├── version.txt
├── .gitmodules
├── .gitignore
├── CITATION.md
├── test_database_update.sh
├── .github
    └── workflows
    │   ├── dockerhub.yml
    │   ├── trigger_action.sh
    │   ├── get_binary_release.sh
    │   ├── binary.yml
    │   ├── ccpp.yml
    │   ├── mac_ccpp.yml
    │   ├── conda.yml
    │   └── mac_conda.yml
├── test_prot.gff
├── LICENSE
├── test_disrupt.expected
├── README.md
├── curl_easy.hpp
├── test_prot.expected
├── columns.hpp
├── fasta2parts.cpp
├── test_amrfinder.sh
├── mutate.cpp
├── amrfinder_index.cpp
├── curl_easy.cpp
├── test_dna.expected
├── common.inc
├── test_prot.fa
├── gff.hpp
├── test_both.expected
├── fasta_extract.cpp
├── Makefile
├── fasta_check.cpp
├── alignment.hpp
├── gff_check.cpp
├── disruption2genesymbol.cpp
├── tsv.hpp
├── amrfinder_update.cpp
├── dna_mutation.cpp
├── test_dna_mut_all.expected
└── gff.cpp


/version.txt:
--------------------------------------------------------------------------------
1 | 4.2.5
2 | 


--------------------------------------------------------------------------------
/.gitmodules:
--------------------------------------------------------------------------------
1 | [submodule "stxtyper"]
2 | 	path = stx
3 | 	url = https://github.com/ncbi/stxtyper.git
4 | 


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
 1 | data/
 2 | *.o
 3 | amr_report
 4 | amrfinder
 5 | amrfinder_index
 6 | amrfinder_update
 7 | amrfinder_customize
 8 | disruption2genesymbol
 9 | dna_mutation
10 | fasta_check
11 | fasta_extract
12 | fasta2parts
13 | gff_check
14 | mutate
15 | *.got
16 | 


--------------------------------------------------------------------------------
/CITATION.md:
--------------------------------------------------------------------------------
1 | Please see our [wiki instructions on citing AMRFinderPlus](https://github.com/ncbi/amr/wiki#citation) for more information on how to cite AMRFinderPlus. Importantly we ask that you include both the software version and database version in your methods so people can reproduce your results.
2 | 


--------------------------------------------------------------------------------
/test_database_update.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/sh
 2 | 
 3 | echo "test_database_update.sh - test update from staging area"
 4 | git status -uno
 5 | echo ""
 6 | echo "Attempts to update from ftp://ftp.ncbi.nlm.nih.gov/pathogen/Technical/AMRFinder_technical/test_database/"
 7 | echo "WARNING: recompiles AMRFinderPlus to use a different update URL"
 8 | echo "To continue press <CR>, to abort ^C"
 9 | read
10 | 
11 | set -x
12 | 
13 | touch amrfinder_update.cpp
14 | make TEST_UPDATE=1
15 | ./amrfinder -U
16 | ./test_amrfinder.sh -n
17 | #touch amrfinder_update.cpp
18 | #make
19 | 
20 | 


--------------------------------------------------------------------------------
/.github/workflows/dockerhub.yml:
--------------------------------------------------------------------------------
 1 | name: dockerhub image
 2 | 
 3 | on:
 4 |     schedule: 
 5 |         - cron: '15 21 * * *' # 9:15pm everyday
 6 |     workflow_dispatch:
 7 |     repository_dispatch:
 8 |         types: [docker-test, install-test]
 9 | 
10 | jobs:
11 | 
12 |   test_dockerhub:
13 |     runs-on: ubuntu-latest
14 |     timeout-minutes: 30
15 |     steps:
16 |     - uses: actions/checkout@v4
17 |     - name: Test docker
18 |       run: docker run hello-world
19 |     - name: Software and DB version
20 |       run: docker run ncbi/amr amrfinder --database_version
21 |     - name: image ls for debugging
22 |       run: docker image ls
23 |     - name: Protein
24 |       run: docker run --rm -v ${PWD}:/data ncbi/amr amrfinder --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got --print_node > test_dna.got
25 |     - name: Check results
26 |       run: diff test_dna.expected test_dna.got
27 |     - name: Combined
28 |       run: docker run --rm -v ${PWD}:/data ncbi/amr amrfinder --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_both.got
29 |     - name: Check combined results
30 |       run: diff test_both.expected test_both.got
31 | 


--------------------------------------------------------------------------------
/test_prot.gff:
--------------------------------------------------------------------------------
 1 | ##gff-version 3
 2 | ##sequence-region contig1 1-50000
 3 | contig01	.	gene	101	961	.	+	.	ID=gene1;Name=blaTEM-156
 4 | contigX	.	gene	1	501	.	+	.	ID=gene2;Name=nimIJ_hmm
 5 | contig02	.	gene	1	1191	.	+	.	ID=gene3;Name=blaPDC-114_blast
 6 | contig03	.	gene	101	802	.	+	.	ID=gene4;Name=blaOXA-436_partial
 7 | contig04	.	gene	101	1147	.	+	.	ID=gene5;Name=vanG
 8 | contig06	.	gene	31	2616	.	+	.	ID=gene6;Name=gyrA
 9 | contig07	.	gene	101	526	.	+	.	ID=gene7;Name=50S_L22
10 | contig09	.	gene	1	675	.	-	.	Name=aph3pp-Ib_partial_5p_neg
11 | contig09	.	gene	715	1377	.	-	.	Name=sul2_partial_3p_neg
12 | contig11	.	gene	113	547	.	+	.	Name=blaTEM-internal_stop
13 | contig12	.	gene	71	637	.	+	.	Name=qacR-curated_blast
14 | contig13	.	gene	1	1137	.	+	.	Name=emrD3-suppressed-in-vibrio
15 | contig13	.	gene	1141	1491	.	+	.	Name=arsR-suppressed-in-escherichia
16 | contig14	.	gene	1093	2181	.	+	.	Name=pmrB_C84R
17 | contig16	.	gene	1	423	.	+	.	Name=nfsA_R15C_K141STOP
18 | contig18	.	gene	279	1238	.	+	.	Name=stxA2a_prot
19 | contig18	Protein Homology	CDS	279	1238	.	+	0	Name=stxA2a_prot
20 | contig18	.	gene	1250	1519	.	+	.	Name=stxB2a_prot
21 | contig18	Protein Homology	CDS	1250	1519	.	+	0	Name=stxB2a_prot
22 | 


--------------------------------------------------------------------------------
/.github/workflows/trigger_action.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/sh
 2 | 
 3 | cat <<END
 4 | Note this requires a ~/.github-token file that contains a github token
 5 | with appropriate permissions
 6 | 
 7 | Actions that can be triggered:
 8 | 
 9 | 1. install-test
10 | 2. linux-compile-test
11 | 3. linux-binary-test
12 | 4. linux-bioconda-test
13 | 5. mac-bioconda-test
14 | 6. docker-test
15 | END
16 | 
17 | echo -n "% "
18 | read action
19 | 
20 | if [ "X$action" == "X" ]
21 | then
22 |     echo "Enter an action to take next time you run"
23 |     exit 1;
24 | fi
25 | 
26 | echo $action
27 | case $action in 
28 |     1|install-test) event=install-test;;
29 |     2|linux-compile-test) event=linux-compile-test;;
30 |     3|linux-binary-test) event=linux-binary-test;;
31 |     4|linux-bioconda-test) event=linux-bioconda-test;;
32 |     5|mac-bioconda-test) event=mac-bioconda-test;;
33 |     6|docker-test) event=docker-test;;
34 |     *) echo "Unknown action. Please try again"
35 |         exit 1;;
36 | esac
37 | 
38 | echo "action=$action event=$event"
39 | 
40 | cmd="
41 | curl \
42 |   -H 'Accept: application/vnd.github.everest-preview+json' \
43 |   -H 'Authorization: token `cat ~/.github-token`' \
44 |   --data '{\"event_type\": \"$event\"}' \
45 |   --request POST \
46 |   https://api.github.com/repos/ncbi/amr/dispatches
47 | "
48 | echo $cmd
49 | echo $cmd | bash
50 | 
51 | 


--------------------------------------------------------------------------------
/.github/workflows/get_binary_release.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | # found and lightly modified these functions
 3 | get_latest_release() {
 4 |     curl --silent "https://api.github.com/repos/$1/releases/latest" |
 5 |     grep '"tag_name":' |
 6 |     cut -d '"' -f 4
 7 | }
 8 | 
 9 | get_tarball_url() {
10 |     curl --silent "https://api.github.com/repos/$1/releases/latest" |
11 |         fgrep '"browser_download_url":' |
12 |         cut -d '"' -f 4
13 | }
14 | 
15 | 
16 | release=$(get_latest_release ncbi/amr)
17 | URL=$(get_tarball_url ncbi/amr)
18 | 
19 | >&2 echo "Downloading AMRFinderPlus version $release"
20 | >&2 echo "Binaries from $URL"
21 | 
22 | # download and unpack AMRFinder binaries
23 |     curl --silent -L -O $URL
24 |     tarball_name=$(echo $URL | perl -pe 's#^.*/(.*)#\1#')
25 |     tar xfz $tarball_name
26 |     rm $tarball_name
27 | 
28 | # download and unpack test
29 |     curl --silent \
30 |          -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.fa \
31 |          -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.fa \
32 |          -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.gff \
33 |          -O https://raw.githubusercontent.com/ncbi/amr/master/test_both.expected \
34 |          -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.expected \
35 |          -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.expected
36 | 
37 | # download database
38 |     ./amrfinder --update
39 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | 
 2 |                             PUBLIC DOMAIN NOTICE
 3 |                National Center for Biotechnology Information
 4 | 
 5 |   This software/database is a "United States Government Work" under the
 6 |   terms of the United States Copyright Act.  It was written as part of
 7 |   the author's official duties as a United States Government employee and
 8 |   thus cannot be copyrighted.  This software/database is freely available
 9 |   to the public for use. The National Library of Medicine and the U.S.
10 |   Government have not placed any restriction on its use or reproduction.
11 | 
12 |   Although all reasonable efforts have been taken to ensure the accuracy
13 |   and reliability of the software and data, the NLM and the U.S.
14 |   Government do not and cannot warrant the performance or results that
15 |   may be obtained by using this software or data. The NLM and the U.S.
16 |   Government disclaim all warranties, express or implied, including
17 |   warranties of performance, merchantability or fitness for any particular
18 |   purpose.
19 | 
20 |   Please cite Feldgarden, Michael, Vyacheslav Brover, Daniel H. Haft, Arjun B.
21 |   Prasad, Douglas J. Slotta, Igor Tolstoy, Gregory H. Tyson et al. "Validating
22 |   the AMRFinder tool and resistance gene database by using antimicrobial
23 |   resistance genotype-phenotype correlations in a collection of isolates."
24 |   Antimicrobial agents and chemotherapy 63, no. 11 (2019): e00483-19. 
25 |   https://pubmed.gov/31427293 in any work or product based on this material.
26 |   
27 | 


--------------------------------------------------------------------------------
/.github/workflows/binary.yml:
--------------------------------------------------------------------------------
 1 | name: binary tarball
 2 | 
 3 | on: 
 4 |     workflow_dispatch:
 5 |     release:
 6 |         branches: [ master ]
 7 |     repository_dispatch:
 8 |         types: [linux-binary-test, install-test]
 9 |     schedule: 
10 |         - cron: '15  15  *   *   *' # 3:15pm every day
11 | jobs:
12 |   build:
13 |     runs-on: ubuntu-latest
14 |     timeout-minutes: 30
15 |     steps:
16 |         - uses: actions/checkout@v4
17 |         - name: prerequisites
18 |           run: |
19 |               sudo apt-get update
20 |               sudo apt-get install -y hmmer ncbi-blast+ curl build-essential
21 |         - name: download
22 |           run: bash -x .github/workflows/get_binary_release.sh
23 |         - name: Software and db version
24 |           run: ./amrfinder --database_version
25 |         - name: run tests included with distribution
26 |           run: |
27 |               ./amrfinder --plus -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_prot.got
28 |               diff test_prot.expected test_prot.got
29 |               ./amrfinder --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got --print_node > test_dna.got
30 |               diff test_dna.expected test_dna.got
31 |               ./amrfinder --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_both.got
32 |               diff test_both.expected test_both.got
33 |         - name: Run tests
34 |           run: |
35 |               # temporarily we need to download the test script. Can remove
36 |               # once we have a new software release and it's included in the
37 |               # distribution
38 |               BASE_URL="https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master"
39 |               echo "BASE_URL=${BASE_URL}"
40 |               curl --silent -L -O ${BASE_URL}/test_amrfinder.sh
41 |               bash -x ./test_amrfinder.sh
42 | 


--------------------------------------------------------------------------------
/test_disrupt.expected:
--------------------------------------------------------------------------------
 1 | Protein id	Contig id	Start	Stop	Strand	Element symbol	Element name	Scope	Type	Subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference	% Identity to reference	Alignment length	Closest reference accession	Closest reference name	HMM accession	HMM description	Hierarchy node
 2 | NA	cirA_A169insTer10	47	5134	+	cirA_A169insTer10	Klebsiella pneumoniae cefiderocol resistant CirA	core	AMR	POINT_DISRUPT	BETA-LACTAM	CEFIDEROCOL	POINTX	1696	657	100.00	99.85	657	WP_002912926.1	catecholate siderophore receptor CirA	NA	NA	cirA
 3 | NA	cirA_K633LfsTer8	13	3644	+	cirA_K633LfsTer8	Klebsiella pneumoniae cefiderocol resistant CirA	core	AMR	POINT_DISRUPT	BETA-LACTAM	CEFIDEROCOL	POINTX	1210	657	100.00	100.00	657	WP_002912926.1	catecholate siderophore receptor CirA	NA	NA	cirA
 4 | NA	cirA_N184NRHSEWTer	69	6059	+	cirA_N184NRHSEWTer	Klebsiella pneumoniae cefiderocol resistant CirA	core	AMR	POINT_DISRUPT	BETA-LACTAM	CEFIDEROCOL	POINTX	1997	657	100.00	100.00	657	WP_002912926.1	catecholate siderophore receptor CirA	NA	NA	cirA
 5 | NA	cirA_N184NRHSEWTer	2058	2930	-	blaCTX-M-15	extended-spectrum class A beta-lactamase CTX-M-15	core	AMR	AMR	BETA-LACTAM	CEPHALOSPORIN	ALLELEX	291	291	100.00	100.00	291	WP_000239590.1	extended-spectrum class A beta-lactamase CTX-M-15	NA	NA	blaCTX-M-15
 6 | NA	cirA_Q562Ter	164	2134	-	cirA_Q562Ter	Klebsiella pneumoniae cefiderocol resistant CirA	core	AMR	POINT_DISRUPT	BETA-LACTAM	CEFIDEROCOL	POINTX	657	657	100.00	99.85	657	WP_002912926.1	catecholate siderophore receptor CirA	NA	NA	cirA
 7 | NA	cirA_T98Ter	14	1973	+	cirA_T98Ter	Klebsiella pneumoniae cefiderocol resistant CirA	core	AMR	POINT_DISRUPT	BETA-LACTAM	CEFIDEROCOL	POINTX	653	657	100.00	95.59	658	WP_002912926.1	catecholate siderophore receptor CirA	NA	NA	cirA
 8 | NA	cirA_Y253CfsTer5	60	833	+	cirA_Y253CfsTer5	Klebsiella pneumoniae cefiderocol resistant CirA	core	AMR	POINT	BETA-LACTAM	CEFIDEROCOL	POINTX	258	258	100.00	100.00	258	WP_002912926.1	catecholate siderophore receptor CirA	NA	NA	cirA
 9 | NA	ompK35_R60LfsTer31	18	1101	+	ompK35_R60LfsTer31	Klebsiella pneumoniae carbapenem resistant OmpK35	core	AMR	POINT_DISRUPT	BETA-LACTAM	CARBAPENEM	POINTX	361	359	100.00	100.00	359	WP_004141771.1	outer membrane porin OmpK35	NA	NA	ompK35
10 | 


--------------------------------------------------------------------------------
/.github/workflows/ccpp.yml:
--------------------------------------------------------------------------------
 1 | name: C++ CI
 2 | 
 3 | on: 
 4 |     workflow_dispatch:
 5 |     push:
 6 |     pull_request:
 7 |     repository_dispatch:
 8 |         types: [linux-compile-test, install-test]
 9 | jobs:
10 |   linux_x86:
11 |     runs-on: ubuntu-latest
12 |     timeout-minutes: 30
13 |     steps:
14 |     - uses: actions/checkout@v4
15 |     - name: prerequisites
16 |       run: |
17 |           sudo apt-get update
18 |           sudo apt-get install -y hmmer ncbi-blast+ git libcurl4-openssl-dev build-essential curl
19 |     - name: submodule checkout
20 |       run: git submodule update --init --recursive
21 |     - name: make
22 |       run: cat version.txt; make -j -O
23 |     - name: download db
24 |       run: ./amrfinder -u
25 |     - name: Software and DB version
26 |       run: ./amrfinder --database_version
27 |     - name: make test
28 |       run: make test
29 |     - name: test for no-overwrite database update (PD-3469 / https://github.com/ncbi/amr/issues/16)
30 |       run: ./amrfinder -u 2>&1 | fgrep 'Skipping update'
31 |     - name: make github_binaries
32 |       run: make github_binaries
33 |     - uses: actions/upload-artifact@v4
34 |       with:
35 |           name: release-binary
36 |           path: amrfinder_binaries_v*.tar.gz
37 |   linux-arm64:
38 |     runs-on: ubuntu-24.04-arm
39 |     timeout-minutes: 30
40 |     steps:
41 |     - uses: actions/checkout@v4
42 |     - name: prerequisites
43 |       run: |
44 |           sudo apt-get update
45 |           sudo apt-get install -y hmmer ncbi-blast+ git libcurl4-openssl-dev build-essential curl
46 |     - name: submodule checkout
47 |       run: git submodule update --init --recursive
48 |     - name: make
49 |       run: cat version.txt; make -j -O
50 |     - name: download db
51 |       run: ./amrfinder -u
52 |     - name: Software and DB version
53 |       run: ./amrfinder --database_version
54 |     - name: make test
55 |       run: make test
56 |     - name: test for no-overwrite database update (PD-3469 / https://github.com/ncbi/amr/issues/16)
57 |       run: ./amrfinder -u 2>&1 | fgrep 'Skipping update'
58 |     - name: make github_binaries
59 |       run: |
60 |         make github_binaries
61 |         version=`cat version.txt`
62 |         mv amrfinder_binaries_v$version.tar.gz amrfinder_binaries_linux_aarch64_v$version.tar.gz
63 |     - uses: actions/upload-artifact@v4
64 |       with:
65 |           name: release-binary-arm
66 |           path: amrfinder_binaries_linux_aarch64_v*.tar.gz
67 | 
68 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | # NCBI Antimicrobial Resistance Gene Finder (AMRFinderPlus)
 2 | 
 3 | This software and the accompanying database are designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences. We have also added "plus" stress, heat, and biocide resistance and virulence factors for [some organisms](https://github.com/evolarjun/amr/wiki/Curated-organisms).
 4 | 
 5 | ## See [the wiki for documentation](https://github.com/ncbi/amr/wiki)
 6 | ## [Citing AMRFinderPlus](https://github.com/ncbi/amr/wiki#how-to-cite)
 7 | ## Please [subscribe to our announce list](https://www.ncbi.nlm.nih.gov/mailman/listinfo/amrfinder-announce) for announcements of database and software updates.
 8 | 
 9 | ----
10 | # Licenses
11 | 
12 | ## PUBLIC DOMAIN NOTICE
13 | 
14 | ### National Center for Biotechnology Information
15 | 
16 | This software/database is a "United States Government Work" under the
17 | terms of the United States Copyright Act.  It was written as part of
18 | the authors' official duties as a United States Government employee and
19 | thus cannot be copyrighted.  This software/database is freely available
20 | to the public for use. The National Library of Medicine and the U.S.
21 | Government have not placed any restriction on its use or reproduction.
22 | 
23 | Although all reasonable efforts have been taken to ensure the accuracy
24 | and reliability of the software and data, the NLM and the U.S.
25 | Government do not and cannot warrant the performance or results that
26 | may be obtained by using this software or data. The NLM and the U.S.
27 | Government disclaim all warranties, express or implied, including
28 | warranties of performance, merchantability or fitness for any particular
29 | purpose.
30 | 
31 | In any work or product derived from this material, proper attribution of the
32 | authors as the source of the software or data should be made, using the
33 | following citation:
34 | 
35 | Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH,
36 | Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W.
37 | AMRFinderPlus and the Reference Gene Catalog facilitate examination of the
38 | genomic links among antimicrobial resistance, stress response, and virulence.
39 | Sci Rep. 2021 Jun 16;11(1):12728. doi: [10.1038/s41598-021-91456-0](https://doi.org/10.1038/s41598-021-91456-0). PMID: [34135355](https://pubmed.ncbi.nlm.nih.gov/34135355/); PMCID: [PMC8208984](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8208984/).
40 | 
41 | 
42 | 


--------------------------------------------------------------------------------
/.github/workflows/mac_ccpp.yml:
--------------------------------------------------------------------------------
 1 | name: MacOS C++ CI
 2 | 
 3 | on: 
 4 |     workflow_dispatch:
 5 |     push:
 6 |     pull_request:
 7 |     repository_dispatch:
 8 |         types: [mac-compile-test, install-test]
 9 | jobs:
10 |   macos_arm:
11 |     runs-on: macos-latest
12 |     timeout-minutes: 30
13 |     steps:
14 |     - uses: actions/checkout@v4
15 |     - name: submodule checkout
16 |       run: git submodule update --init --recursive
17 |     - name: prerequisites
18 |       run: |
19 |           /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
20 |           brew install blast
21 |           brew install hmmer
22 |     - name: make
23 |       run: make -j
24 |     - name: download db
25 |       run: ./amrfinder -u
26 |     - name: Software and DB versions
27 |       run: |
28 |           cat version.txt
29 |           ./amrfinder --database_version
30 |     - name: make test
31 |       run: make test
32 |     - name: test for no-overwrite database update (PD-3469 / https://github.com/ncbi/amr/issues/16)
33 |       run: ./amrfinder -u 2>&1 | fgrep 'Skipping update'
34 |     - name: make github_binaries
35 |       run: |
36 |           make github_binaries
37 |           version=`cat version.txt`
38 |           mv amrfinder_binaries_v$version.tar.gz amrfinder_binaries_macos_aarch64_v$version.txt
39 |     - uses: actions/upload-artifact@v4
40 |       with:
41 |           name: release-binary
42 |           path: amrfinder_binaries_macos_aarch64_v*.tar.gz
43 |   macos_x86_64:
44 |     runs-on: macos-15-intel
45 |     timeout-minutes: 30
46 |     steps:
47 |     - uses: actions/checkout@v4
48 |     - name: submodule checkout
49 |       run: git submodule update --init --recursive
50 |     - name: prerequisites
51 |       run: |
52 |           /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
53 |           brew install blast
54 |           brew install hmmer
55 |     - name: make
56 |       run: make -j
57 |     - name: download db
58 |       run: ./amrfinder -u
59 |     - name: Software and DB versions
60 |       run: |
61 |           cat version.txt
62 |           ./amrfinder --database_version
63 |     - name: make test
64 |       run: make test
65 |     - name: test for no-overwrite database update (PD-3469 / https://github.com/ncbi/amr/issues/16)
66 |       run: ./amrfinder -u 2>&1 | fgrep 'Skipping update'
67 |     - name: make github_binaries
68 |       run: |
69 |           make github_binaries
70 |           version=`cat version.txt`
71 |           mv amrfinder_binaries_v$version.tar.gz amrfinder_binaries_macos_x86_64_v$version.txt
72 |     - uses: actions/upload-artifact@v4
73 |       with:
74 |           name: release-binary
75 |           path: amrfinder_binaries_macos_x86_64_v*.tar.gz
76 | 


--------------------------------------------------------------------------------
/.github/workflows/conda.yml:
--------------------------------------------------------------------------------
 1 | name: Linux bioconda 
 2 | 
 3 | on:
 4 |     workflow_dispatch:
 5 |     schedule:
 6 |         - cron: '15 3 * * *' # 3:15am everyday
 7 |     repository_dispatch:
 8 |         types: [linux-bioconda-test, install-test]
 9 | jobs:
10 |   conda_linux_x86_64:
11 |     runs-on: ubuntu-latest
12 |     timeout-minutes: 30
13 |     steps:
14 |     - name: When was this run
15 |       run: date
16 |     - name: configure conda
17 |       run: |
18 |           . $CONDA/bin/activate
19 |           conda config --add channels defaults
20 |           conda config --add channels bioconda
21 |           conda config --add channels conda-forge
22 |     - name: install AMRFinderPlus
23 |       run: |
24 |           . $CONDA/bin/activate
25 |           conda install --update-deps -c conda-forge -c bioconda -y ncbi-amrfinderplus
26 |           amrfinder --version
27 |     - name: download latest AMRFinderPlus database
28 |       run: |
29 |           source /usr/share/miniconda/bin/activate
30 |           echo CONDA_PREFIX = ${CONDA_PREFIX}
31 |           /usr/share/miniconda/bin/amrfinder --force_update
32 |     - name: Software and DB version
33 |       run: |
34 |           source /usr/share/miniconda/bin/activate
35 |           amrfinder --database_version
36 |     - name: download tests
37 |       run: |
38 |           BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master
39 |           curl --silent -L -O ${BASE_URL}/test_amrfinder.sh
40 |     - name: run tests
41 |       run: |
42 |           source /usr/share/miniconda/bin/activate
43 |           echo CONDA_PREFIX = $CONDA_PREFIX
44 |           bash ./test_amrfinder.sh -p
45 |   conda_linux_aarch64:
46 |     runs-on: ubuntu-24.04-arm
47 |     timeout-minutes: 30
48 |     steps:
49 |     - uses: conda-incubator/setup-miniconda@v3
50 |       with:
51 |         auto-update-conda: true
52 |     - name: When was this run
53 |       run: date
54 |     - name: configure conda
55 |       shell: bash -el {0}
56 |       run: |
57 |           conda config --add channels defaults
58 |           conda config --add channels bioconda
59 |           conda config --add channels conda-forge
60 |     - name: install AMRFinderPlus
61 |       shell: bash -el {0}
62 |       run: |
63 |           conda install --update-deps -c conda-forge -c bioconda -y ncbi-amrfinderplus
64 |           amrfinder --version
65 |     - name: download latest AMRFinderPlus database
66 |       shell: bash -el {0}
67 |       run: amrfinder --force_update
68 |     - name: Software and DB version
69 |       shell: bash -el {0}
70 |       run: amrfinder --database_version
71 |     - name: download tests
72 |       run: |
73 |           BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master
74 |           curl --silent -L -O ${BASE_URL}/test_amrfinder.sh
75 |     - name: run tests
76 |       shell: bash -el {0}
77 |       run: bash ./test_amrfinder.sh -p
78 | 


--------------------------------------------------------------------------------
/curl_easy.hpp:
--------------------------------------------------------------------------------
 1 | // curl_easy.hpp
 2 | 
 3 | /*===========================================================================
 4 | *
 5 | *                            PUBLIC DOMAIN NOTICE                          
 6 | *               National Center for Biotechnology Information
 7 | *                                                                          
 8 | *  This software/database is a "United States Government Work" under the   
 9 | *  terms of the United States Copyright Act.  It was written as part of    
10 | *  the author's official duties as a United States Government employee and 
11 | *  thus cannot be copyrighted.  This software/database is freely available 
12 | *  to the public for use. The National Library of Medicine and the U.S.    
13 | *  Government have not placed any restriction on its use or reproduction.  
14 | *                                                                          
15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
16 | *  and reliability of the software and data, the NLM and the U.S.          
17 | *  Government do not and cannot warrant the performance or results that    
18 | *  may be obtained by using this software or data. The NLM and the U.S.    
19 | *  Government disclaim all warranties, express or implied, including       
20 | *  warranties of performance, merchantability or fitness for any particular
21 | *  purpose.                                                                
22 | *                                                                          
23 | *  Please cite the author in any work or product based on this material.   
24 | *
25 | * ===========================================================================
26 | *
27 | * Author: Vyacheslav Brover
28 | *
29 | * Dependencies: curl.{h,c}
30 | *
31 | * File Description:
32 | *   curl_easy functions
33 | *
34 | */
35 | 
36 | 
37 | #ifdef _MSC_VER
38 |   #error "UNIX is required"
39 | #endif
40 | 
41 | 
42 | #include <unistd.h>
43 | extern "C" 
44 | {
45 |   #include <curl/curl.h>
46 |     // Linking requires:  -lcurl
47 | }
48 | 
49 | #include "common.hpp"
50 | using namespace Common_sp;
51 | 
52 | 
53 | 
54 | 
55 | namespace CURL_sp
56 | {
57 |   
58 |   
59 | SoftwareVersion getLibVersion ();
60 | 
61 |   
62 | 
63 | struct Curl
64 | {
65 |   CURL* eh {nullptr};
66 | 
67 | 
68 |   Curl ()
69 |     : eh (curl_easy_init ())
70 |     { if (! eh)
71 |         throw runtime_error ("Cannot initialize curl_easy");        
72 |       // Override the libcurl system-wide default
73 |       // PD-5495 / https://github.com/ncbi/amr/issues/170
74 |       if (const char *env_ca_bundle = getenv ("CURL_CA_BUNDLE"))          
75 |         curl_easy_setopt (eh, CURLOPT_CAINFO, env_ca_bundle);  
76 |     }
77 |  ~Curl ()
78 |    { curl_easy_cleanup (eh); }
79 | 
80 | 
81 |   void download (const string &url,
82 |                  const string &fName);
83 |   string read (const string &url);
84 | private:
85 |   void process (const string &url,
86 |                 const string &error_msg_action);
87 | };
88 | 
89 | 	
90 | 
91 | 
92 | }  // namespace
93 | 
94 | 
95 | 


--------------------------------------------------------------------------------
/test_prot.expected:
--------------------------------------------------------------------------------
 1 | Protein id	Contig id	Start	Stop	Strand	Element symbol	Element name	Scope	Type	Subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference	% Identity to reference	Alignment length	Closest reference accession	Closest reference name	HMM accession	HMM description	Hierarchy node
 2 | blaTEM-156	contig01	101	961	+	blaTEM-156	class A beta-lactamase TEM-156	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	ALLELEP	286	286	100.00	100.00	286	WP_061158039.1	class A beta-lactamase TEM-156	NF000531.2	TEM family class A beta-lactamase	blaTEM-156
 3 | blaPDC-114_blast	contig02	1	1191	+	blaPDC	PDC family class C beta-lactamase	core	AMR	AMR	BETA-LACTAM	CEPHALOSPORIN	BLASTP	397	397	100.00	99.75	397	WP_061189306.1	class C beta-lactamase PDC-114	NF000422.6	PDC family class C beta-lactamase	blaPDC
 4 | blaOXA-436_partial	contig03	101	802	+	blaOXA	OXA-48 family class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALP	233	265	87.92	100.00	233	WP_058842180.1	OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436	NF012161.0	class D beta-lactamase	blaOXA-48_fam
 5 | vanG	contig04	101	1147	+	vanG	D-alanine--D-serine ligase VanG	core	AMR	AMR	GLYCOPEPTIDE	VANCOMYCIN	EXACTP	349	349	100.00	100.00	349	WP_063856695.1	D-alanine--D-serine ligase VanG	NF000091.3	D-alanine--D-serine ligase VanG	vanG
 6 | aph3pp-Ib_partial_5p_neg	contig09	1	675	-	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIAL_CONTIG_ENDP	225	267	81.27	100.00	217	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NF032896.1	APH(3'') family aminoglycoside O-phosphotransferase	aph(3'')-Ib
 7 | sul2_partial_3p_neg	contig09	715	1377	-	sul2	sulfonamide-resistant dihydropteroate synthase Sul2	core	AMR	AMR	SULFONAMIDE	SULFONAMIDE	PARTIALP	221	271	81.55	100.00	221	WP_001043265.1	sulfonamide-resistant dihydropteroate synthase Sul2	NA	NA	sul2
 8 | blaTEM-internal_stop	contig11	113	547	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALP	144	286	50.35	97.22	144	WP_000027057.1	broad-spectrum class A beta-lactamase TEM-1	NA	NA	blaTEM
 9 | qacR-curated_blast	contig12	71	637	+	qacR	multidrug-binding transcriptional regulator QacR	plus	STRESS	BIOCIDE	QUATERNARY AMMONIUM	QUATERNARY AMMONIUM	BLASTP	188	188	100.00	99.47	188	ADK23698.1	multidrug-binding transcriptional regulator QacR	NA	NA	qacR
10 | emrD3-suppressed-in-vibrio	contig13	1	1137	+	emrD3	multidrug efflux MFS transporter EmrD-3	plus	AMR	AMR	EFFLUX	EFFLUX	EXACTP	379	379	100.00	100.00	379	ABQ18953.1	multidrug efflux MFS transporter EmrD-3	NA	NA	emrD3
11 | pmrB_C84R	contig14	1093	2181	+	pmrB_C84R	Escherichia colistin resistant PmrB	core	AMR	POINT	COLISTIN	COLISTIN	POINTP	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA	pmrB
12 | nfsA_R15C_K141STOP	contig16	1	423	+	nfsA_R15C	Escherichia nitrofurantoin resistant NfsA	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTP	140	240	58.33	99.29	140	WP_089631889.1	nitroreductase NfsA	NA	NA	nfsA
13 | stxA2a_prot	contig18	279	1238	+	stxA2	Shiga toxin Stx2 subunit A	plus	VIRULENCE	VIRULENCE	STX2	stxA2	EXACTP	319	319	100.00	100.00	319	TJA36680.1	Shiga toxin Stx2 subunit A	NF041702.1	Shiga toxin Stx2 subunit A	stxA2_acd
14 | stxB2a_prot	contig18	1250	1519	+	stxB2	Shiga toxin Stx2a subunit B	plus	VIRULENCE	VIRULENCE	STX2	stxB2a	EXACTP	89	89	100.00	100.00	89	AAM90978.1	Shiga toxin Stx2a subunit B	NF033660.0	Shiga toxin Stx2 subunit B	stxB2a
15 | nimIJ_hmm	contigX	1	501	+	nimIJ	NimIJ family 5-nitroimidazole reductase	core	AMR	AMR	NITROIMIDAZOLE	NITROIMIDAZOLE	HMM	166	165	98.18	76.54	162	WP_005812825.1	NimIJ family 5-nitroimidazole reductase	NF000262.1	NimIJ family 5-nitroimidazole reductase	nimIJ
16 | 


--------------------------------------------------------------------------------
/columns.hpp:
--------------------------------------------------------------------------------
 1 | // columns.hpp
 2 | 
 3 | /*===========================================================================
 4 | *
 5 | *                            PUBLIC DOMAIN NOTICE                          
 6 | *               National Center for Biotechnology Information
 7 | *                                                                          
 8 | *  This software/database is a "United States Government Work" under the   
 9 | *  terms of the United States Copyright Act.  It was written as part of    
10 | *  the author's official duties as a United States Government employee and 
11 | *  thus cannot be copyrighted.  This software/database is freely available 
12 | *  to the public for use. The National Library of Medicine and the U.S.    
13 | *  Government have not placed any restriction on its use or reproduction.  
14 | *                                                                          
15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
16 | *  and reliability of the software and data, the NLM and the U.S.          
17 | *  Government do not and cannot warrant the performance or results that    
18 | *  may be obtained by using this software or data. The NLM and the U.S.    
19 | *  Government disclaim all warranties, express or implied, including       
20 | *  warranties of performance, merchantability or fitness for any particular
21 | *  purpose.                                                                
22 | *                                                                          
23 | *  Please cite the author in any work or product based on this material.   
24 | *
25 | * ===========================================================================
26 | *
27 | * Author: Vyacheslav Brover
28 | *
29 | * File Description:
30 | *   AMRFinderPlus column names
31 | *
32 | */
33 | 
34 | 
35 | 
36 | // Columns
37 | // PD-5085
38 | constexpr const char* prot_colName = "Protein id";   // PD-2534  
39 | constexpr const char* contig_colName = "Contig id";
40 | // Target 
41 | constexpr const char* start_colName = "Start"; 
42 | constexpr const char* stop_colName = "Stop";
43 | constexpr const char* strand_colName = "Strand";
44 | //        
45 | constexpr const char* genesymbol_colName = "Element symbol";  // PD-4924 
46 | constexpr const char* elemName_colName = "Element name";  // PD-4910
47 | constexpr const char* scope_colName = "Scope";  // PD-2825 
48 | // PD-1856
49 | constexpr const char* type_colName = "Type";
50 | constexpr const char* subtype_colName = "Subtype";
51 | constexpr const char* class_colName = "Class";
52 | constexpr const char* subclass_colName = "Subclass";
53 | //        
54 | constexpr const char* method_colName = "Method";
55 | constexpr const char* targetLen_colName = "Target length";  // was: "Element length" (temporarily)
56 | constexpr const char* refLen_colName = "Reference sequence length";
57 | constexpr const char* refCov_colName = "% Coverage of reference";
58 | constexpr const char* refIdent_colName = "% Identity to reference";
59 | constexpr const char* alignLen_colName = "Alignment length";
60 | constexpr const char* closestRefAccession_colName = "Closest reference accession";
61 | constexpr const char* closestRefName_colName = "Closest reference name";
62 | constexpr const char* hmmAccession_colName = "HMM accession";
63 | constexpr const char* hmmDescr_colName = "HMM description";
64 | constexpr const char* hierarchyNode_colName = "Hierarchy node";
65 | 
66 | 
67 | // PD-5155
68 | constexpr const char* fusion_infix = "::";  // was: "/"
69 |   
70 | constexpr const char* na = "NA";
71 | 
72 | constexpr const char* disruption_delim = "_@";
73 | 
74 | 
75 | // Methods
76 | constexpr const char* frameshift_Name       = "FRAMESHIFT";
77 | constexpr const char* internalStop_Name     = "INTERNAL_STOP";
78 | constexpr const char* partial_Name          = "PARTIAL";
79 | constexpr const char* partialContigEnd_Name = "PARTIAL_CONTIG_END";
80 | 
81 | 


--------------------------------------------------------------------------------
/fasta2parts.cpp:
--------------------------------------------------------------------------------
  1 | // fasta2parts.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Split the sequences a FASTA file into chunks without breaking sequences
 31 | *
 32 | */
 33 |    
 34 |    
 35 | #undef NDEBUG 
 36 | 
 37 | #include "common.hpp"
 38 | using namespace Common_sp;
 39 | 
 40 | #include "common.inc"
 41 | 
 42 | 
 43 | 
 44 | namespace 
 45 | {
 46 | 
 47 | 
 48 | 
 49 | struct ThisApplication final : Application
 50 | {
 51 |   ThisApplication ()
 52 |     : Application ("Split the sequences a FASTA file into parts without breaking sequences")
 53 |     {
 54 |       addPositional ("in", "FASTA file");
 55 |       addPositional ("parts_max", "Max. number of parts (>= 2)");
 56 |       addPositional ("dir", "Output directory where chunks are saved named by integers starting with 1");
 57 | 	    version = SVN_REV;
 58 |     }
 59 | 
 60 | 
 61 | 
 62 |   void body () const final
 63 |   {
 64 |     const string fName     =               getArg ("in");
 65 |     const size_t parts_max = str2<size_t> (getArg ("parts_max"));
 66 |     const string dirName   =               getArg ("dir");
 67 |     
 68 |     if (parts_max <= 1)
 69 |       throw runtime_error ("Number of parts must be >= 2");
 70 |       
 71 | 
 72 |     const size_t chunk_min = (size_t) getFileSize (fName) / parts_max + 1;
 73 | 
 74 |     size_t part = 0;
 75 |     unique_ptr<OFStream> out;
 76 |     size_t seqSize = 0;
 77 |     LineInput f (fName); 
 78 |     while (f. nextLine ())
 79 |     {
 80 |       trimTrailing (f. line);
 81 |       if (f. line. empty ())
 82 |       	continue;
 83 |     	if (   f. line [0] == '>'
 84 |     	    && seqSize >= chunk_min
 85 |     	    && part < parts_max
 86 |     	   )
 87 |     	{
 88 |     	  out. reset ();
 89 |     	  seqSize = 0;
 90 |     	}
 91 |     	if (! out. get ())
 92 |     	{
 93 |     	  part++;
 94 |     	  ASSERT (part <= parts_max);
 95 |     	  out. reset (new OFStream (dirName, toString (part), ""));
 96 |     	}
 97 |    		*out << f. line << endl;
 98 |    		seqSize += f. line. size ();
 99 | 	  }
100 |   }
101 | };
102 | 
103 | 
104 | 
105 | }  // namespace
106 | 
107 | 
108 | 
109 | int main (int argc, 
110 |           const char* argv[])
111 | {
112 |   ThisApplication app;
113 |   return app. run (argc, argv);  
114 | }
115 | 
116 | 
117 | 
118 | 


--------------------------------------------------------------------------------
/.github/workflows/mac_conda.yml:
--------------------------------------------------------------------------------
 1 | name: Mac bioconda
 2 | on:
 3 |     workflow_dispatch:
 4 |     schedule:
 5 |         - cron: '15 9 * * *' # 9:15am everyday
 6 |     repository_dispatch:
 7 |         types: [mac-bioconda-test, install-test]
 8 | jobs:
 9 |   conda_macos_aarch64:
10 |     runs-on: macos-latest
11 |     timeout-minutes: 30
12 |     steps:
13 |     - name: Install conda because built-in conda is borked
14 |       run: |
15 |           curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
16 |           bash ./Miniconda3-latest-MacOSX-x86_64.sh -b -p /Users/runner/miniconda3
17 |     - name: Configure conda
18 |       run: |
19 |           source /Users/runner/miniconda3/bin/activate
20 |           conda init
21 |           # THIS DOESN"T WORK! Just install miniconda myself
22 |           # . $CONDA/bin/activate
23 |           conda config --add channels defaults
24 |           conda config --add channels bioconda
25 |           conda config --add channels conda-forge
26 |           # permissions are messed up on the mac runner
27 |           # Is this faster than installing miniconda myself?
28 |           # sudo chown -R 501:20 $CONDA
29 |           conda update conda
30 |     - name: Install AMRFinderPlus
31 |       run: |
32 |           source /Users/runner/miniconda3/bin/activate
33 |           conda install --update-deps -c bioconda -c conda-forge -y ncbi-amrfinderplus
34 |     - name: Download AMRFinderPlus database
35 |       run: |
36 |           source /Users/runner/miniconda3/bin/activate
37 |           /Users/runner/miniconda3/bin/amrfinder -u
38 |     - name: Software and DB version
39 |       run: |
40 |           source /Users/runner/miniconda3/bin/activate
41 |           amrfinder --database_version
42 |     - name: Download tests
43 |       run: |
44 |           BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master
45 |           curl --silent -L -O ${BASE_URL}/test_amrfinder.sh
46 |     - name: Run tests
47 |       run: |
48 |           source /Users/runner/miniconda3/bin/activate
49 |           echo CONDA_PREFIX = $CONDA_PREFIX
50 |           bash ./test_amrfinder.sh -p 
51 |   conda_macos_x86_64:
52 |     runs-on: macos-15-intel
53 |     timeout-minutes: 30
54 |     steps:
55 |     - name: Install conda because built-in conda is borked
56 |       run: |
57 |           curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
58 |           bash ./Miniconda3-latest-MacOSX-x86_64.sh -b -p /Users/runner/miniconda3
59 |     - name: Configure conda
60 |       run: |
61 |           source /Users/runner/miniconda3/bin/activate
62 |           conda init
63 |           # THIS DOESN"T WORK! Just install miniconda myself
64 |           # . $CONDA/bin/activate
65 |           conda config --add channels defaults
66 |           conda config --add channels bioconda
67 |           conda config --add channels conda-forge
68 |           # permissions are messed up on the mac runner
69 |           # Is this faster than installing miniconda myself?
70 |           # sudo chown -R 501:20 $CONDA
71 |           conda update conda
72 |     - name: Install AMRFinderPlus
73 |       run: |
74 |           source /Users/runner/miniconda3/bin/activate
75 |           conda install --update-deps -c bioconda -c conda-forge -y ncbi-amrfinderplus
76 |     - name: Download AMRFinderPlus database
77 |       run: |
78 |           source /Users/runner/miniconda3/bin/activate
79 |           /Users/runner/miniconda3/bin/amrfinder -u
80 |     - name: Software and DB version
81 |       run: |
82 |           source /Users/runner/miniconda3/bin/activate
83 |           amrfinder --database_version
84 |     - name: Download tests
85 |       run: |
86 |           BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master
87 |           curl --silent -L -O ${BASE_URL}/test_amrfinder.sh
88 |     - name: Run tests
89 |       run: |
90 |           source /Users/runner/miniconda3/bin/activate
91 |           echo CONDA_PREFIX = $CONDA_PREFIX
92 |           bash ./test_amrfinder.sh -p
93 | 


--------------------------------------------------------------------------------
/test_amrfinder.sh:
--------------------------------------------------------------------------------
  1 | #!/bin/bash
  2 | 
  3 | AMRFINDER_OPTS=" --plus --print_node --threads 6 "
  4 | path=0
  5 | no_download=0
  6 | print_help=0
  7 | while getopts "pnh" opt; do
  8 |     case $opt in
  9 |         p) path=1 ;;
 10 |         n) no_download=1 ;;
 11 |         h) print_help=1 ;;
 12 |     esac
 13 | done
 14 | 
 15 | if [ "$print_help" -gt 0 ]
 16 | then
 17 |     echo "test_amrfinder.sh - Run tests"
 18 |     echo "Options: "
 19 |     echo "    -p Test the amrfinder command in path instead of ./amrfinder"
 20 |     echo "    -n Don't attempt to download fresh test data, use the test data in $PWD"
 21 |     echo "    -h print this help message"
 22 |     exit 1
 23 | fi
 24 | 
 25 | # some color macros
 26 | if [ "$TERM" == "" ] || [ "$TERM" == "dumb" ] || [ ! -t 1 ]
 27 | then
 28 |     green='' # no colors
 29 |     red=''
 30 |     reset=''
 31 | else
 32 |     green=`tput setaf 2`  # Set green foreground color (code 2)
 33 |     red=`tput setaf 1`    # Set red foreground color (code 1)
 34 |     reset=`tput sgr0`     # Reset color to default
 35 | fi
 36 | 
 37 | if [ "$path" -gt 0 ]
 38 | then
 39 |     echo "Testing amrfinder command in your \$PATH"
 40 |     which amrfinder
 41 |     AMRFINDER=amrfinder
 42 | else
 43 |     echo "Testing ./amrfinder"
 44 |     AMRFINDER=./amrfinder
 45 | fi
 46 | 
 47 | if [ "$no_download" -gt 0 ]
 48 | then
 49 |     echo "-n option detected, skipping download of test data and using tests in"
 50 |     echo "$PWD.  Note test data may not match the latest database release."
 51 | else
 52 |     echo Downloading fresh test data...
 53 |     BASE_URL=https://raw.githubusercontent.com/ncbi/amr/master
 54 |     curl --silent --location \
 55 |        -O ${BASE_URL}/test_dna.fa \
 56 |        -O ${BASE_URL}/test_prot.fa \
 57 |        -O ${BASE_URL}/test_prot.gff \
 58 |        -O ${BASE_URL}/test_both.expected \
 59 |        -O ${BASE_URL}/test_dna.expected \
 60 |        -O ${BASE_URL}/test_dna_mut_all.expected \
 61 |        -O ${BASE_URL}/test_prot.expected \
 62 |        -O ${BASE_URL}/test_disrupt.fa \
 63 |        -O ${BASE_URL}/test_disrupt.expected
 64 | 
 65 |     if [ $? != 0 ]
 66 |     then
 67 |         echo "${red}WARNING: Could not download new test data.${reset}"
 68 |         echo "Will attempt to use test data in $PWD."
 69 |         echo "Test data included with installation may not match the latest database release."
 70 |     fi
 71 | fi
 72 | 
 73 | TESTS=0
 74 | TEST_TEXT=""
 75 | FAILURES=0
 76 | 
 77 | function test_input_file {
 78 |     local test_base="$1"
 79 |     local options="$2"
 80 | 
 81 |     TESTS=$(( $TESTS + 1 ))
 82 | 
 83 |     if ! $AMRFINDER $options $AMRFINDER_OPTS > "$test_base.got"
 84 |     then
 85 |         echo "${red}not ok: $AMRFINDER returned a non-zero exit value indicating a failure of the software${reset}"
 86 |         echo "#   $AMRFINDER $options $AMRFINDER_OPTS > $test_base.got"
 87 |         return 1
 88 |     else
 89 |         if ! diff -q "$test_base.expected" "$test_base.got"
 90 |         then
 91 |             echo "${red}not ok: $AMRFINDER returned output different from expected.${reset}"
 92 |             echo "#   diff $test_base.expected $test_base.got"
 93 |             echo "#   To approve run: "
 94 |             echo "#         mv $test_base.got $test_base.expected"
 95 |             TEST_TEXT="$TEST_TEXT"$'\n'"${red}Failed $test_base${reset}";
 96 |             echo ""
 97 |             return 1
 98 |         else
 99 |             echo "${green}ok:${reset} $test_base"
100 |             return 0
101 |         fi
102 |     fi
103 | }
104 | 
105 | test_input_file "test_prot" "-p test_prot.fa -g test_prot.gff -O Escherichia"
106 | FAILURES=$(( $? + $FAILURES ))
107 | 
108 | test_input_file "test_dna" "-n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got"
109 | FAILURES=$(( $? + $FAILURES ))
110 | 
111 | test_input_file "test_both" "-n test_dna.fa -g test_prot.gff -p test_prot.fa -O Escherichia"
112 | FAILURES=$(( $? + $FAILURES ))
113 | 
114 | test_input_file "test_disrupt" "-n test_disrupt.fa -O Klebsiella_pneumoniae"
115 | FAILURES=$(( $? + $FAILURES ))
116 | 
117 | # gzipped input
118 | # gzip -c test_prot.fa > test_prot.fa.gz 
119 | # gzip -c test_dna.fa > test_dna.fa.gz
120 | # gzip -c test_prot.gff > test_prot.gff.gz
121 | # test_input_file "test_prot" "-n test_dna.fa.gz -p test_prot.fa.gz -g test_prot.gff.gz --protein_output test_prot.gz.fa --nucleotide_output test_dna.gz.out"
122 | 
123 | echo "Done."
124 | echo "$TEST_TEXT"
125 | echo ""
126 | if [ "$FAILURES" -gt 0 ]
127 | then
128 |     PASSED=$(( $TESTS - $FAILURES ))
129 |     echo "${red}not ok overall: $FAILURES out of $TESTS amrfinder tests failed${reset}"
130 |     exit 1
131 | else
132 |     echo "${green}ok: all $TESTS amrfinder tests passed ${reset}"
133 |     echo "Success!"
134 | fi
135 | 


--------------------------------------------------------------------------------
/mutate.cpp:
--------------------------------------------------------------------------------
  1 | // mutate.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Mutate a FASTA file
 31 | *
 32 | */
 33 | 
 34 | 
 35 | #undef NDEBUG
 36 | 
 37 | #include "common.hpp"
 38 | using namespace Common_sp;
 39 | #include "alignment.hpp"
 40 | using namespace Alignment_sp;
 41 | #include "seq.hpp"
 42 | using namespace Seq_sp;
 43 | 
 44 | #include "common.inc"
 45 | 
 46 | 
 47 | 
 48 | namespace 
 49 | {
 50 | 
 51 | 
 52 | 
 53 | struct ThisApplication final : Application
 54 | {
 55 |   ThisApplication ()
 56 |     : Application ("Mutate a FASTA file")
 57 |     {
 58 |   	  addPositional ("in", "Input FASTA file");
 59 |   	  addPositional ("mut", "AmrMutation table: <seq_id> <1-based pos> <mutation_std> <mutation_report>");
 60 |   	  addFlag ("aa", "Protein/DNA");
 61 |   	  addFlag ("orig", "Add the original, non-mutated sequences");
 62 | 
 63 |  	    version = SVN_REV;  
 64 |     }
 65 | 
 66 | 
 67 | 	
 68 | 	void body () const final
 69 |   {
 70 | 	  const string inFName  = getArg ("in");
 71 | 	  const string mutFName = getArg ("mut");
 72 | 	  const bool aa         = getFlag ("aa");
 73 | 	  const bool orig       = getFlag ("orig");
 74 |   
 75 |   
 76 |     map <string/*seqId*/,Vector<AmrMutation>> id2mutation;
 77 |     {
 78 |       LineInput in (mutFName);
 79 |       Istringstream iss;
 80 |       while (in. nextLine ())
 81 |       {
 82 |         iss. reset (in. line);
 83 |         string seqId;
 84 |         size_t pos;
 85 |         string mutation_std;
 86 |         string mutation_report;
 87 |         iss >> seqId >> pos >> mutation_std >> mutation_report;
 88 |         QC_ASSERT (! mutation_report. empty ());
 89 |         AmrMutation mut (pos, mutation_std, mutation_report, "X", "X", "X");
 90 |         mut. qc ();
 91 |         id2mutation [seqId] << std::move (mut);
 92 |       }
 93 |     }
 94 |   
 95 |   
 96 | 	  Multifasta fIn (inFName, aa);
 97 | 	  while (fIn. next ())
 98 | 	  {
 99 |  	    unique_ptr<const Seq> seq;
100 | 	    try
101 |   	  {
102 |   	    if (aa)
103 |   	    {
104 |   	      auto pep = new Peptide (fIn, 1000, false);  // PAR
105 |   	      pep->pseudo = true;
106 |   	      seq. reset (pep);  
107 |   	    }
108 |   	    else
109 |   	      seq. reset (new Dna     (fIn, 100000, false));  // PAR
110 |   	    seq->qc ();
111 |   	    if (orig)
112 |   	      seq->saveText (cout);
113 |   	    if (const Vector<AmrMutation>* muts = findPtr (id2mutation, seq->getId ()))
114 |   	      for (const AmrMutation& mut : *muts)
115 |     	    {
116 |     	      unique_ptr<Seq> seq1 (seq->copy ());
117 |     	      mut. apply (seq1->seq);
118 |     	      if (! aa)
119 |     	        strLower (seq1->seq);
120 |       	    seq1->name += ":" + to_string (mut. pos_real + 1) + ":" + mut. geneMutation;
121 |       	    seq1->qc ();
122 |       	    seq1->saveText (cout);
123 |     	    }
124 |   	  }
125 |   	  catch (const exception &e)
126 |   	  {
127 |   	    if (seq)
128 |   	      throw runtime_error (seq->name + "\n" + e. what ());
129 |   	    throw;
130 |   	  }
131 |   	}
132 |   }
133 | };
134 | 
135 | 
136 | 
137 | }  // namespace
138 | 
139 | 
140 | 
141 | 
142 | int main (int argc, 
143 |           const char* argv[])
144 | {
145 |   ThisApplication app;
146 |   return app. run (argc, argv);  
147 | }
148 | 
149 | 
150 | 
151 | 


--------------------------------------------------------------------------------
/amrfinder_index.cpp:
--------------------------------------------------------------------------------
  1 | // amrfinder_index.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Indexing of AMRFinder data
 31 | *
 32 | * Dependencies: NCBI BLAST, HMMer
 33 | *
 34 | * Release changes: see amrfinder.cpp
 35 | *
 36 | */
 37 | 
 38 | 
 39 | 
 40 | 
 41 | #ifdef _MSC_VER
 42 |   #error "UNIX is required"
 43 | #endif
 44 |    
 45 | #undef NDEBUG 
 46 | #include "common.hpp"
 47 | using namespace Common_sp;
 48 | 
 49 | #include "common.inc"
 50 | 
 51 | 
 52 | 
 53 | 
 54 | namespace 
 55 | {
 56 | 
 57 | 
 58 | 	
 59 | // ThisApplication
 60 | 
 61 | struct ThisApplication final : ShellApplication
 62 | {
 63 |   ThisApplication ()
 64 |     : ShellApplication ("Index the database for AMRFinder", true, false, true, true)
 65 |     {
 66 |     	addPositional ("DATABASE", "Directory with AMRFinder database");
 67 |     	addKey ("blast_bin", "Directory for BLAST", "", '\0', "BLAST_DIR");
 68 |     	addKey ("hmmer_bin", "Directory for HMMer", "", '\0', "HMMER_DIR");
 69 | 	    version = SVN_REV;
 70 |     }
 71 | 
 72 | 
 73 | 
 74 |   void shellBody () const final
 75 |   {
 76 |     string dbDir     = getArg ("DATABASE");
 77 |     string blast_bin = getArg ("blast_bin");
 78 |     string hmmer_bin = getArg ("hmmer_bin");
 79 | 
 80 |     addDirSlash (dbDir);
 81 |     addDirSlash (blast_bin);
 82 |     addDirSlash (hmmer_bin);
 83 |     
 84 |         
 85 |     const Verbose vrb (qc_on);
 86 |     
 87 |     
 88 |     if (! directoryExists (dbDir))
 89 |       throw runtime_error ("Database directory " + dbDir + " does not exist");
 90 |                             
 91 |     if (! blast_bin. empty ())
 92 |       prog2dir ["makeblastdb"] = blast_bin;
 93 |     findProg ("makeblastdb");    
 94 | 
 95 |     if (! hmmer_bin. empty ())
 96 |       prog2dir ["hmmpress"] = hmmer_bin;
 97 |     findProg ("hmmpress");
 98 |     
 99 | 
100 |     // Cf. amrfinder_update.cpp
101 |     StringVector dnaPointMuts;
102 |     {
103 |       LineInput f (dbDir + "taxgroup.tsv", verbose () ? 1 : 0);
104 |       while (f. nextLine ())
105 |       {
106 |    	    if (isLeft (f. line, "#"))
107 | 	 	      continue;
108 |         string taxgroup = f. line;
109 |         const int n        = str2<int> (rfindSplit (taxgroup, '\t'));
110 |         const string gpipe =            rfindSplit (taxgroup, '\t');
111 |         QC_ASSERT (n >= 0);
112 |         QC_ASSERT (! contains (taxgroup, ' '));
113 |         if (n)
114 |           dnaPointMuts << taxgroup;
115 |       }
116 |     }    
117 |     
118 |     stderr. section ("Indexing");
119 |     exec (fullProg ("hmmpress") + " -f " + shellQuote (dbDir + "AMR.LIB") + " > /dev/null 2> " + tmp + "/hmmpress.err", tmp + "/hmmpress.err");
120 |     setSymlink (dbDir, tmp + "/db", true);
121 | 	  exec (fullProg ("makeblastdb") + " -in " + tmp + "/db/AMRProt.fa" + "  -dbtype prot  -logfile " + tmp + "/makeblastdb.AMRProt", tmp + "/makeblastdb.AMRProt");  
122 | 	  exec (fullProg ("makeblastdb") + " -in " + tmp + "/db/AMR_CDS.fa" + "  -dbtype nucl  -logfile " + tmp + "/makeblastdb.AMR_CDS", tmp + "/makeblastdb.AMR_CDS");  
123 |     for (const string& dnaPointMut : dnaPointMuts)
124 |   	  exec (fullProg ("makeblastdb") + " -in " + tmp + "/db/AMR_DNA-" + dnaPointMut + ".fa  -dbtype nucl  -logfile " + tmp + "/makeblastdb.AMR_DNA-" + dnaPointMut, tmp + "/makeblastdb.AMR_DNA-" + dnaPointMut);
125 |   }
126 | };
127 | 
128 | 
129 | 
130 | }  // namespace
131 | 
132 | 
133 | 
134 | int main (int argc, 
135 |           const char* argv[])
136 | {
137 |   ThisApplication app;
138 |   return app. run (argc, argv);  
139 | }
140 | 
141 | 
142 | 
143 | 


--------------------------------------------------------------------------------
/curl_easy.cpp:
--------------------------------------------------------------------------------
  1 | // curl_easy.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   curl_easy functions
 31 | *
 32 | */
 33 | 
 34 | 
 35 | #undef NDEBUG
 36 | 
 37 | #include "curl_easy.hpp"
 38 | using namespace Common_sp;
 39 | 
 40 | #include "common.inc"
 41 | 
 42 | 
 43 | 
 44 | namespace CURL_sp
 45 | {
 46 |   
 47 |   
 48 |   
 49 | SoftwareVersion getLibVersion ()
 50 | {
 51 |   if (const curl_version_info_data* ver = curl_version_info (CURLVERSION_NOW))
 52 |   {
 53 |     const uint major = (ver->version_num >> 16) & 0xff;
 54 |     const uint minor = (ver->version_num >> 8)  & 0xff;
 55 |     const uint patch = ver->version_num         & 0xff;
 56 |     return SoftwareVersion (major, minor, patch);
 57 |   }
 58 |   return SoftwareVersion ();
 59 | }
 60 | 
 61 | 
 62 |   
 63 | 
 64 | // Curl
 65 | 
 66 | namespace 
 67 | {
 68 |   size_t write_stream_cb (char* ptr,
 69 |                           size_t size, 
 70 |                           size_t nMemb, 
 71 |                           void* userData)
 72 |   {
 73 |     ASSERT (ptr);
 74 |     ASSERT (size == 1);
 75 |     ASSERT (userData);
 76 |     
 77 |     OFStream& f = * static_cast <OFStream*> (userData);
 78 |     FOR (size_t, i, nMemb)
 79 |       f << ptr [i];
 80 |     
 81 |     return nMemb;
 82 |   }
 83 | 
 84 | 
 85 | 
 86 |   size_t write_string_cb (char* ptr,
 87 |                           size_t size, 
 88 |                           size_t nMemb, 
 89 |                           void* userData)
 90 |   {
 91 |     ASSERT (ptr);
 92 |     ASSERT (size == 1);
 93 |     ASSERT (userData);
 94 |     
 95 |     string& s = * static_cast <string*> (userData);
 96 |     FOR (size_t, i, nMemb)
 97 |       s += ptr [i];
 98 |     
 99 |     return nMemb;
100 |   }
101 | }
102 | 
103 | 
104 |  	
105 | void Curl::download (const string &url,
106 |                      const string &fName) 
107 | {
108 |   ASSERT (! fName. empty ());  
109 |   
110 |   {
111 |     OFStream f (fName);
112 |     curl_easy_setopt (eh, CURLOPT_WRITEFUNCTION, write_stream_cb);
113 |     curl_easy_setopt (eh, CURLOPT_WRITEDATA, & f);
114 |     process (url, "download");
115 |   }
116 |   
117 |   IFStream f (fName);
118 |   string s;
119 |   f >> s;
120 |   if (s == "<?xml")
121 |     throw runtime_error ("Cannot download " + strQuote (fName));
122 | }
123 | 
124 | 
125 | 
126 | string Curl::read (const string &url)
127 | {
128 |   string s;  s. reserve (1024);  // PAR  
129 |   curl_easy_setopt (eh, CURLOPT_WRITEFUNCTION, write_string_cb);
130 |   curl_easy_setopt (eh, CURLOPT_WRITEDATA, & s);
131 |   process (url, "read");
132 |   
133 |   return s;
134 | }
135 | 
136 | 
137 | 
138 | void Curl::process (const string &url,
139 |                     const string &error_msg_action)
140 | {
141 |   QC_ASSERT (! url. empty ());  
142 | 
143 |   char err [CURL_ERROR_SIZE + 1] = "";
144 |   curl_easy_setopt (eh, CURLOPT_ERRORBUFFER, err);
145 |   
146 |   curl_easy_setopt (eh, CURLOPT_URL, url. c_str ());
147 |   if (isLeft (url, "ftp://"))
148 |     curl_easy_setopt (eh, CURLOPT_FTP_USE_EPSV, 0);
149 | 
150 |   const CURLcode cc = curl_easy_perform (eh);
151 |   if (cc)
152 |   {
153 |     const SoftwareVersion ver (CURL_sp::getLibVersion ());
154 |     throw runtime_error ("CURL: Cannot " + error_msg_action
155 |                          + "\n  from " + url 
156 |                          + "\n  code=" + to_string ((int) cc) 
157 |                          + "\n  error: " + err
158 |                          + "\n  version: " + ver. str ()
159 |                          );
160 |   }
161 | }
162 | 
163 | 
164 | 
165 | 
166 | }  // namespace
167 | 
168 | 
169 | 


--------------------------------------------------------------------------------
/test_dna.expected:
--------------------------------------------------------------------------------
 1 | Protein id	Contig id	Start	Stop	Strand	Element symbol	Element name	Scope	Type	Subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference	% Identity to reference	Alignment length	Closest reference accession	Closest reference name	HMM accession	HMM description	Hierarchy node
 2 | NA	contig01	1	984	+	blaTEMp_G162T	Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter	core	AMR	POINT	BETA-LACTAM	AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID	POINTN	984	1176	83.67	99.80	984	NZ_CP095603.1:148777-149952	blaTEM promoter region	NA	NA	NA
 3 | NA	contig01	101	958	+	blaTEM-156	class A beta-lactamase TEM-156	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	ALLELEX	286	286	100.00	100.00	286	WP_061158039.1	class A beta-lactamase TEM-156	NA	NA	blaTEM-156
 4 | NA	contig02	1	1191	+	blaPDC	PDC family class C beta-lactamase	core	AMR	AMR	BETA-LACTAM	CEPHALOSPORIN	BLASTX	397	397	100.00	99.75	397	WP_061189306.1	class C beta-lactamase PDC-114	NA	NA	blaPDC
 5 | NA	contig03	101	802	+	blaOXA	OXA-48 family class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	234	265	88.30	100.00	234	WP_058842180.1	OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436	NA	NA	blaOXA-48_fam
 6 | NA	contig04	101	1147	+	vanG	D-alanine--D-serine ligase VanG	core	AMR	AMR	GLYCOPEPTIDE	VANCOMYCIN	EXACTX	349	349	100.00	100.00	349	WP_063856695.1	D-alanine--D-serine ligase VanG	NA	NA	vanG
 7 | NA	contig04	1261	2391	+	blaEC	BlaEC family class C beta-lactamase	plus	AMR	AMR	BETA-LACTAM	BETA-LACTAM	BLASTX	377	377	100.00	98.14	377	WP_063610930.1	extended-spectrum class C beta-lactamase EC-15	NA	NA	blaEC
 8 | NA	contig08	1	700	+	blaTEMp_G162T	Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter	core	AMR	POINT	BETA-LACTAM	AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID	POINTN	700	1176	59.52	99.71	700	NZ_CP095603.1:148777-149952	blaTEM promoter region	NA	NA	NA
 9 | NA	contig08	101	700	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIAL_CONTIG_ENDX	200	286	69.93	100.00	200	WP_061158039.1	class A beta-lactamase TEM-156	NA	NA	blaTEM
10 | NA	contig09	1	651	-	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIAL_CONTIG_ENDX	217	267	81.27	100.00	217	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NA	NA	aph(3'')-Ib
11 | NA	contig09	715	1377	-	sul2	sulfonamide-resistant dihydropteroate synthase Sul2	core	AMR	AMR	SULFONAMIDE	SULFONAMIDE	PARTIAL_CONTIG_ENDX	221	271	81.55	100.00	221	WP_001043265.1	sulfonamide-resistant dihydropteroate synthase Sul2	NA	NA	sul2
12 | NA	contig10	486	1307	+	blaOXA	OXA-9 family oxacillin-hydrolyzing class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	274	274	100.00	99.64	274	WP_000722315.1	oxacillin-hydrolyzing class D beta-lactamase OXA-9	NA	NA	blaOXA-9_fam
13 | NA	contig11	1	984	+	blaTEMp_G162T	Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter	core	AMR	POINT	BETA-LACTAM	AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID	POINTN	984	1176	83.67	96.04	984	NZ_CP095603.1:148777-149952	blaTEM promoter region	NA	NA	NA
14 | NA	contig11	101	958	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	286	286	100.00	93.01	286	WP_061158039.1	class A beta-lactamase TEM-156	NA	NA	blaTEM
15 | NA	contig12	71	634	+	qacR	multidrug-binding transcriptional regulator QacR	plus	STRESS	BIOCIDE	QUATERNARY AMMONIUM	QUATERNARY AMMONIUM	BLASTX	188	188	100.00	99.47	188	ADK23698.1	multidrug-binding transcriptional regulator QacR	NA	NA	qacR
16 | NA	contig13	1	1137	+	emrD3	multidrug efflux MFS transporter EmrD-3	plus	AMR	AMR	EFFLUX	EFFLUX	EXACTX	379	379	100.00	100.00	379	ABQ18953.1	multidrug efflux MFS transporter EmrD-3	NA	NA	emrD3
17 | NA	contig14	1	1089	+	pmrB_C84R	Escherichia colistin resistant PmrB	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA	pmrB
18 | NA	contig14	1093	2181	+	pmrB_C84R	Escherichia colistin resistant PmrB	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA	pmrB
19 | NA	contig15	1	2905	+	23S_A2058T	Escherichia azithromycin/erythromycin/telithromycin resistant 23S	core	AMR	POINT	MACROLIDE	AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA	NA
20 | NA	contig16	1	720	+	nfsA_K141Ter	Escherichia nitrofurantoin resistant NfsA	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA	nfsA
21 | NA	contig16	1	720	+	nfsA_R15C	Escherichia nitrofurantoin resistant NfsA	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA	nfsA
22 | NA	contig17	1	247	+	ampC_T-14TGT	Escherichia cephalosporin resistant ampC promoter	core	AMR	POINT	BETA-LACTAM	CEPHALOSPORIN	POINTN	247	245	100.00	99.19	247	NZ_CP041538.1:1149245-1149489	ampC/blaEC promoter region	NA	NA	NA
23 | NA	contig18	279	1235	+	stxA2	Shiga toxin Stx2 subunit A	plus	VIRULENCE	VIRULENCE	STX2	stxA2	EXACTX	319	319	100.00	100.00	319	TJA36680.1	Shiga toxin Stx2 subunit A	NA	NA	stxA2_acd
24 | NA	contig18	279	1516	+	stx2a_operon	stx2a operon	plus	VIRULENCE	STX_TYPE	STX2	STX2A	COMPLETE	1238	NA	NA	100.00	408	AAS07600.1,AAM90978.1	Shiga toxin stx2a	NA	NA	stxA2a::stxB2a
25 | NA	contig18	1250	1516	+	stxB2	Shiga toxin Stx2a subunit B	plus	VIRULENCE	VIRULENCE	STX2	stxB2a	EXACTX	89	89	100.00	100.00	89	AAM90978.1	Shiga toxin Stx2a subunit B	NA	NA	stxB2a
26 | 


--------------------------------------------------------------------------------
/common.inc:
--------------------------------------------------------------------------------
  1 | // common.inc
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Common macros
 31 | *   To be included into .cpp-files AFTER all headers
 32 | *
 33 | */
 34 | 
 35 | 
 36 | #define FOR_START(type,i,start,end)  for (type i = (start); i < (end); i++)  
 37 | #define FOR(type,i,end)  FOR_START (type, i, 0, (end))
 38 | // Fast FOR: precomputed end
 39 | #define FFOR_START(type,i,start,end)  for (type i = (start), i ## _end_ = (end); i < i ## _end_; i++)  
 40 | #define FFOR(type,i,end)  FFOR_START (type, i, 0, (end))
 41 | //
 42 | #define FOR_REV_END(type,i,end,start)  for (type i = (start); i-- > (end);)  
 43 | #define FOR_REV(type,i,start)  FOR_REV_END(type, i, 0, (start))
 44 | // FOR(type,i,a) and FOR_REV(type,i,a) iterate over the same i
 45 | // FOR_START(type,i,a,b) and FOR_REV_END(type,i,a,b) iterate over the same i
 46 | 
 47 | #define ITER(ContainerType,iter,container) \
 48 |   for (ContainerType::iterator iter = (container). begin (); iter != (container). end (); iter++)
 49 | #define CONST_ITER(ContainerType,iter,container) \
 50 |   for (ContainerType::const_iterator iter = (container). begin (); iter != (container). end (); iter++)
 51 | #define ITER_REV(ContainerType,iter,container) \
 52 |   for (ContainerType::reverse_iterator iter = (container). rbegin (); iter != (container). rend (); iter++)
 53 | #define CONST_ITER_REV(ContainerType,iter,container) \
 54 |   for (ContainerType::const_reverse_iterator iter = (container). rbegin (); iter != (container). rend (); iter++)
 55 | 
 56 | 
 57 | #define  Case     break; case
 58 | #define  Default  break; default
 59 | 
 60 | 
 61 | // Exceptions
 62 | 
 63 | #include <string>
 64 | #include <exception>
 65 | 
 66 | 
 67 | #ifdef _MSC_VER
 68 |   #define FUNC  std::string (__FUNCSIG__) + ":\n"
 69 | #else
 70 |   #define FUNC  std::string (__PRETTY_FUNCTION__) + ":\n"
 71 | #endif
 72 | 
 73 | 
 74 | #define ERROR_MSG(msg)                     \
 75 |   { if (! std::uncaught_exceptions ())     \
 76 |       throwf (std::string ("\"" __FILE__ "\", line ") + to_string (__LINE__) + ", in " + (FUNC) + (msg));  \
 77 |     exit (1);                              \
 78 |   }
 79 | #define ERROR            ERROR_MSG ("ERROR")
 80 | #define NOT_IMPLEMENTED  ERROR_MSG ("NOT IMPLEMENTED")
 81 | #define NEVER_CALL       ERROR_MSG ("NEVER CALL")
 82 | 
 83 | 
 84 | #define QC_ASSERT(cond)  { errno = 0; if (! (cond)) ERROR_MSG (#cond) }
 85 | 
 86 | 
 87 | namespace 
 88 | {
 89 |   const bool debugP = 
 90 |     #ifdef NDEBUG
 91 |       false
 92 |     #else
 93 |       true
 94 |     #endif
 95 |     ;
 96 | }
 97 | 
 98 | 
 99 | // Logic errors
100 | #ifdef NDEBUG                                       
101 |   #define ASSERT(cond)
102 | #else
103 |   #define ASSERT(cond)  QC_ASSERT (cond)
104 | #endif
105 | 
106 | 
107 | #ifdef NDEBUG                                       
108 |   #define EXEC_ASSERT(cond)  cond
109 | #else
110 |   #define EXEC_ASSERT(cond)  { const bool c_ = (cond); if (! c_) ERROR_MSG (#cond); }
111 | #endif
112 | 
113 | 
114 | #define IMPLY(a,b)     { if (a) { ASSERT (b) }}
115 | #define QC_IMPLY(a,b)  { if (a) { QC_ASSERT (b) }}
116 | 
117 | #define ASSERT_EQ(x,y,delta)     ASSERT    (std::fabs((x) - (y)) <= (delta))
118 | #define QC_ASSERT_EQ(x,y,delta)  QC_ASSERT (std::fabs((x) - (y)) <= (delta))
119 | 
120 | 
121 | 
122 | #define MODULE_INIT   static bool run = false; \
123 |                       if (run)                 \
124 |                         return true;           \
125 |                       run = true;
126 | 
127 | 
128 | #define LESS_PART(x,y,part)  { if ((x).part < (y).part)  return true; \
129 |                                if ((y).part < (x).part)  return false; }
130 | #define LESS_COMP(comp)  { const ebool c = comp; if (c == etrue) return true; if (c == efalse) return false; }
131 | #define COMP_PART(x,y,part)  { if ((x).part < (y).part)  return -1; \
132 |                                if ((y).part < (x).part)  return  1; }
133 | 
134 | 
135 | 
136 | #define PRINT(x)  { Offset::newLn (cout); cout << #x << " = " << (x); }
137 | 
138 | #define LOG(x)  { if (logPtr) *logPtr << (x) << endl; }
139 | 
140 | #define XSTR(s) STR(s)
141 | #define STR(s)  #s
142 | 
143 | 
144 | 


--------------------------------------------------------------------------------
/test_prot.fa:
--------------------------------------------------------------------------------
 1 | >blaTEM-156
 2 | MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLS
 3 | RVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNIGDHVTRL
 4 | DRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGS
 5 | RGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
 6 | >blaPDC-114_blast BLAST (100% length, but 1 mismatch)
 7 | MRDTRFPCLCGIAASTLLFATTPAIAGEAPADRLKALVDAAVQPVMKANDIPGLAVAISLKGEPHYFSYGLASKEDGRRV
 8 | TPETLFEIGSVSKTFTATLAGYALTQDKMRLDDRASQHWPALVGSRFDGISLLDLATYTAGGLPLQFPDSVQKDQAQIRD
 9 | YYRQWQPTYAPGSQRLYSNPSIGLFGYLAARSLGQPFERLMEQQVFPALGLEQTHLDVPEAALAQYAQGYGKDDRPLRAG
10 | PGPLDAEGYGVKTSAADLLRFVDANLHPERLDRPWAQALDATHRGYYKVGDMTQGLGWEAYDWPISLKRLQAGNSTPMAL
11 | QPHRIARLPAPQALEGQRLLNKTGSTNGFGAYVAFVPGRDLGLVILANRNYPNAERVKIAYAILSGLEQQGKVPLKR
12 | >blaOXA-436_partial (Should be partial OXA-48 family
13 | MRALALSAVLMVTTMIGMPAVAKEWQENKSWNAHFSEHKTQGVVVLWNENTQQGFTNDLKRANQAFLPASTFKIPNSLIA
14 | LDLGVVKDEHQVFKWDGQTRDIAAWNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNLDSFWLDG
15 | GIRISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANADYIIRAKTGYSVRIEPKIGWWVGWIELDDNVW
16 | >vanG
17 | MQNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTWFEDSKN
18 | LCPVVVSQNRSVKGFLEIASDKYRIIKVDLVFPVLHGKNGENGTLQGIFELAGIPVVGCDTLSSALCMDK
19 | DRAHKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQELDAAIELAF
20 | EHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQ
21 | EAAVTIYKALGCSGFSRVDMFYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYVE
22 | >gyrA  T86I  Campylobacter
23 | MENIFSKDSDIELVDIENSIKGSYLDYSMSVIIGRALPDARDGLKPVHRRILYAMQNDEAKSRTDFVKSARIVGAVIGRYHPHGDAAVYDALVRMAQDFSMRYPSITGQGNFGSIDGDSAAAMRYTEAKMSKLSHELLKD
24 | IDKDTVDFVPNYDGSESEPDVLPSRVPNLLLNGSSGIAVGMATNIPPHSLNELIDGLLYLLDSKDASLEE
25 | IMQFIKGPDFPTGGIIYGKKGIIEAYRTGRGRVKVRAKTHIEKKTNKDVIVIDELPYQTNKARLIEQIAE
26 | LVKEKQIEGISEVRDESNKEGIRVVIELKREAMSEIVLNNLFKSTTMESTFGVIMLAIHNKEPKIFSLLE
27 | LLNLFLTHRKTVIIRRTIFELQKARARAHILEGLKIALDNIDEVIALIKNSSDNNTARDSLVAKFGLSEL
28 | QANAILDMKLGRLTGLEREKIENELAELMKEIARLEEILKSETLLENLIRDELKEIRSKFDVPRITQIED
29 | DYDDIDIEDLIPNENMVVTITHRGYIKRVPSKQYEKQKRGGKGKLAVTTYDDDFIESFFTANTHDTLMFV
30 | TDRGQLYWLKVYKIPEGSRTAKGKAVVNLINLQAEEKIMAIIPTTDFDESKSLCFFTKNGIVKRTNLSEY
31 | QNIRSVGVRAINLDENDELVTAIIVQRDEDEIFATGGEENLENQEIENLDDENLENEESVSTQGKMLFAV
32 | TKKGMCIKFPLAKVREIGRVSRGVTAIKFKEKNDELVGAVVIENDEQEILSISAKGIGKRTNAGEYRLQS
33 | RGGKGVICMKLTEKTKDLISVVIVDETMDLMALTSSGKMIRVDMQSIRKAGRNTSGVIVVNVENDEVVSI
34 | AKCPKEENDEDELSDENFGLDL
35 | >50S_L22 Campylobacter 50S_L22:A103V
36 | MSKALIKFIRLSSTKARLIAREVQGMNAELAMASLKFMPNKGAKYIANAISSAVANGGFEANEVIVKSCRVDAAAVLKRF
37 | RPRARGSASRIRKPTSHILVEVVKAEVKAEEKKTVAKKTTTTKAPAKKTTSTKKATAKKES
38 | 
39 | >nimIJ_hmm  WP_027455679.1 NimIJ family nitroimidazole resistance protein [Prevotella brevis]
40 | MSEFREMRRKRQQLTDADSIAVLQKATSGTLALLGDNDYPYAVPISYVYDNGKLYFHSAMAGHKVDAIRR
41 | CNKASFCVIEKDDVRPEKYTTYFRSVIAFGRIEIVEDEAEKRTIMHMMGNRFNPNHDDALQKELESGLAH
42 | MLAIRMDIEHLTGKEAIELVRQRGGN
43 | 
44 | >aph3pp-Ib_partial_5p_neg  NZ_QKNQ01000001.1 Providencia rettgeri strain Pret_2032, whole genome shotgun sequence  2160922-2162737  150-1527  704-137
45 | IRKLKEPPLNRTNIFFGESHSDWLPVRGGESGDFVFRRGDGHAFAKIAPASRRGELAGERDRLIWLKGRGVACPEVINWQEEQEGACLVITAIPGVPAADLSGADLLKAWPSMGQQLGAVHSLSVDQCPFERRLSRMFGRAVDVVSRNAVNPDFLPDEDKSTPQLDLLARVERELPVRLDQERTDMVVCHGDPCMPNFMVDPKTLQCTGLIDLGRLGTADRYADL
46 | 
47 | >sul2_partial_3p_neg   NZ_QKNQ01000001.1 Providencia rettgeri strain Pret_2032, whole genome shotgun sequence  2160922-2162737  150-1377  2-667
48 | SSNPDAAPVSSDTEIERIAPVLDALKADGIPVSLDSYQPATQAYALSRGVAYLNDIRGFPDAAFYPQLAKSSAKLVVMHSVQDGQADRREAPAGDIMDHIAAFFDARIAALTGAGIKRNRLVLDPGMGFFLGAAPETSLSVLARFDELRLRFDLPVLLSVSRKSFLRALTGRGPGDVGAATLAAELAAAAGGADFIRTHEPRPLRDGLAVLAALKETARIR
49 | 
50 | >blaTEM-internal_stop
51 | HFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVNYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSCVDAG
52 | QEQLGRSIHYSQNDLVEYSPVTEKHLTDGMTLRELCSAAITMSDNTAANLLLTTIGGPKELTA
53 | 
54 | >qacR-curated_blast  (ADK23698.1)
55 | MKLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKENLFLEILNIEESKWQEQWKKEQI
56 | KCKTNREKFYLYNELSLTTEYYYPLQNAIIEFYTEYYKTNSINEKMNKLENKYIDAYHVIFKEGNLNGEW
57 | CINDVNAVSKIAANAVNGIVTFTHEQNINERIKLMNKFSQIFLNGLSK
58 | 
59 | >arsR-suppressed-in-escherichia BAE77793.1  arsR_K-12 As(III)-sensing_metalloregulatory_transcriptional_repressor_ArsR
60 | MSFLLPIQLFKILADETRLGIVLLLSELGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAW
61 | AAKIIDEAWRCEQEKVQAIVRNLARQNCSGDSKNICS
62 | 
63 | >emrD3-suppressed-in-vibrio ABQ18953.1
64 | MKTKPSLWLMVIMLMFPQIVETIYSPVLGSIARSFSVSDAQAAQTLSVYFLAFALGVVIWGVLADKWGRRPTMLVGLLIY
65 | GSATFIAMQTDSFTILMLARVFSAFGIAVGSVVTQTILRDVFSGHELRKVFSLMGIGISISPVLGMLLGGQLAFAGGHQL
66 | VFLALFFIALVLFVYNLCQLPETQQVKPKIALGCLVARMFKDRQVLLSALLVALYNVALFSYYQLGAFIFSDLGLDAEQF
67 | GYSGIALGLGSLIGSFLNKTLLAKQVPQRALLLLAALLLIMGTIGVSLTLDSIGFVAAMILVVIAYGMAIPNILSTALVE
68 | YKSQAGSAGALFGLLYYLLIGSGLALTGLVQRLGVVLLMCAGITLLATLARSSHIARLP
69 | 
70 | >pmrB_C84R
71 | MHFLRRPISLRQRLILTIGAILLVFELISVFWLWHESTEQIQLFEQALRDNRNNDRHIMREIREAVASLIVPGVFMVSLTLFIRYQAVRRITRPLAELQKELEARTADNLTPIAIHSATLEIEAVVSALNDLVSRLTSTLDNERLFTADVAHELRTPLAGVRLHLELLAKTHHIDVAPLVARLDQMMESVSQLLQLARAGQSFSSGNYQHVKLLEDVILPSYDELSTMLDQRQQTLLLPESAADITVQGDATLLRMLLRNLVENAHRYSPQGSNIMIKLQEDDGAVMAVEDEGPGIDESKCGELSKAFVRMDSRYGGIGLGLSIVSRITQLHHGQFFLQNRQETSGTRAWVRLKKDQYVANQI
72 | 
73 | >nfsA_R15C_K141STOP 
74 | MTPTIELICGHRSICHFTDEPISEAQREAIINSARATSSSSFLQYSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVT
75 | 
76 | >stxA2a_prot EHY1938862.1 Shiga toxin Stx2a subunit A [Escherichia coli]
77 | MKCILFKWVLCLLLGFSSVSYSREFTIDFSTQQSYVSSLNSIRTEISTPLEHISQGTTSVSVINHTPPGSYFAVDIRGLD
78 | VYQARFDHLRLIIEQNNLYVAGFVNTATNTFYRFSDFTHISVPGVTTVSMTTDSSYTTLQRVAALERSGMQISRHSLVSS
79 | YLALMEFSGNTMTRDASRAVLRFVTVTAEALRFRQIQREFRQALSETAPVYTMTPGDVDLTLNWGRISNVLPEYRGEDGV
80 | RVGRISFNNISAILSTVAVILNCHHQGARSVRAVNEESQPECQITGDRPVIKINNTLWESNTAAAFLNRKSQFLYTTGK
81 | >stxB2a_prot EHY1938863.1 Shiga toxin Stx2a subunit B [Escherichia coli]
82 | MKKMFMAVLFALVSVNAMAADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSG
83 | FAEVQFNND
84 | 


--------------------------------------------------------------------------------
/gff.hpp:
--------------------------------------------------------------------------------
  1 | // gff.hpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   .gff file reader
 31 | *
 32 | */
 33 |    
 34 | 
 35 | #ifndef GFF_HPP
 36 | #define GFF_HPP
 37 | 
 38 | 
 39 | #include "common.hpp"
 40 | using namespace Common_sp;
 41 | 
 42 | 
 43 | 
 44 | namespace GFF_sp
 45 | {
 46 | 
 47 | 
 48 | 
 49 | struct Locus 
 50 | {
 51 |   static constexpr size_t end_delta = 3;  // PAR
 52 |   size_t lineNum {0};
 53 |     // >= 1
 54 |     // 0 - unknown
 55 |   string contig;
 56 |     // DNA FASTA id
 57 |   size_t start {0};
 58 |   size_t stop {0};
 59 |     // start <= stop
 60 |   bool strand {false};
 61 |   bool partial {false};
 62 |   size_t contigLen {0};
 63 |     // 0 <=> unknown
 64 |   bool crossOrigin {false};
 65 |   string gene;
 66 |   string product;
 67 | 
 68 |   
 69 |   Locus (size_t lineNum_arg,
 70 |          const string &contig_arg,
 71 |          size_t start_arg,
 72 |          size_t stop_arg,
 73 |          bool strand_arg,
 74 |          bool partial_arg,
 75 |          size_t crossOriginSeqLen,
 76 |          string gene_arg,
 77 |          string product_arg);
 78 |   Locus () = default;
 79 |     
 80 | 
 81 |   bool empty () const
 82 |     { return contig. empty (); }
 83 |   void print (ostream &os) const
 84 |     { os        << contig 
 85 |          << ' ' << start 
 86 |          << ' ' << stop 
 87 |          << ' ' << strand 
 88 |          << ' ' << contigLen 
 89 |          << ' ' << crossOrigin 
 90 |          << ' ' << gene 
 91 |          << ' ' << product 
 92 |          << endl; 
 93 |     }
 94 |   bool operator< (const Locus& other) const;
 95 |   size_t size () const
 96 |     { return crossOrigin
 97 |                ? contigLen - stop + start
 98 |                : stop - start;            
 99 |     }
100 |   bool atContigStart () const
101 |     { return start <= end_delta; }
102 |   bool atContigStop () const
103 |     { return contigLen && contigLen - stop <= end_delta;}
104 | };
105 | 
106 | 
107 | 
108 | struct Gff
109 | {
110 |   enum Type  {bakta, genbank, microscope, patric, pgap, prodigal, prokka, pseudomonasdb, rast, standard/*PD-4548*/};
111 |     // Alphabetic order
112 |   static const StringVector names;
113 |   static Type name2type (const string &name);
114 | };
115 | 
116 | 
117 | 
118 | struct Annot final : Root
119 | {	
120 |   // Protein GFF id is a function of attributes (column in GFF)
121 |   map<string/*protein GFF id*/,Set<Locus>> prot2loci; 
122 |   map<string/*protein FASTA id*/,string/*protein GFF id*/> fasta2gff_prot;  
123 |     // empty() => protein FASTA id = protein GFF id
124 | 
125 | 
126 |   Annot (const string &fName,
127 |          Gff::Type gffType,
128 |          bool protMatch,
129 |          bool lcl);
130 |     // GFF
131 | 		// https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
132 | 		// https://github.com/ncbi/amr/issues/91
133 | 		// Input: protMatch: property of protein FASTA:  
134 | 		//                     genbank: "[locus_tag=...]" in comment
135 | 		//                     microscope: "><acc>|ID:<num>|<gene>|
136 | 		//                     prodigal: "ID=" in comment
137 | 		//        lcl: property of DNA FASTA: >lcl|...
138 |     /*
139 |       gffType        protein GFF id
140 |       -------        --------------
141 |       bakta          ID=       
142 |       genbank        locus_tag=[project:]acc  // if pseudo or protMatch
143 |                      Name=[project:]acc       // else                    
144 |       microscope     ID=
145 |       patric         ID=...;locus_tag=...
146 |       pgap           Name=    
147 |       prodigal       ID=            
148 |       prokka         ID=      
149 |       pseudomonasdb  Alias= (or locus=)
150 |       rast           ID=       
151 |       standard       Name=         
152 |         
153 |                      ["]acc["]
154 |     */
155 |   explicit Annot (const string &fName);
156 |     // Bed
157 | 		// https://genome.ucsc.edu/FAQ/FAQformat.html#format1
158 | 		
159 | 		
160 |   void load_fasta2gff_prot (const string &fName);
161 |     // Input: fName: file is created by gff_check.cpp -gff_prot_match
162 |     // Output: fasta2gff_prot
163 |   void load_fasta2gff_dna (const string &fName);
164 |     // Input: fName: file is created by gff_check.cpp -gff_dna_match
165 |     // Output: Locus::contig
166 |   const Set<Locus>& findLoci (const string &fasta_prot) const;
167 |     // Return: !empty()
168 |     // throw if not found
169 | };
170 | 
171 | 
172 | 
173 | 
174 | }
175 | 
176 | 
177 | 
178 | #endif
179 | 


--------------------------------------------------------------------------------
/test_both.expected:
--------------------------------------------------------------------------------
 1 | Protein id	Contig id	Start	Stop	Strand	Element symbol	Element name	Scope	Type	Subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference	% Identity to reference	Alignment length	Closest reference accession	Closest reference name	HMM accession	HMM description	Hierarchy node
 2 | NA	contig01	1	984	+	blaTEMp_G162T	Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter	core	AMR	POINT	BETA-LACTAM	AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID	POINTN	984	1176	83.67	99.80	984	NZ_CP095603.1:148777-149952	blaTEM promoter region	NA	NA	NA
 3 | blaTEM-156	contig01	101	961	+	blaTEM-156	class A beta-lactamase TEM-156	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	ALLELEP	286	286	100.00	100.00	286	WP_061158039.1	class A beta-lactamase TEM-156	NF000531.2	TEM family class A beta-lactamase	blaTEM-156
 4 | blaPDC-114_blast	contig02	1	1191	+	blaPDC	PDC family class C beta-lactamase	core	AMR	AMR	BETA-LACTAM	CEPHALOSPORIN	BLASTP	397	397	100.00	99.75	397	WP_061189306.1	class C beta-lactamase PDC-114	NF000422.6	PDC family class C beta-lactamase	blaPDC
 5 | blaOXA-436_partial	contig03	101	802	+	blaOXA	OXA-48 family class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALP	233	265	87.92	100.00	233	WP_058842180.1	OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-436	NF012161.0	class D beta-lactamase	blaOXA-48_fam
 6 | vanG	contig04	101	1147	+	vanG	D-alanine--D-serine ligase VanG	core	AMR	AMR	GLYCOPEPTIDE	VANCOMYCIN	EXACTP	349	349	100.00	100.00	349	WP_063856695.1	D-alanine--D-serine ligase VanG	NF000091.3	D-alanine--D-serine ligase VanG	vanG
 7 | NA	contig04	1261	2391	+	blaEC	BlaEC family class C beta-lactamase	plus	AMR	AMR	BETA-LACTAM	BETA-LACTAM	BLASTX	377	377	100.00	98.14	377	WP_063610930.1	extended-spectrum class C beta-lactamase EC-15	NA	NA	blaEC
 8 | NA	contig08	1	700	+	blaTEMp_G162T	Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter	core	AMR	POINT	BETA-LACTAM	AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID	POINTN	700	1176	59.52	99.71	700	NZ_CP095603.1:148777-149952	blaTEM promoter region	NA	NA	NA
 9 | NA	contig08	101	700	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIAL_CONTIG_ENDX	200	286	69.93	100.00	200	WP_061158039.1	class A beta-lactamase TEM-156	NA	NA	blaTEM
10 | aph3pp-Ib_partial_5p_neg	contig09	1	675	-	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIAL_CONTIG_ENDP	225	267	81.27	100.00	217	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NF032896.1	APH(3'') family aminoglycoside O-phosphotransferase	aph(3'')-Ib
11 | sul2_partial_3p_neg	contig09	715	1377	-	sul2	sulfonamide-resistant dihydropteroate synthase Sul2	core	AMR	AMR	SULFONAMIDE	SULFONAMIDE	PARTIAL_CONTIG_ENDP	221	271	81.55	100.00	221	WP_001043265.1	sulfonamide-resistant dihydropteroate synthase Sul2	NA	NA	sul2
12 | NA	contig10	486	1307	+	blaOXA	OXA-9 family oxacillin-hydrolyzing class D beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	274	274	100.00	99.64	274	WP_000722315.1	oxacillin-hydrolyzing class D beta-lactamase OXA-9	NA	NA	blaOXA-9_fam
13 | NA	contig11	1	984	+	blaTEMp_G162T	Escherichia amoxicillin-clavulanic acid/piperacillin-tazobactam/ticarcillin-clavulanic acid resistant blaTEM promoter	core	AMR	POINT	BETA-LACTAM	AMOXICILLIN-CLAVULANIC_ACID/PIPERACILLIN-TAZOBACTAM/TICARCILLIN-CLAVULANIC_ACID	POINTN	984	1176	83.67	96.04	984	NZ_CP095603.1:148777-149952	blaTEM promoter region	NA	NA	NA
14 | blaTEM-internal_stop	contig11	113	547	+	blaTEM	TEM family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	INTERNAL_STOP	144	286	50.35	97.22	144	WP_000027057.1	broad-spectrum class A beta-lactamase TEM-1	NA	NA	blaTEM
15 | qacR-curated_blast	contig12	71	637	+	qacR	multidrug-binding transcriptional regulator QacR	plus	STRESS	BIOCIDE	QUATERNARY AMMONIUM	QUATERNARY AMMONIUM	BLASTP	188	188	100.00	99.47	188	ADK23698.1	multidrug-binding transcriptional regulator QacR	NA	NA	qacR
16 | emrD3-suppressed-in-vibrio	contig13	1	1137	+	emrD3	multidrug efflux MFS transporter EmrD-3	plus	AMR	AMR	EFFLUX	EFFLUX	EXACTP	379	379	100.00	100.00	379	ABQ18953.1	multidrug efflux MFS transporter EmrD-3	NA	NA	emrD3
17 | NA	contig14	1	1089	+	pmrB_C84R	Escherichia colistin resistant PmrB	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA	pmrB
18 | pmrB_C84R	contig14	1093	2181	+	pmrB_C84R	Escherichia colistin resistant PmrB	core	AMR	POINT	COLISTIN	COLISTIN	POINTP	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA	pmrB
19 | NA	contig15	1	2905	+	23S_A2058T	Escherichia azithromycin/erythromycin/telithromycin resistant 23S	core	AMR	POINT	MACROLIDE	AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA	NA
20 | NA	contig16	1	720	+	nfsA_K141Ter	Escherichia nitrofurantoin resistant NfsA	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA	nfsA
21 | NA	contig16	1	720	+	nfsA_R15C	Escherichia nitrofurantoin resistant NfsA	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA	nfsA
22 | NA	contig17	1	247	+	ampC_T-14TGT	Escherichia cephalosporin resistant ampC promoter	core	AMR	POINT	BETA-LACTAM	CEPHALOSPORIN	POINTN	247	245	100.00	99.19	247	NZ_CP041538.1:1149245-1149489	ampC/blaEC promoter region	NA	NA	NA
23 | stxA2a_prot	contig18	279	1238	+	stxA2	Shiga toxin Stx2 subunit A	plus	VIRULENCE	VIRULENCE	STX2	stxA2	EXACTP	319	319	100.00	100.00	319	TJA36680.1	Shiga toxin Stx2 subunit A	NF041702.1	Shiga toxin Stx2 subunit A	stxA2_acd
24 | NA	contig18	279	1516	+	stx2a_operon	stx2a operon	plus	VIRULENCE	STX_TYPE	STX2	STX2A	COMPLETE	1238	NA	NA	100.00	408	AAS07600.1,AAM90978.1	Shiga toxin stx2a	NA	NA	stxA2a::stxB2a
25 | stxB2a_prot	contig18	1250	1519	+	stxB2	Shiga toxin Stx2a subunit B	plus	VIRULENCE	VIRULENCE	STX2	stxB2a	EXACTP	89	89	100.00	100.00	89	AAM90978.1	Shiga toxin Stx2a subunit B	NF033660.0	Shiga toxin Stx2 subunit B	stxB2a
26 | nimIJ_hmm	contigX	1	501	+	nimIJ	NimIJ family 5-nitroimidazole reductase	core	AMR	AMR	NITROIMIDAZOLE	NITROIMIDAZOLE	HMM	166	165	98.18	76.54	162	WP_005812825.1	NimIJ family 5-nitroimidazole reductase	NF000262.1	NimIJ family 5-nitroimidazole reductase	nimIJ
27 | 


--------------------------------------------------------------------------------
/fasta_extract.cpp:
--------------------------------------------------------------------------------
  1 | // fasta_check.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Extract sequences out of a FASTA file
 31 | *
 32 | */
 33 |    
 34 |    
 35 | #undef NDEBUG 
 36 | 
 37 | #include "common.hpp"
 38 | using namespace Common_sp;
 39 | 
 40 | #include "common.inc"
 41 | 
 42 | 
 43 | 
 44 | namespace 
 45 | {
 46 |   
 47 |   
 48 |   
 49 | struct Segment
 50 | // not circular
 51 | {
 52 |   size_t start {0};
 53 |   size_t stop {0};
 54 |   bool strand {true};
 55 |     // false <=> negative
 56 |   string genesymbol;
 57 |   string name;
 58 |   
 59 |   
 60 |   bool isDna () const
 61 |     { return stop; }
 62 |   size_t size () const
 63 |     { return stop - start; }
 64 |   void saveText (ostream &os) const
 65 |     { os         << start 
 66 |          << '\t' << stop 
 67 |          << '\t' << strand 
 68 |          << '\t' << genesymbol 
 69 |          << '\t' << name
 70 |          << endl;
 71 |     }
 72 | };
 73 | 
 74 | 
 75 | 
 76 | char complementaryNucleotide (char wildNucleotide)
 77 | {
 78 |   char r = ' ';
 79 |   switch (toLower (wildNucleotide))
 80 |   {
 81 |     case 'a': r = 't'; break;
 82 |     case 'c': r = 'g'; break;
 83 |     case 'g': r = 'c'; break;
 84 |     case 't': r = 'a'; break;
 85 |     case 'm': r = 'k'; break;
 86 |     case 'r': r = 'y'; break;
 87 |     case 'w': r = 'w'; break;
 88 |     case 's': r = 's'; break;
 89 |     case 'y': r = 'r'; break;
 90 |     case 'k': r = 'm'; break;
 91 |     case 'v': r = 'b'; break;
 92 |     case 'h': r = 'd'; break;
 93 |     case 'd': r = 'h'; break;
 94 |     case 'b': r = 'v'; break;
 95 |     case 'n': r = 'n'; break;
 96 |     case '-': r = '-'; break;
 97 |     default: 
 98 |     	throw runtime_error ("Bad nucleotide " + to_string (wildNucleotide));
 99 |   }
100 |   if (isupper (wildNucleotide))
101 |     r = toUpper (r);
102 | 
103 |   return r;
104 | }
105 | 
106 | 
107 | 
108 | bool process (const string &id, 
109 |               string &seq, 
110 |               const map<string/*id*/,Vector<Segment>> &id2segments)
111 | {
112 |   if (id. empty ())
113 |     return false;
114 |   const Vector<Segment>* segments = findPtr (id2segments, id);
115 |   if (! segments)
116 |     return false;
117 |     
118 |   replaceStr (seq, "-", "");
119 |   QC_ASSERT (! seq. empty ());
120 |   
121 |   for (Segment& seg : var_cast (*segments))
122 |   {
123 |     cout << '>' << id;
124 |     if (seg. isDna ())
125 |     {
126 |       QC_ASSERT (seg. start <= seq. size ());
127 |       minimize (seg. stop, seq. size ());
128 |       QC_ASSERT (seg. start < seg. stop);
129 |       cout << ':' << seg. start + 1 << '-' << seg. stop << ' ' << "strand:" << (seg. strand ? '+' : '-');
130 |     }
131 |     cout << ' ' << seg. genesymbol << ' ' << seg. name << endl;
132 |     string seq1 (seq);
133 |     if (seg. isDna ())
134 |     {
135 |       ASSERT (seg. stop <= seq1. size ());
136 |       seq1 = seq1. substr (seg. start, seg. size ());
137 |       if (! seg. strand)
138 |       {
139 |         reverse (seq1);
140 |         for (char &c : seq1)
141 |           c = complementaryNucleotide (c);
142 |       }
143 |     //strLower (seq1);  // Letter case can indicate nucleotide quality
144 |     }    
145 |   //else
146 |     //strUpper (seq1);
147 |     constexpr size_t line_len = 60;  // PAR
148 |     for (size_t i = 0; i < seq1. size (); i += line_len)
149 |       cout << seq1. substr (i, line_len) << endl;
150 |   }
151 |   
152 |   return true;
153 | }
154 | 
155 | 
156 | 
157 | struct ThisApplication final : Application
158 | {
159 |   ThisApplication ()
160 |     : Application ("Extract sequences out of a FASTA file")
161 |     {
162 |       addPositional ("fasta", "FASTA file");
163 |       addPositional ("target", "Target identifiers in the FASTA file to extract.\n\
164 | Line format for amino acid sequences : <id> <gene symbol> <product name>\n\
165 | Line format for nucleotide sequences : <id> <start (>=1)> <stop (>= start)> <strand (+/-)> <gene symbol> <product name>\
166 | ");
167 |       addFlag ("aa", "Amino acid sequenes, otherwise nucleotide");
168 | 	    version = SVN_REV;
169 |     }
170 | 
171 | 
172 | 
173 |   void body () const final
174 |   {
175 |     const string fName       = getArg ("fasta");
176 |     const string targetFName = getArg ("target");
177 |     const bool aa            = getFlag ("aa");
178 |     
179 |     
180 |     map<string/*id*/,Vector<Segment>> id2segments;
181 |     {
182 |       LineInput f (targetFName);
183 |       string id;
184 |       Istringstream iss;
185 |       while (f. nextLine ())
186 |       {
187 |         iss. reset (f. line);
188 |         Segment seg;
189 |         iss >> id;
190 |         if (! aa)
191 |         {
192 |           char strand = '\0';
193 |           iss >> seg. start >> seg. stop >> strand;
194 |           QC_ASSERT (seg. start);
195 |           QC_ASSERT (seg. start <= seg. stop);
196 |           seg. start--;
197 |           QC_ASSERT (   strand == '+' 
198 |                      || strand == '-'
199 |                     );
200 |           seg. strand = (strand == '+');
201 |         }
202 |         iss >> seg. genesymbol;
203 |         seg. name = f. line. substr ((size_t) iss. tellg ());
204 |         trim (seg. name);
205 |         QC_ASSERT (aa == ! seg. isDna ());
206 |         id2segments [id] << std::move (seg);
207 |       }
208 |     }
209 |     if (verbose ())
210 |       for (const auto& it : id2segments)
211 |       {
212 |         cout << it. first << ": " << endl;
213 |         for (const Segment& seg : it. second)
214 |         {
215 |           cout << "  ";
216 |           seg. saveText (cout);
217 |         }
218 |       }
219 |     if (id2segments. empty ())
220 |       return;
221 |     
222 | 
223 |     size_t processed = 0;
224 |     {
225 |       LineInput f (fName); 
226 |       string id;
227 |       string seq;
228 |       while (f. nextLine ())
229 |       {
230 |         trimTrailing (f. line);
231 |         if (f. line. empty ())
232 |         	continue;
233 |       	if (f. line [0] == '>')
234 |       	{
235 |       	  processed += process (id, seq, id2segments);
236 |       		size_t pos = 1;
237 |       		while (pos < f. line. size () && ! isspace (f. line [pos]))
238 |       		  pos++;
239 |       		id = f. line. substr (1, pos - 1);
240 |       		seq. clear ();
241 |       	}
242 |       	else 
243 |       	  seq += f. line;
244 |   	  }
245 |    	  processed += process (id, seq, id2segments);
246 |    	}
247 |    	if (processed != id2segments. size ())  
248 |    	  throw runtime_error ("Requested identifiers: " + to_string (id2segments. size ()) + ", but processed: " + to_string (processed));
249 |    	  // Assumed: no duplicate identifiers in FASTA
250 |   }
251 | };
252 | 
253 | 
254 | 
255 | }  // namespace
256 | 
257 | 
258 | 
259 | int main (int argc, 
260 |           const char* argv[])
261 | {
262 |   ThisApplication app;
263 |   return app. run (argc, argv);  
264 | }
265 | 
266 | 
267 | 
268 | 


--------------------------------------------------------------------------------
/Makefile:
--------------------------------------------------------------------------------
  1 | ##############################################################################
  2 | # PUBLIC DOMAIN NOTICE This software/database is "United States Government
  3 | # Work" under the terms of the United States Copyright Act. It was written as
  4 | # part of the authors' official duties for the United States Government and
  5 | # thus cannot be copyrighted. This software/database is freely available to the
  6 | # public for use without a copyright notice. Restrictions cannot be placed on
  7 | # its present or future use.
  8 | #
  9 | # Although all reasonable efforts have been taken to ensure the accuracy and
 10 | # reliability of the software and data, the National Center for Biotechnology
 11 | # Information (NCBI) and the U.S. Government do not and cannot warrant the
 12 | # performance or results that may be obtained by using this software or data.
 13 | # NCBI, NLM, and the U.S. Government disclaim all warranties as to performance,
 14 | # merchantability or fitness for any particular purpose.
 15 | #
 16 | # In any work or product derived from this material, proper attribution of the
 17 | # authors as the source of the software or data should be made, using:
 18 | # https://ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/ as the
 19 | # citation.
 20 | ###############################################################################
 21 | 
 22 | # the SVNREV is set automatically here for convenience,
 23 | # but when actually building we should override it like:
 24 | # make all SVNREV=-D\'SVN_REV=\"$VERSION\"\' or use
 25 | # a version.txt file
 26 | ifeq ($(wildcard version.txt),)
 27 | 	VERSION_STRING := $(shell git describe --tags)
 28 | else
 29 | 	VERSION_STRING := $(shell cat version.txt)
 30 | endif
 31 | SVNREV := -D'SVN_REV="$(VERSION_STRING)"'
 32 | 
 33 | INSTALL=install
 34 | 
 35 | # make it possible to hard define a database directory
 36 | # Define default paths
 37 | # This is a little convoluted because I broke things and don't want
 38 | # to change two different ways of defining the paths. This could
 39 | # be simplified in a later release
 40 | PREFIX ?= /usr/local
 41 | ifneq '$(INSTALL_DIR)' ''
 42 | 	bindir=$(INSTALL_DIR)
 43 | endif
 44 | bindir ?= $(PREFIX)/bin
 45 | ifneq '$(CONDA_DB_DIR)' ''
 46 | 	DBDIR := -D'CONDA_DB_DIR="$(CONDA_DB_DIR)"'
 47 | endif
 48 | ifneq '$(DEFAULT_DB_DIR)' ''
 49 | 	DBDIR := -D'CONDA_DB_DIR="$(DEFAULT_DB_DIR)"'
 50 | endif
 51 | 
 52 | # for testing database updates using 
 53 | ifdef TEST_UPDATE
 54 | 	TEST_UPDATE_DB := '-D TEST_UPDATE'
 55 | endif
 56 | 
 57 | # detect system architecture and set appropriate flags
 58 | # this is probably not the best way (i.e. M1 Mac would be arm64)
 59 | # but it works for Nvidia Jetson boards (aarch64) 
 60 | ARCH := $(shell uname -m)
 61 | OS := $(shell uname -s)
 62 | # "hack": if amd64 we can set to aarch64
 63 | # as AArch64 and ARM64 refer to the same thing
 64 | # this should build for Mac M1 and other arm64 chips
 65 | ifeq ($(ARCH),arm64)
 66 |   ARCH := aarch64
 67 | endif
 68 | # report detected OS and arch in stdout
 69 | $(info Dectected architecture: $(OS) $(ARCH))
 70 | # set CFLAGS based on arch
 71 | ifeq ($(ARCH),aarch64)
 72 |   # set arm CFLAGS
 73 |   CPPFLAGS = -std=gnu++17 -pthread --signed-char -falign-jumps -fno-math-errno -O3 
 74 | else
 75 |   # set x86_x64 CFLAGS
 76 |   CPPFLAGS = -std=gnu++17 -pthread -malign-double -fno-math-errno -O3
 77 | endif
 78 | # was: -std=gnu++14 
 79 | 
 80 | CXX=g++
 81 | COMPILE.cpp= $(CXX) $(CPPFLAGS) $(SVNREV) $(DBDIR) $(TEST_UPDATE_DB) -c 
 82 | 
 83 | 
 84 | .PHONY: all clean install release stxtyper test
 85 | 
 86 | BINARIES= amr_report amrfinder amrfinder_index amrfinder_update fasta_check \
 87 | 		  fasta_extract fasta2parts gff_check dna_mutation mutate disruption2genesymbol
 88 | 
 89 | all:	$(BINARIES) stxtyper
 90 | 
 91 | release: clean
 92 | 	svnversion . > version.txt
 93 | 	make all
 94 | 
 95 | common.o:	common.hpp common.inc
 96 | curl_easy.o: curl_easy.hpp common.hpp common.inc
 97 | gff.o: gff.hpp common.hpp common.inc
 98 | alignment.o:	alignment.hpp seq.hpp common.hpp common.inc
 99 | seq.o: seq.hpp graph.hpp common.hpp common.inc
100 | 
101 | amr_report.o:	common.hpp common.inc gff.hpp alignment.hpp tsv.hpp seq.hpp columns.hpp version.txt
102 | amr_reportOBJS=amr_report.o common.o gff.o alignment.o seq.o graph.o
103 | amr_report:	$(amr_reportOBJS)
104 | 	$(CXX) $(LDFLAGS) -o $@ $(amr_reportOBJS)
105 | 
106 | amrfinder.o:  common.hpp common.inc gff.hpp seq.hpp tsv.hpp columns.hpp version.txt
107 | amrfinderOBJS=amrfinder.o common.o gff.o tsv.o
108 | amrfinder:	$(amrfinderOBJS)
109 | 	$(CXX) $(LDFLAGS) -o $@ $(amrfinderOBJS) -pthread $(DBDIR)
110 | 
111 | amrfinder_update.o:  common.hpp common.inc curl_easy.hpp version.txt
112 | amrfinder_updateOBJS=amrfinder_update.o common.o curl_easy.o
113 | amrfinder_update:      $(amrfinder_updateOBJS) 
114 | 	@if [ "$(TEST_UPDATE)" != "" ]  ; \
115 | 	then  \
116 | 		touch amrfinder_update.cpp ;\
117 | 	fi # make sure the next make command rebuilds amrfinder_update
118 | 	$(CXX) $(LDFLAGS) -o $@ $(amrfinder_updateOBJS) -lcurl 
119 | 
120 | amrfinder_index.o:  common.hpp common.inc version.txt
121 | amrfinder_indexOBJS=amrfinder_index.o common.o
122 | amrfinder_index:      $(amrfinder_indexOBJS) 
123 | 	$(CXX) $(LDFLAGS) -o $@ $(amrfinder_indexOBJS) 
124 | 
125 | fasta_check.o:	common.hpp common.inc version.txt
126 | fasta_checkOBJS=fasta_check.o common.o 
127 | fasta_check:	$(fasta_checkOBJS)
128 | 	$(CXX) $(LDFLAGS) -o $@ $(fasta_checkOBJS)
129 | 
130 | fasta_extract.o:	common.hpp common.inc version.txt
131 | fasta_extractOBJS=fasta_extract.o common.o
132 | fasta_extract:	$(fasta_extractOBJS)
133 | 	$(CXX) $(LDFLAGS) -o $@ $(fasta_extractOBJS)
134 | 
135 | fasta2parts.o:	common.hpp common.inc version.txt
136 | fasta2partsOBJS=fasta2parts.o common.o
137 | fasta2parts:	$(fasta2partsOBJS)
138 | 	$(CXX) $(LDFLAGS) -o $@ $(fasta2partsOBJS)
139 | 
140 | gff_check.o:	common.hpp common.inc gff.hpp version.txt
141 | gff_checkOBJS=gff_check.o common.o gff.o
142 | gff_check:	$(gff_checkOBJS)
143 | 	$(CXX) $(LDFLAGS) -o $@ $(gff_checkOBJS)
144 | 
145 | dna_mutation.o:	common.hpp common.inc alignment.hpp seq.hpp tsv.hpp columns.hpp version.txt
146 | dna_mutationOBJS=dna_mutation.o common.o alignment.o seq.o graph.o
147 | dna_mutation:	$(dna_mutationOBJS)
148 | 	$(CXX) $(LDFLAGS) -o $@ $(dna_mutationOBJS)
149 | 
150 | mutate.o:	common.hpp common.inc alignment.hpp seq.hpp version.txt
151 | mutateOBJS=mutate.o common.o alignment.o seq.o graph.o
152 | mutate:	$(mutateOBJS)
153 | 	$(CXX) -o $@ $(mutateOBJS)
154 | 
155 | disruption2genesymbol.o:	common.hpp common.inc seq.hpp version.txt
156 | disruption2genesymbolOBJS=disruption2genesymbol.o common.o alignment.o seq.o graph.o
157 | disruption2genesymbol:	$(disruption2genesymbolOBJS)
158 | 	$(CXX) -o $@ $(disruption2genesymbolOBJS)
159 | 
160 | stxtyper:
161 | 		$(MAKE) -C stx
162 | 
163 | clean:
164 | 	rm -f *.o
165 | 	rm -f $(BINARIES)
166 | 	$(MAKE) -C stx clean
167 | 
168 | install:
169 | 	@if [ ! -e $(DESTDIR)$(bindir) ]; \
170 | 	then \
171 | 		mkdir -p $(DESTDIR)$(bindir); \
172 | 	fi
173 | 	$(INSTALL) $(BINARIES) $(DESTDIR)$(bindir)
174 | 	make -C stx install PREFIX=$(PREFIX) bindir=$(bindir)
175 | 	mkdir $(DESTDIR)$(bindir)/stx
176 | 	ln -s ../stxtyper $(DESTDIR)$(bindir)/stx/stxtyper
177 | 
178 | # amrfinder binaries for github binary release
179 | GITHUB_FILE=amrfinder_binaries_v$(VERSION_STRING)
180 | GITHUB_FILES = test_amrfinder.sh test_*.expected test_*.fa test_*.gff $(BINARIES)
181 | 
182 | github_binaries:
183 | 	@if [ ! -e version.txt ]; \
184 | 	then \
185 | 		echo >&2 "version.txt required to make a distribution file"; \
186 | 		false; \
187 | 	fi
188 | #   first recompile amrfinder.o to pick up the new version info
189 | #	and remove leaky NCBI paths
190 | 	make clean
191 | #	make all CXX=/usr/bin/g++ LD_RUN_PATH= 
192 | 	make all LD_RUN_PATH= 
193 | 	mkdir $(GITHUB_FILE)
194 | 	echo $(VERSION_STRING) > $(GITHUB_FILE)/version.txt
195 | 	cp $(GITHUB_FILES) $(GITHUB_FILE)
196 | #	make -C stx
197 | #	make -C stx install INSTALL_DIR=../$(GITHUB_FILE)/stx CXX=/usr/bin/g++ LD_RUN_PATH=
198 | 	make -C stx install INSTALL_DIR=../$(GITHUB_FILE)/stx LD_RUN_PATH=
199 | 	cp stx/test_stxtyper.sh stx/version.txt $(GITHUB_FILE)/stx
200 | 	mkdir $(GITHUB_FILE)/stx/test
201 | 	cp -R stx/test/*.fa stx/test/*.expected $(GITHUB_FILE)/stx/test
202 | 	if [ -e $(GITHUB_FILE).tar.gz ]; then rm $(GITHUB_FILE).tar.gz; fi
203 | 	cd $(GITHUB_FILE); ln -s stx/stxtyper .; tar cvfz ../$(GITHUB_FILE).tar.gz *
204 | 	rm -r $(GITHUB_FILE)/*
205 | 	rmdir $(GITHUB_FILE)
206 | 
207 | test: $(DISTFILES) Makefile *.cpp *.hpp *.inc test_dna.fa test_prot.fa test_prot.gff test_dna.fa test_dna.expected test_prot.expected test_both.expected
208 | 	make -C stx test
209 | 	# test the amrfinder in the current directory 
210 | 	# with the data in the current directory
211 | 	./test_amrfinder.sh -n 
212 | 


--------------------------------------------------------------------------------
/fasta_check.cpp:
--------------------------------------------------------------------------------
  1 | // fasta_check.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Check the correctness of a FASTA file
 31 | *
 32 | */
 33 |    
 34 |    
 35 | #undef NDEBUG 
 36 | 
 37 | #include "common.hpp"
 38 | using namespace Common_sp;
 39 | 
 40 | #include "common.inc"
 41 | 
 42 | 
 43 | 
 44 | namespace 
 45 | {
 46 | 
 47 | 
 48 | 
 49 | struct ThisApplication final : Application
 50 | {
 51 |   ThisApplication ()
 52 |     : Application ("Check the correctness of a FASTA file. Exit with an error if it is incorrect. Print the number of sequences, max. sequence length and total sequence length")
 53 |     {
 54 |       addPositional ("in", "FASTA file");
 55 |       addFlag ("aa", "Amino acid sequenes, otherwise nucleotide");
 56 |       addFlag ("hyphen", "Hyphens are allowed");
 57 |       addFlag ("ambig", "Ambiguous characters are allowed");
 58 |       addKey ("ambig_max", "Max. number of ambiguous characters in sequences", "0");
 59 |       addFlag ("stop_codon", "Stop codons ('*') in the protein sequence are allowed");
 60 |       addKey ("len", "Output file with lines: <sequence id> <length>");
 61 |       addKey ("out", "Output FASTA file with some of the issues fixed");
 62 | 	    version = SVN_REV;
 63 |     }
 64 | 
 65 | 
 66 | 
 67 |   void body () const final
 68 |   {
 69 |     const string fName     = getArg ("in");
 70 |     const bool aa          = getFlag ("aa");
 71 |     const bool hyphen      = getFlag ("hyphen");
 72 |     const bool ambig       = getFlag ("ambig");
 73 |     const size_t ambig_max = str2<size_t> (getArg ("ambig_max"));
 74 |     const bool stop_codon  = getFlag ("stop_codon");
 75 |     const string lenFName  = getArg ("len");
 76 |     const string outFName  = getArg ("out");
 77 |     
 78 |     QC_IMPLY (stop_codon, aa);
 79 |     
 80 | 
 81 |     unique_ptr<OFStream> lenF;
 82 |     if (! lenFName. empty ())
 83 |       lenF. reset (new OFStream (lenFName));
 84 |     unique_ptr<OFStream> outF;
 85 |     if (! outFName. empty ())
 86 |       outF. reset (new OFStream (outFName));
 87 |     size_t lines = 0;
 88 |     StringVector ids;  ids. reserve (100000);  // PAR
 89 |     size_t seqSize_max = 0;
 90 |     size_t seqSize_sum = 0;
 91 |   //string errorS;
 92 |     // One sequence
 93 |     size_t xs = 0;
 94 |     string header;
 95 |     string seq;
 96 |     
 97 |     auto processSeq = [&] () 
 98 |   	  {
 99 |   	    if (! lines)
100 |   	      return;
101 |  	  		ASSERT (! header. empty ());
102 |  	  		ASSERT (! ids. empty ());
103 |  	  		const string id (ids. back ());
104 |   	    if (aa && ! stop_codon)
105 |   	    {  	    
106 |     	    while (! seq. empty () && seq. back () == '*')
107 |    	  		  if (outF)
108 |    	  		    seq. erase (seq. size () - 1);
109 |    	  		  else
110 |     		      throw runtime_error (id + ": '*' at the sequence end");
111 |     		}
112 |   	    if (seq. empty ())
113 |  	  		  throw runtime_error (id + ": Empty sequence");
114 |  	  		bool skip = false;
115 |   	    if (! ambig && xs > ambig_max)
116 |   	    {
117 |  	  		  if (outF)
118 |  	  		    skip = true;
119 |  	  		  else
120 |   		      throw runtime_error (id + ": Too many ambiguities");
121 |   		  }
122 |   		  if (skip)
123 |   		    { LOG ("Skipping " + id); }
124 |   		  else
125 |   		  {
126 |      	  	if (lenF. get ())
127 |      	  	  *lenF << id << '\t' << seq. size () << endl;
128 |   	      if (outF)
129 |   	        *outF << header << endl << seq << endl;
130 |    	  	  maximize (seqSize_max, seq. size ());
131 |    	  	  seqSize_sum += seq. size ();
132 |    	  	}
133 |     	  xs = 0;
134 |     	  header. clear ();
135 |     	  seq. clear ();
136 |  	    };
137 |     
138 |     size_t nuc = 0;   
139 |     {
140 |       LineInput f (fName); 
141 |       string id;
142 |       while (f. nextLine ())
143 |       {
144 |         trimTrailing (f. line);
145 |         if (f. line. empty ())
146 |         	continue;
147 |       	const string errorS ("File " + fName + ", " + f. lineStr (false) + ": ");
148 |       	if (f. line [0] == '>')
149 |       	{
150 |       		size_t pos = 1;
151 |       		while (pos < f. line. size () && ! isspace (f. line [pos]))
152 |       		  pos++;
153 |       		id = f. line. substr (1, pos - 1);
154 |       		if (id. empty ())
155 |       			throw runtime_error (errorS + "Empty sequence identifier");
156 |         #if 0
157 |       		if (id. size () > 1000)  // PAR
158 |       			throw runtime_error (errorS + "Too long sequence identifier");
159 |         #endif
160 |       	  for (const char c : id)
161 |       	  	if (! printable (c))
162 |       	  		throw runtime_error (errorS + "Non-printable character in the sequence identifier: " + to_string ((int) c));
163 |       	  // BLAST: PD-4548
164 |       	  if (! aa)
165 |       	  {
166 |         	  if (id. front () == '?')
167 |        	  		throw runtime_error (errorS + "Sequence identifier starts with '?'");
168 |        	  	for (const char c : {',', ';', '.', '~'})
169 |           	  if (id. back () == c)
170 |          	  		throw runtime_error (errorS + "Sequence identifier ends with " + strQuote (string (1, c)));
171 |         	  if (contains (id, "\\t"))
172 |        	  		throw runtime_error (errorS + "Sequence identifier contains '\\t'");
173 |         	  if (contains (id, ",,"))
174 |        	  		throw runtime_error (errorS + "Sequence identifier contains ',,'");
175 |        	  }
176 |      	    processSeq ();
177 |       	  header = f. line;
178 |       	  ids << id;
179 |       	}
180 |       	else 
181 |       	{
182 |       		if (! lines)
183 |       			throw runtime_error (errorS + "FASTA should start with '>'");
184 |       	  for (const char c : f. line)
185 |       	  {
186 |       	    bool skip = false;
187 |       	  	if (c == '-')
188 |       	  		if (hyphen)
189 |       	  			;
190 |       	  		else
191 |       	  		{
192 |       	  		  if (outF)
193 |       	  		    skip = true;
194 |       	  		  else
195 |   	    	  		  throw runtime_error (errorS + "Hyphen in the sequence");  	    	  		  
196 |   	    	    }
197 |   	    	  else
198 |   	    	  {
199 |   	    	  	const char c1 = toLower (c);
200 |   	    	  	if (aa)
201 |   	    	  	{
202 |   		    	  	if (! charInSet (c1, "acdefghiklmnpqrstvwyxbzjuoacdefghiklmnpqrstvwyxbzjuo*"))
203 |   		    	  		throw runtime_error (errorS + "Wrong amino acid character: (code = " + to_string ((int) c) + ") '" + c + "'");
204 |   		    	    if (charInSet (c1, "acgt"))
205 |   		    	    	nuc++;
206 |   		    	    if (charInSet (c1, "xbzjuo"))
207 |   		    	      xs++;
208 |   		    	  }
209 |   	    	  	else
210 |   	    	  	{
211 |   		    	  	if (! charInSet (c1, "acgtbdhkmnrsvwyacgtbdhkmnrsvwy"))
212 |   		    	  		throw runtime_error (errorS + "Wrong nucleotide character: (code = " + to_string ((int) c) + ") '" + c + "'");
213 |   		    	    if (charInSet (c1, "bdhkmnrsvwy"))
214 |   		    	      xs++;
215 |   		    	  }
216 |   		    	}
217 |   		    	if (! skip)
218 |   		    	  seq += c;
219 |   		    }
220 |       	}
221 |       	lines++;
222 |   	  }
223 |   	}
224 |     processSeq ();	// Last sequence
225 | 	  if (! lines)
226 | 	  	throw runtime_error ("Empty file"); 
227 |   	if (aa && (double) nuc / (double) seqSize_sum > 0.9)  // PAR
228 |   		throw runtime_error ("Protein sequences looks like a nucleotide sequences");
229 |   		
230 | 	  ids. sort ();
231 | 	  const size_t index = ids. findDuplicate ();
232 | 	  if (index != no_index)
233 | 	  	throw runtime_error ("Duplicate identifier: " + ids [index]);
234 | 	  	
235 | 	  cout << ids. size () << endl
236 | 	       << seqSize_max << endl
237 | 	       << seqSize_sum << endl;
238 |   }
239 | };
240 | 
241 | 
242 | 
243 | }  // namespace
244 | 
245 | 
246 | 
247 | int main (int argc, 
248 |           const char* argv[])
249 | {
250 |   ThisApplication app;
251 |   return app. run (argc, argv);  
252 | }
253 | 
254 | 
255 | 
256 | 


--------------------------------------------------------------------------------
/alignment.hpp:
--------------------------------------------------------------------------------
  1 | // alignment.hpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Protein or DNA mutations library.
 31 | *
 32 | */
 33 |    
 34 |    
 35 | #include "common.hpp"
 36 | using namespace Common_sp;
 37 | #include "seq.hpp"
 38 | using namespace Seq_sp;
 39 | 
 40 | 
 41 |    
 42 | 
 43 | namespace Alignment_sp
 44 | {
 45 | 
 46 | 
 47 | 
 48 | static constexpr char pm_delimiter = '_';
 49 | 
 50 | 
 51 | 
 52 | struct AmrMutation final : Root
 53 | // Database
 54 | {
 55 | 	size_t pos_real {0};  
 56 | 	  // In whole reference sequence
 57 | 	  // = start of reference
 58 | 	
 59 | 	string geneMutation_std;
 60 |   // Function of geneMutation_std
 61 |   // Upper-case
 62 |   string reference;
 63 | 	string allele;
 64 | 	string gene;
 65 | 	int pos_std {0};  
 66 | 	size_t frameshift {no_index};
 67 | 	  // Position of '*' after getStop()
 68 | 	int frameshift_insertion {0};
 69 | 
 70 | 	// To be reported
 71 | 	// !empty()
 72 | 	string geneMutation;
 73 | 	string classS;
 74 | 	string subclass;
 75 | 	string name;
 76 | 	  // Species binomial + resistance
 77 | 	
 78 | 	
 79 |   // Input: pos_arg: 1-based
 80 | 	AmrMutation (size_t pos_real_arg,
 81 |   		 				 const string &geneMutation_std_arg,
 82 |   		 				 const string &geneMutation_arg,
 83 |   			 			 const string &class_arg,    
 84 |   				 		 const string &subclass_arg, 
 85 |   					 	 const string &name_arg);    
 86 | 	AmrMutation (size_t pos_arg,
 87 |   		 				 const string &geneMutation_std_arg)
 88 |     : AmrMutation (pos_arg, geneMutation_std_arg, geneMutation_std_arg, "X", "X", "X")
 89 |     {}
 90 | 	AmrMutation () = default;
 91 | private:
 92 | 	static void parse (const string &geneMutation_std,
 93 | 	                   string &reference,
 94 | 	                   string &allele,
 95 |                      string &gene,
 96 |                      int &pos_std,
 97 |                      size_t &frameshift,
 98 |                      int &frameshift_insertion);
 99 | public:
100 |   void qc () const override;
101 |   void saveText (ostream &os) const override
102 |     { if (empty ())
103 |         os << "empty";
104 |       else
105 |         os        << pos_real + 1 
106 |            << ' ' << geneMutation 
107 |            << ' ' << frameshift_insertion 
108 |            << ' ' << name; 
109 |     }
110 |   bool empty () const override
111 |     { return geneMutation_std. empty (); }
112 | 
113 | 
114 |   size_t getStop () const
115 |     { return pos_real + reference. size (); }
116 |   string wildtype () const
117 |     { return gene + "_" + reference + to_string (pos_std + 1) + reference; }
118 |   bool operator< (const AmrMutation &other) const;
119 |   bool operator== (const AmrMutation &other) const
120 |     { return geneMutation_std == other. geneMutation_std; }
121 |   void apply (string &seq) const
122 |     { if (pos_real >= seq. size ())
123 |         throw runtime_error ("AmrMutation position " + to_string (pos_real) + " is outside the sequence: " + seq);
124 |       if (frameshift != no_index)
125 |         throw runtime_error ("AmrMutation is a frameshift");
126 |       if (verbose ())
127 |         cerr         << seq. substr (0, pos_real) 
128 |              << endl << allele 
129 |              << endl << seq. substr (pos_real + reference. size ())
130 |              << endl;
131 |       seq = seq. substr (0, pos_real) + allele + seq. substr (pos_real + reference. size ());
132 |     }
133 | };
134 | 
135 | 
136 | 
137 | struct Alignment;
138 | 
139 | 
140 | 
141 | struct SeqChange final : Root
142 | // Observation
143 | {
144 |   const Alignment* al {nullptr};
145 |     // !nullptr    
146 | //bool fromAllele {false};
147 |   
148 |   // In alignment
149 |   size_t start {0};
150 |   size_t len {0};
151 |   
152 |   // No '-'
153 |   string reference;
154 |     // Insertion => start is artifically decremented and len is incremented => !empty()
155 |   string allele;
156 |   // empty() <=> frame shift
157 | 
158 |   size_t start_ref {0};
159 |   size_t stop_ref {0};
160 |   size_t start_target {0};
161 | 	double neighborhoodMismatch {0.0};
162 | 	  // 0..1
163 | 	  
164 | 	VectorPtr<AmrMutation> mutations;
165 | 	  // !nullptr
166 | 	  // Matching AmrMutation's
167 |     		  
168 | 	Disruption disr;
169 | 
170 | 	const SeqChange* replacement {nullptr}; 
171 | 	  // !nullptr => *this is replaced by *replacement
172 |   
173 |   
174 |   SeqChange () = default;
175 |   explicit SeqChange (const Alignment* al_arg/*,
176 |              bool fromAllele_arg*/)
177 |     : al (al_arg)
178 |   //, fromAllele (fromAllele_arg)
179 |     {}
180 |   SeqChange (const Alignment* al_arg,
181 |              const AmrMutation* mutation_arg)
182 |     : al (al_arg)
183 |     { mutations << checkPtr (mutation_arg); }
184 |   SeqChange (const Alignment* al_arg,
185 |              const Disruption &disr_arg)
186 |     : al (al_arg)
187 |     , disr (disr_arg)
188 |     {}
189 |   void qc () const override;
190 |   void saveText (ostream &os) const override
191 |     { os        << start + 1 
192 |          << ' ' << len 
193 |          << ' ' << strQuote (reference) << " -> " << strQuote (allele)
194 |          << ' ' << start_ref + 1 << ".." << stop_ref
195 |          << ' ' << start_target + 1 
196 |          << ' ' << neighborhoodMismatch;
197 |       if (! disr. empty ())
198 |         disr. saveText (os);
199 |       for (const AmrMutation* mutation : mutations)
200 |       { os << ' ' ;
201 |         mutation->saveText (os);
202 |       }
203 |       os << endl; 
204 |     }
205 |   bool empty () const override
206 |     { return ! len && disr. empty (); }
207 |     
208 |     
209 |   bool hasMutation () const
210 |     { return ! empty () && ! mutations. empty () && ! replacement; }
211 |   bool hasFrameshift () const
212 |     { return hasMutation () && mutations [0] -> frameshift != no_index; }
213 |   bool isFrameshift () const
214 |     { return reference. empty (); }
215 |   string getMutationStr () const;
216 |   size_t getStop () const
217 |     { return start + len; }
218 |   bool operator< (const SeqChange &other) const;
219 |   bool better (const SeqChange &other) const;
220 |   bool finish (const string &refSeq,
221 |                size_t flankingLen);
222 |     // Return: good match
223 |     // Invokes: finishPos()
224 |   bool finishPos (size_t flankingLen);
225 |     // Return: good match
226 | private:
227 |   void setSeq ();
228 |   void setStartStopRef ();
229 |   void setStartTarget ();
230 |   void setNeighborhoodMismatch (size_t flankingLen);
231 | public:
232 |   bool matchesMutation (const AmrMutation& mut) const;
233 | };
234 | 
235 | 
236 | 
237 | struct Alignment : Hsp
238 | {
239 |   AmrMutation refMutation;
240 |     // !empty() => qseq contains AmrMutation::allele
241 | //int ref_offset {0};
242 | 
243 |   Vector<SeqChange> seqChanges;
244 | 
245 |   
246 |   Alignment (const string &line,
247 |              bool qProt_arg,  
248 |              bool sProt_arg)
249 |     : Hsp (line, qProt_arg, sProt_arg, qProt_arg || sProt_arg /*aProt*/, /*false*/ qProt_arg /*qStopCodon*/, true/*bacterialStartCodon*/)
250 |     {}
251 |   Alignment () = default;  
252 | protected:
253 |   void setSeqChanges (const Vector<AmrMutation> &refMutations,
254 |                       size_t flankingLen/*,
255 |                       bool allMutationsP*/);
256 |     // Input: flankingLen: valid if > 0
257 | private:
258 |   size_t refMutation2refSeq_pos ();
259 |     // Return: no_index <=> refMutation is not detected
260 | public:
261 |   void qc () const override;
262 |   void saveText (ostream &os) const override
263 |     { Hsp::saveText (os);
264 |       if (! refMutation. empty ())
265 |         os << ' ' << refMutation;
266 | 	    os << " #seqChanges:" << seqChanges. size ();
267 |     }
268 | 
269 | 
270 |   bool hasMutation () const
271 |     { for (const SeqChange& seqChange : seqChanges)
272 |         if (seqChange. hasMutation ())
273 |           return true;
274 |       return false;
275 |     }
276 |   bool hasDeclarativeFrameshift () const
277 |     { return seqChanges. size () == 1 && seqChanges [0]. hasFrameshift (); }
278 | };
279 | 
280 | 
281 | 
282 | 
283 | }  // namespace
284 | 
285 | 
286 | 


--------------------------------------------------------------------------------
/gff_check.cpp:
--------------------------------------------------------------------------------
  1 | // gff_check.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Check the correctness of a GFF file
 31 | *
 32 | */
 33 |    
 34 |    
 35 | #undef NDEBUG 
 36 | 
 37 | #include "common.hpp"
 38 | using namespace Common_sp;
 39 | #include "gff.hpp"
 40 | using namespace GFF_sp;
 41 | 
 42 | #include "common.inc"
 43 | 
 44 | 
 45 | 
 46 | namespace 
 47 | {
 48 | 
 49 | 
 50 | const string locus_tagS ("[locus_tag=");
 51 | const string prodigal_ID (" ID=");
 52 | const string noFile ("emptystring");
 53 | 
 54 | 
 55 | 
 56 | struct ThisApplication final : Application
 57 | {
 58 |   ThisApplication ()
 59 |     : Application ("Check the correctness of a GFF file. Exit with an error if it is incorrect.")
 60 |     {
 61 |       // Input
 62 |       addPositional ("gff", "GFF file, if " + strQuote (noFile) + " then exit 0");
 63 |       addKey ("gfftype", "Type of GFF file: " + Gff::names. toString (", "), "genbank");
 64 |       addKey ("prot", "Protein FASTA file");
 65 |       addKey ("dna", "DNA FASTA file");
 66 |       addFlag ("lcl", "Nucleotide FASTA created by PGAP has \"lcl|\" prefix in accessions");  
 67 |       // Output
 68 |       addKey ("gff_prot_match", "Output file with pairs: \"<protein FASTA id> <protein GFF id>\", \n\
 69 | where for genbank: <protein GFF id> is from " + strQuote (locus_tagS + "<id>") + " in the protein FASTA comment, \n\
 70 | for microscope: <protein GFF id> is ID:<num> from '><acc>|ID:<num>|<gene>|', \n\
 71 | and for prodigal: <protein GFF id> is ID=<num> in the protein FASTA comment\n\
 72 | ");
 73 |       addKey ("gff_dna_match",  "Output file with pairs: \"<DNA FASTA id> <DNA GFF id>\", where for pseudomonasdb: <DNA GFF id> is the suffix after '|' in the DNA FASTA identifier");
 74 | 	    version = SVN_REV;
 75 |     }
 76 | 
 77 | 
 78 | 
 79 |   void body () const final
 80 |   {
 81 |     const string    gffName        = getArg ("gff");
 82 |     const Gff::Type type           = Gff::name2type (getArg ("gfftype"));
 83 |     const string    protFName      = getArg ("prot");
 84 |     const string    dnaFName       = getArg ("dna");
 85 |     const string    protMatchFName = getArg ("gff_prot_match");
 86 |     const string    dnaMatchFName  = getArg ("gff_dna_match");
 87 |     const bool      lcl            = getFlag ("lcl"); 
 88 |     
 89 |     if (lcl && type != Gff::pgap)
 90 |       throw runtime_error ("-lcl requires type pgap");
 91 |     
 92 |     
 93 |     if (isRight (gffName, noFile))
 94 |     	return;
 95 |     
 96 | 
 97 |     const Annot annot (gffName, type, ! protMatchFName. empty (), lcl);
 98 |     
 99 |     
100 |     if (! protFName. empty ())
101 |     {
102 | 	    StringVector gffIds;  gffIds. reserve (10000);  // PAR
103 |     	{
104 | 	    	OFStream outF;
105 | 	    	if (! protMatchFName. empty ())
106 | 	    		outF. open ("", protMatchFName, "");
107 | 	    	StringVector fastaIds;  fastaIds. reserve (gffIds. capacity ());
108 | 			  LineInput f (protFName /*, 100 * 1024, 1*/);
109 |     		Istringstream iss;
110 |     		string line_orig;
111 |      		string fastaId;
112 | 			  while (f. nextLine ())
113 | 			  {
114 |           trimTrailing (f. line);
115 | 			    if (f. line. empty ())
116 | 			      continue;
117 | 		    	if (f. line [0] != '>')
118 | 		    	  continue;
119 | 	    		line_orig = f. line;
120 | 	    		iss. reset (f. line. substr (1));
121 | 	    		fastaId. clear ();
122 |     		  iss >> fastaId;
123 |     		  QC_ASSERT (! fastaId. empty ());
124 | 	    		ASSERT (! contains (fastaId, ' '));
125 |     			fastaIds << fastaId;
126 |     		  // gffId
127 |     			string gffId (fastaId);
128 | 	    		if (! protMatchFName. empty ())
129 | 	    		  switch (type)
130 | 	    		  {
131 | 	    		    case Gff::genbank:
132 |       	    		{
133 |       	    			const size_t pos = f. line. find (locus_tagS);
134 |       	    			if (pos == string::npos)
135 |       	    				throw runtime_error (__FILE__ ": " + strQuote (locus_tagS) + " is not found in: " + line_orig);
136 |       	    			gffId = f. line. substr (pos + locus_tagS. size ());
137 |       	    			const size_t end = gffId. find (']');
138 |       	    			if (end == string::npos)
139 |       	    				throw runtime_error (__FILE__ ": ']' is not found after " + strQuote (locus_tagS) + " in: " + line_orig);
140 |       	    		  gffId. erase (end);
141 |       	    		}
142 |       	    		break;
143 |       	    	case Gff::microscope:
144 |       	    	  {
145 |       	    	    string s (std::move (gffId));
146 |       	    	    findSplit (s, '|');
147 |       	    	    gffId = findSplit (s, '|');
148 |       	    	    const string idS ("ID:");
149 |       	    	    if (! isLeft (gffId, idS))
150 |       	    	      throw runtime_error (__FILE__ ": 'ID:' is not found in: " + line_orig);
151 |       	    	    gffId. erase (0, idS. size ());
152 |       	    	  }      	    	  
153 |       	    	  break;
154 | 	    		    case Gff::prodigal:
155 |       	    		{
156 |       	    			const size_t pos = f. line. find (prodigal_ID);
157 |       	    			if (pos == string::npos)
158 |       	    				throw runtime_error (__FILE__ ": " + strQuote (prodigal_ID) + " is not found in: " + line_orig);
159 |       	    			gffId = f. line. substr (pos + prodigal_ID. size ());
160 |       	    			const size_t end = gffId. find (';');
161 |       	    			if (end == string::npos)
162 |       	    				throw runtime_error (__FILE__ ": ';' is not found after " + strQuote (prodigal_ID) + " in: " + line_orig);
163 |       	    		  gffId. erase (end);
164 |       	    		}
165 |       	    		break;
166 |       	      default: break;
167 |       	    }
168 | 	    	  //
169 | 	    		if (contains (gffId, ' '))
170 | 	    			throw runtime_error (__FILE__ ": " + strQuote (gffId) + " contains space");
171 | 	    		if (gffId. empty ())
172 | 	    			throw runtime_error (__FILE__ ": No protein identifier in: " + line_orig);
173 |     			gffIds << gffId;
174 |     			if (outF. is_open ())
175 |     				outF << fastaId << '\t' << gffId << endl;
176 | 			  }
177 | 			  const size_t n = fastaIds. size ();
178 | 			  fastaIds. sort ();
179 | 			  fastaIds. uniq ();
180 | 			  if (fastaIds. size () != n)
181 | 			  	throw runtime_error (__FILE__ ": Duplicate FASTA ids");
182 | 			  gffIds. sort ();
183 | 			  {
184 |   			  const string* s_prev = nullptr;
185 |   			  for (const string& s : gffIds)
186 |   			  {
187 |   			    if (s_prev && *s_prev == s)
188 |     			  	throw runtime_error (__FILE__ ": GFF identifier " + strQuote (s) + " is not unique");
189 |   			    s_prev = & s;
190 |   			  }
191 |   			}
192 | 			  ASSERT (gffIds. size () == fastaIds. size ());
193 | 			}
194 | 			if (verbose ())
195 | 			  cout << "# Proteins in GFF: " << annot. prot2loci. size () << endl;
196 | 		  for (const string& seqid : gffIds)
197 | 		  	if (! contains (annot. prot2loci, seqid))
198 | 		  		throw runtime_error (__FILE__ ": Protein FASTA id " + strQuote (seqid) + " is not in the GFF file");
199 |     #if 0
200 | 		  for (const auto& it : annot. prot2loci)
201 | 		    if (! gffIds. containsFast (it. first))
202 | 		  		throw runtime_error (__FILE__ ": GFF protein id " + strQuote (it. first) + " is not in the protein FASTA file");  // pseudogene ??
203 | 		#endif
204 |     }   
205 | 
206 | 
207 |     if (! dnaFName. empty ())
208 |     {
209 |     	StringVector contigIds;  contigIds. reserve (10000);  // PAR
210 |     	StringVector gffIds;  gffIds. reserve (10000);  // PAR
211 |     	{
212 |       	OFStream outF;
213 |       	if (! dnaMatchFName. empty ())
214 |       		outF. open ("", dnaMatchFName, "");
215 | 			  LineInput f (dnaFName /*, 100 * 1024, 1*/);
216 |     		Istringstream iss;
217 |     		string contigId;
218 | 			  while (f. nextLine ())
219 | 	    	{
220 |           trimTrailing (f. line);
221 | 			    if (f. line. empty ())
222 | 			      continue;
223 | 		    	if (f. line [0] != '>')
224 | 		    	  continue;
225 | 	    		iss. reset (f. line. substr (1));
226 | 	    		contigId. clear ();
227 |     		  iss >> contigId;
228 | 	    		ASSERT (! contains (contigId, ' '));
229 |     		  // gffId
230 |     			string gffId (contigId);
231 | 	    		if (! dnaMatchFName. empty ())
232 | 	    		  switch (type)
233 | 	    		  {
234 | 	    		    case Gff::pseudomonasdb:
235 |       	    		{
236 |       	    			const size_t pos = gffId. rfind ('|');
237 |       	    			if (pos != string::npos)
238 |       	    				gffId. erase (0, pos + 1);
239 |       	    		}
240 |       	    		break;
241 |       	      default: break;
242 |       	    }
243 |       	  //
244 | 	    		if (gffId. empty ())
245 | 	    			throw runtime_error (__FILE__ ": No contig identifier in:\n" + f. line);
246 | 	    		if (lcl && ! isLeft (gffId, "lcl|"))
247 | 	    			throw runtime_error (__FILE__ ": Contig identifier does not start with " + strQuote ("lcl|") + ":\n" + f. line);
248 |     			gffIds << gffId;
249 |     			contigIds << contigId;
250 |     			if (outF. is_open ())
251 |     				outF << contigId << '\t' << gffId << endl;
252 | 	    	}
253 | 			}
254 | 			ASSERT (contigIds. size () == gffIds. size ());
255 | 		  gffIds. sort ();
256 | 		  {
257 | 			  const string* s_prev = nullptr;
258 | 			  for (const string& s : gffIds)
259 | 			  {
260 | 			    if (s_prev && *s_prev == s)
261 |   			  	throw runtime_error (__FILE__ ": DNA GFF identifier " + strQuote (s) + " is not unique");
262 | 			    s_prev = & s;
263 | 			  }
264 | 			}
265 | 		  contigIds. sort ();
266 | 		  {
267 | 			  const string* s_prev = nullptr;
268 | 			  for (const string& s : contigIds)
269 | 			  {
270 | 			    if (s_prev && *s_prev == s)
271 |   			  	throw runtime_error (__FILE__ ": DNA contig identifier " + strQuote (s) + " is not unique");
272 | 			    s_prev = & s;
273 | 			  }
274 | 			}
275 | 			for (const auto& it : annot. prot2loci)
276 | 			  for (const Locus& cds : it. second)
277 | 			    if (! gffIds. contains (cds. contig))
278 |   		  		throw runtime_error (__FILE__ ": GFF contig id " + strQuote (cds. contig) + " is not in the DNA FASTA file");
279 |     }   
280 |   }
281 | };
282 | 
283 | 
284 | 
285 | }  // namespace
286 | 
287 | 
288 | 
289 | int main (int argc, 
290 |           const char* argv[])
291 | {
292 |   ThisApplication app;
293 |   return app. run (argc, argv);  
294 | }
295 | 
296 | 
297 | 
298 | 


--------------------------------------------------------------------------------
/disruption2genesymbol.cpp:
--------------------------------------------------------------------------------
  1 | // disruption2genesymbol.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Convert Disruption::genesymbol_raw() to a gene symbol
 31 | *
 32 | */
 33 | 
 34 | 
 35 | #undef NDEBUG
 36 | 
 37 | #include "common.hpp"
 38 | using namespace Common_sp;
 39 | #include "seq.hpp"
 40 | using namespace Seq_sp;
 41 | 
 42 | #include "common.inc"
 43 | 
 44 | 
 45 | 
 46 | namespace 
 47 | {
 48 |   
 49 |   
 50 | constexpr char no_aa {'?'};
 51 | 
 52 |   
 53 |   
 54 | struct SymbolRaw final : Root
 55 | {
 56 |   static constexpr size_t del_size {10};  // PAR
 57 | 
 58 |   // Input
 59 |   string contig;
 60 |   string prot;
 61 |   Disruption::Type type {Disruption::eNone};
 62 |   // 0-based  
 63 |   size_t qstart {no_index}; 
 64 |   size_t qend {no_index};
 65 |     // aa
 66 |   size_t sstart {no_index};
 67 |   size_t send {no_index};
 68 |     // bp
 69 |   //
 70 |   Strand strand {0};
 71 |   bool stop {false};
 72 |   string rest;
 73 |   
 74 |   // Output
 75 |   string ref;
 76 |   string allele;
 77 | 
 78 | 
 79 |   explicit SymbolRaw (const string &line)
 80 |     {
 81 |       string s;
 82 |       {
 83 |         istringstream iss (line);
 84 |         iss >> contig >> prot >> s;
 85 |         QC_ASSERT (! s. empty ());
 86 |         ASSERT (! contig. empty ());
 87 |         ASSERT (! prot. empty ());
 88 | 
 89 |         constexpr size_t rest_size = 1024;
 90 |         char rest_ [rest_size];
 91 |         iss. getline (rest_, rest_size);
 92 |         rest = rest_;
 93 |       }
 94 | 
 95 |       if (trimSuffix (s, Disruption::stopSuf))
 96 |         stop = true;
 97 | 
 98 |       // strand
 99 |       {
100 |         const string strandS = rfindSplit (s, '_');
101 |         if (strandS == "0")
102 |           strand = -1;
103 |         else if (strandS == "1")
104 |           strand = 1;
105 |         else
106 |           throw runtime_error ("Unknown strand: " + strQuote (strandS));
107 |       }
108 |           
109 |       send   = str2<size_t> (rfindSplit (s, '_'));
110 |       sstart = str2<size_t> (rfindSplit (s, '_'));      
111 |       qend   = str2<size_t> (rfindSplit (s, '_'));
112 |       qstart = str2<size_t> (rfindSplit (s, '_'));       
113 |       QC_ASSERT (qstart <= qend);
114 |       QC_ASSERT (sstart <= send);
115 |       
116 |       type = Disruption::name2type (s);
117 |       QC_ASSERT (type != Disruption::eNone);
118 |       QC_ASSERT (type != Disruption::eSmooth);
119 |     }  
120 |   void saveText (ostream &os) const final
121 |     { 
122 |       ASSERT (! ref. empty ());
123 |       os         << contig  // 0
124 |          << '\t' << prot    // 1 
125 |          << '\t';
126 |       if (verbose ())
127 |         os << '\t' << Disruption::typeNames [type]
128 |            << '\t' << qstart
129 |            << '\t' << qend
130 |            << '\t' << sstart
131 |            << '\t' << send
132 |            << '\t' << (int) strand
133 |            << '\t' << stop
134 |            << '\t' << ref
135 |            << '\t' << allele
136 |            << '\t';           
137 |       ASSERT (! contains (ref, '*'));
138 |       string allele_ (allele);
139 |       const bool alleleStop = trimSuffix (allele_, "*");
140 |       const size_t allele_size = allele_. size ();  // Without stop codon
141 |     //QC_IMPLY (type != Disruption::eFrameshift, alleleStop == stop);
142 |       QC_IMPLY (stop, alleleStop);
143 |       constexpr size_t display_max = 1/*reference aa*/ + 5;  // PAR  // PD-5395
144 |       if (allele_size > display_max)
145 |         allele_ = "ins";
146 |       if (alleleStop)
147 |         allele_ += terminatorWord;
148 |       ASSERT (! contains (allele_, '*'));
149 |       // Standard gene symbol        
150 |       // 2      
151 |       if (ref. size () > display_max)
152 |         os        << ref. front () << qstart + 1 
153 |            << '_' << ref. back ()  << qstart + ref. size ();
154 |       else
155 |         os << ref << qstart + 1;  
156 |       switch (type)
157 |       {
158 |         case Disruption::eFrameshift:
159 |           ASSERT (ref. size () == 1)
160 |           ASSERT (! allele. empty ());
161 |           if (alleleStop && allele_size == 0)            
162 |             os << terminatorWord;
163 |           else
164 |             os << allele [0];
165 |           os << Disruption::typeNames [type];
166 |           if (alleleStop)
167 |             os << terminatorWord << allele_size;
168 |           break;
169 |         case Disruption::eDeletion:  // Or replacement
170 |           if (allele_. empty ())
171 |             os << Disruption::typeNames [type];
172 |           else
173 |           {
174 |             os << allele_;
175 |             if (allele_size > display_max)
176 |               os << allele_size - 1/*reference aa*/;
177 |           }
178 |           break;
179 |         case Disruption::eInsertion:
180 |           ASSERT (ref. size () == 1);
181 |           ASSERT (! allele_. empty ());
182 |           os << allele_;
183 |           if (allele_size > display_max)
184 |             os << allele_size - 1/*reference aa*/;
185 |           break;
186 |         default:
187 |           break;
188 |       }
189 |       // 3
190 |       os << '\t' 
191 |          // = <Disruption::genesymbol_raw()>
192 |          // Opposite to SymbolRaw::SymbolRaw(line)
193 |          << Disruption::typeNames [type] << '_' << qstart << '_' << qend << '_' << sstart << '_' << send << '_' << (strand == 1 ? 1 : 0);
194 |       if (stop)
195 |         os << Disruption::stopSuf;
196 |          //
197 |       os << '\t' << rest  // 4
198 |          << '\n';
199 |     }
200 |     
201 |     
202 |   char contig2aa (const Dna &dna,
203 |                   size_t offset,
204 |                   Gencode gencode) const
205 |     // Input: offset: from sstart/send
206 |     // Return: no_aa <=> offset is outside dna
207 |     {
208 |       QC_ASSERT (send <= dna. seq. size ());
209 |       
210 |       if (strand == 1)
211 |       {
212 |         const size_t i = sstart + offset * 3;
213 |         if (i + 3 > send)
214 |           return no_aa;
215 |         return codon2aa (& dna. seq [i], gencode, false);
216 |       }
217 |       
218 |       ASSERT (strand == -1);
219 |       if (send < (offset + 1) * 3)
220 |         return no_aa;
221 |       const size_t i = send - (offset + 1) * 3;
222 |       ASSERT (i + 3 <= dna. seq. size ());
223 |       if (i < sstart)
224 |         return no_aa;
225 |       string s (dna. seq. substr (i, 3));
226 |       reverseDna (s);
227 |       return codon2aa (s. c_str (), gencode, false);
228 |     }
229 | };
230 | 
231 | 	
232 | 	
233 | struct ThisApplication final : Application
234 | {
235 |   static constexpr char id_delim {'|'};
236 |   
237 |   
238 |   ThisApplication ()
239 |     : Application ("Convert Disruption::genesymbol_raw() to standard gene symbols according to https://hgvs-nomenclature.org/stable/recommendations/protein/frameshift/.\n\
240 | A stop codon is '" + string (terminatorWord) + "'.\n\
241 | Print: <tab row> where <genesymbol> is inserted before <Disruption::genesymbol_raw()>"
242 | )
243 | 	  {
244 | 		  addPositional ("nucl", "Input nucleotide FASTA file");
245 | 		  addPositional ("prot", "Input protein FASTA file");
246 | 		  addPositional ("tab", "Table with lines: <contig identifier in <nucl>>  <protein identifier in <prot>>  <Disruption::genesymbol_raw()>");
247 | 		  addKey ("gencode", "NCBI genetic code for translated BLAST", "11");
248 | 	    addKey ("prot_id_pos", string ("Position of protein id in qseqid delimited by ") + id_delim + ", 1-based. 0 - use qseqid as a whole", "0");
249 | 	  }
250 | 
251 |   
252 |   
253 | 	void body () const final
254 |   {
255 | 	  const string nuclFName   = getArg ("nucl");
256 | 	  const string protFName   = getArg ("prot");
257 | 	  const string tabFName    = getArg ("tab");
258 |     const Gencode gencode    = (Gencode) arg2uint ("gencode"); 
259 |     const size_t prot_id_pos = str2<size_t> (getArg ("prot_id_pos"));
260 |     
261 | 	  
262 | 	  Vector<SymbolRaw> symbolRaws;
263 | 	  {
264 | 	    LineInput f (tabFName);
265 | 	    while (f. nextLine ())
266 | 	      symbolRaws << std::move (SymbolRaw (f. line));
267 | 	  }
268 | 	  if (symbolRaws. empty ())
269 | 	    return;
270 | 	  
271 | 	  // SymbolRaw::allele
272 | 		{
273 | 		  Multifasta fa (nuclFName, false);
274 | 		  while (fa. next ())
275 | 		  {
276 | 	      const Dna dna (fa, 100000/*PAR*/, true);
277 | 		    dna. qc ();	
278 | 		    const string id (dna. getId ());
279 | 		    for (SymbolRaw& symbolRaw : symbolRaws)
280 | 		      if (symbolRaw. contig == id)
281 |   		      for (size_t offset = 0; ; offset++)
282 |   		      {
283 |   		        const char aa = symbolRaw. contig2aa (dna, offset, gencode);
284 |   		        if (aa == no_aa)
285 |   		          break;
286 |   		        symbolRaw. allele += aa;
287 |   		        if (aa == '*')
288 |   		          break;
289 |   		      }
290 | 		  }
291 | 		}
292 | 
293 |     // SymbolRaw::{ref, allele for "del"}
294 | 		{
295 | 		  Multifasta fa (protFName, true);
296 | 		  while (fa. next ())
297 | 		  {
298 | 		    const Peptide pep (fa, 1000/*PAR*/, true);
299 | 		    pep. qc ();	
300 | 		    
301 | 		    string id;
302 | 		    const string id_whole (pep. getId ());
303 | 		    if (prot_id_pos)
304 | 		    {
305 |     		  const StringVector vec (id_whole, id_delim, true);
306 |     		  if (prot_id_pos - 1 >= vec. size ())
307 |     		    throw runtime_error ("Protein identifier position " + to_string (prot_id_pos) + " is outside of the list of identifiers: " + strQuote (id_whole));
308 |     		  id = vec [prot_id_pos - 1];
309 |     		}
310 | 		    else
311 | 		      id = id_whole;
312 |     		
313 | 		    for (SymbolRaw& symbolRaw : symbolRaws)
314 | 		      if (symbolRaw. prot == id)
315 | 		        symbolRaw. ref = pep. seq. substr (symbolRaw. qstart, symbolRaw. qend - symbolRaw. qstart);
316 | 		  }
317 | 		}
318 | 		
319 | 		// symbolRaw's
320 | 		for (const SymbolRaw& symbolRaw : symbolRaws)
321 | 		  symbolRaw. saveText (cout);
322 |   }
323 | };
324 | 
325 | 
326 | }  // namespace
327 | 
328 | 
329 | 
330 | 
331 | int main (int argc, 
332 |           const char* argv[])
333 | {
334 |   ThisApplication app;
335 |   return app. run (argc, argv);
336 | }
337 | 
338 | 
339 | 
340 | 


--------------------------------------------------------------------------------
/tsv.hpp:
--------------------------------------------------------------------------------
  1 | // tsv.hpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   TSV-table
 31 | *
 32 | */
 33 | 
 34 | 
 35 | #ifndef TSV_HPP
 36 | #define TSV_HPP
 37 | 
 38 | 
 39 | #include "common.hpp"
 40 | using namespace Common_sp;
 41 | 
 42 | 
 43 | 
 44 | namespace Common_sp
 45 | {
 46 | 
 47 | 
 48 | 
 49 | struct Date : Root
 50 | {
 51 |   enum Format {fmt_Year, fmt_YMD, fmt_None};  // not complete list ??
 52 |   short year {0};
 53 |   char month {0};
 54 |     // 0 .. 12 - 1
 55 |   char day {0};
 56 |     // 0 .. days[month] - 1  // leap year ??
 57 |   
 58 |   
 59 |   Date () = default;
 60 |   explicit Date (short year_arg,
 61 |                  char month_arg = 0,
 62 |                  char day_arg = 0)
 63 |     : year (year_arg)
 64 |     , month (month_arg)
 65 |     , day (day_arg)
 66 |     {}
 67 |   static bool isYear (short n)
 68 |     { return n > 1000 && n < 2500; }  // PAR
 69 |   static bool isMonth  (short n)
 70 |     { return between<short> (n, 0, 12); }  
 71 |   static bool isDay  (short n)
 72 |     { return between<short> (n, 0, 31); }   // Must depend on month ??
 73 |   static Date parse (const string &s,
 74 |                      Format fmt);
 75 |     // Return: !empty() <=> success
 76 |   bool empty () const final
 77 |     { return    ! year 
 78 |              && ! month
 79 |              && ! day; 
 80 |     }
 81 |   void saveText (ostream &os) const final
 82 |     { os << std::setfill('0') << std::setw(4) <<       year      << '-' 
 83 |          << std::setfill('0') << std::setw(2) << (int) month + 1 << '-' 
 84 |          << std::setfill('0') << std::setw(2) << (int) day   + 1; 
 85 |     }
 86 |   JsonMap* toJson (JsonContainer* parent, 
 87 |                    const string& name = noString) const override
 88 |     { auto j = new JsonMap (parent, name);
 89 |       new JsonInt (year,  j, "year");
 90 |       new JsonInt (month, j, "month");
 91 |       new JsonInt (day,   j, "day");
 92 |       return j;
 93 |     }
 94 |     
 95 |     
 96 |   bool operator== (const Date &other) const
 97 |     { return    year  == other. year
 98 |              && month == other. month
 99 |              && day   == other. day;
100 |     }
101 |   bool less (const Date &other,
102 |              bool equal) const;
103 |   bool operator<= (const Date &other) const
104 |     { return less (other, true); }
105 |   bool operator< (const Date &other) const
106 |     { return less (other, false); }
107 |   Date operator- (const Date &other) const;
108 |     // Requires: other <= *this
109 |   bool year_divisible () const
110 |     { return ! month && ! day; }
111 |   bool quarter_divisible () const
112 |     { return ! (month % 3) && ! day; }
113 |   bool month_divisible () const
114 |     { return ! day; }
115 | };
116 |   
117 |   
118 | 
119 | struct TextTable : Named
120 | // Tab-separated value (tsv) table with a header
121 | // name: file name or empty()
122 | {
123 |   bool pound {false};
124 |     // '#' in the beginning of header
125 |   bool saveHeader {true};
126 |   
127 |   
128 |   struct Header : Named
129 |   { 
130 |     size_t len_max {0};
131 |       // For trim()'ed fields
132 |     // Type
133 |     bool numeric {true};
134 |     // Valid if numeric
135 |     bool scientific {false};
136 |     streamsize decimals {0};
137 |     bool null {false};
138 |       // = can be empty()
139 |     static constexpr size_t choices_max {7};  // PAR
140 |     Set<string> choices;
141 |       // size() <= choices_max + 1
142 |       
143 |     Header () = default;
144 |     explicit Header (const string &name_arg)
145 |       : Named (name_arg)
146 |       {}
147 |     void qc () const override;
148 |     void saveText (ostream& os) const override
149 |       { os         << name 
150 |            << '\t' << len_max 
151 |            << '\t' << (numeric ? ((scientific ? "float" : "int") + string ("(") + to_string (decimals) + ")") : "char") 
152 |            << '\t' << (null ? "null" : "not null"); 
153 |       }
154 |       
155 |     void saveSql (ostream& os) const;
156 |   };
157 |   Vector<Header> header;
158 |     // Header::name's are unique
159 |     // size() = number of columns
160 |     
161 |     
162 |   Vector<StringVector> rows;
163 |     // StringVector::size() = header.size()
164 |     // Values are trim()'ed
165 |   typedef  size_t  ColNum;
166 |     // no_index <=> no column
167 |   typedef  size_t  RowNum;
168 |     // no_index <=> no row
169 |   static constexpr char aggr_sep {','};  // PAR
170 |     
171 |     
172 |   struct Error : runtime_error
173 |   {
174 |     Error (const TextTable &tab,
175 |            const string &what)
176 |       : runtime_error (what + "\nIn table file: " + tab. name)
177 |       {}
178 |   };
179 |     
180 | 
181 |   explicit TextTable (const string &tableFName,
182 |                       const string &columnSynonymsFName = noString,
183 |                       bool headerP = true,
184 |                       uint displayPeriod = 0);
185 |     // Input: tableFName: format: [{'#' <comment> <EOL>}* '#'] <header> <EOL> {<row> <EOL>>}*
186 |     //                    empty lines are skipped
187 |     //        columnSynonymsFName: <syn_format>
188 |     // Rows where number of columns < header size are added empty values
189 |   static constexpr const char* syn_format {"Column synonyms file with the format: {<main synonym> <eol> {<synonym> <eol>}* {<eol>|<eof>}}*"};
190 |   TextTable () = default;
191 |   TextTable (bool pound_arg,
192 |              const Vector<Header> &header_arg)
193 |     : pound (pound_arg)
194 |     , header (header_arg)
195 |     {}
196 | private:
197 |   void setHeader ();
198 | public:
199 |   static Vector<Header> str2header (const string &s,
200 |                                     char sep = ',')
201 |     { const StringVector vec (s, sep, true);
202 |       Vector<Header> header;  header. reserve (vec. size ());
203 |       for (const string& name : vec)
204 |         header << std::move (Header (name));
205 |       return header;
206 |     }
207 |   void qc () const override;
208 |   void saveText (ostream &os) const override;    
209 |         
210 |   
211 |   void printHeader (ostream &os) const;
212 |   ColNum col2num_ (const string &columnName) const;
213 |     // Return: no_index <=> no columnName
214 |   ColNum col2num (const string &columnName) const
215 |     { const ColNum i = col2num_ (columnName);
216 |       if (i == no_index)
217 |         throw Error (*this, "Table has no column " + strQuote (columnName));
218 |       return i;
219 |     }
220 |   Vector<ColNum> columns2nums (const StringVector &columns) const
221 |     { Vector<ColNum> nums;  nums. reserve (columns. size ());
222 |       for (const string &s : columns)
223 |         nums << col2num (s);
224 |       return nums;
225 |     }
226 |   bool hasColumn (const string &columnName) const
227 |     { return col2num_ (columnName) != no_index; }
228 |   void duplicateColumn (const string &columnName_from,
229 |                         const string &columnName_to);
230 |   void substitueColumn (string &columnName_from,
231 |                         const string &columnName_to)
232 |     { duplicateColumn (columnName_from, columnName_to);
233 |       columnName_from = columnName_to;
234 |     }
235 |   ColNum findDate (Date::Format &fmt) const;
236 |     // Date column is not empty and has the same format fmt in all rows
237 |     // Return: no_index <=> not found
238 |     // Output: fmt, valid if return != no_index
239 |   bool isKey (ColNum colNum) const;
240 | private:
241 |   int compare (const StringVector& row1,
242 |                const StringVector& row2,
243 |                ColNum column) const;
244 | public:
245 |   void filterColumns (const StringVector &newColumnNames);
246 |     // Input: newColumnNames: in header::name's
247 |     //          can be repeated
248 |     //          ordered
249 |   void sort (const StringVector &by);
250 |   void deredundify (const StringVector &equivCols,
251 |                     const CompareInt& equivBetter);
252 |     // Input: equivBetter(row1,row2) = 1 <=> row1 is better than row2
253 |     //          Requires: row1 and row2 are in the class of equivCols-equivalent rows
254 |     // Sorts by equivCols
255 |   void group (const StringVector &by,
256 |               const StringVector &sum,
257 |               const StringVector &minV,
258 |               const StringVector &maxV,
259 |               const StringVector &aggr);
260 |     // aggr: slow
261 |     // Invokes: sort(by), filterColumns(by + sum + aggr)
262 | private:
263 |   void merge (RowNum toRowNum,
264 |               RowNum fromRowNum,
265 |               const Vector<ColNum> &sum,
266 |               const Vector<ColNum> &minV,
267 |               const Vector<ColNum> &maxV,
268 |               const Vector<ColNum> &aggr);
269 | public:
270 |   static StringVector aggr2values (const string &aggr)
271 |     { StringVector v (aggr, aggr_sep, true);
272 |       v. sort ();
273 |       v. uniq ();
274 |       return v;
275 |     }
276 |   void colNumsRow2values (const Vector<ColNum> &colNums,
277 |                           RowNum row_num,
278 |                           StringVector &values) const;
279 |     // Output: values
280 |   RowNum find (const Vector<ColNum> &colNums,
281 |                const StringVector &targetValues,
282 |                RowNum rowNum_start) const;
283 |   StringVector col2values (ColNum col) const;
284 | 
285 | 
286 |   struct Key
287 |   {
288 |     const Vector<ColNum> colNums;
289 |     unordered_map<StringVector,RowNum,StringVector::Hasher> data;
290 | 
291 |     Key (const TextTable &tab,
292 |          const StringVector &columns);
293 |          
294 |     RowNum find (const StringVector &values) const
295 |       { const auto& it = data. find (values);
296 |         if (it != data. end ())
297 |           return it->second;
298 |         return no_index;
299 |       }
300 |   };
301 | 
302 | 
303 |   struct Index
304 |   {
305 |     const Vector<ColNum> colNums;
306 |     unordered_map<StringVector,Vector<RowNum>,StringVector::Hasher> data;
307 | 
308 |     Index (const TextTable &tab,
309 |            const StringVector &columns);
310 |          
311 |     const Vector<RowNum>* find (const StringVector &values) const
312 |       { const auto& it = data. find (values);
313 |         if (it == data. end ())
314 |           return nullptr;
315 |         return & it->second;
316 |       }
317 |   };
318 | };
319 | 
320 | 
321 | 		
322 | struct TsvOut
323 | {
324 | private:
325 |   ostream* os {nullptr};
326 |   unique_ptr<const ONumber> on;
327 |   size_t lines {0};
328 |   size_t fields_max {0};
329 |   size_t fields {0};
330 | public:
331 |   bool usePound {true};
332 |   
333 |   
334 |   explicit TsvOut (ostream* os_arg,
335 |                    streamsize precision = 6,
336 | 	                 bool scientific = false)
337 | 	  : os (os_arg)
338 | 	  , on (os_arg ? new ONumber (*os_arg, precision, scientific) : nullptr)
339 | 	  {}
340 | 	  // !os_arg <=> disabled
341 |   explicit TsvOut (ostream &os_arg,
342 |                    streamsize precision = 6,
343 | 	                 bool scientific = false)
344 | 	  : TsvOut (& os_arg, precision, scientific)
345 | 	  {}
346 |  ~TsvOut ()
347 |     { if (fields)
348 |         errorExitStr ("TsvOut: unfinished line with " + to_string (fields) + " fields"); 
349 |     }
350 |     
351 |     
352 |   bool live () const
353 |     { return os; }
354 |   bool empty () const
355 |     { return    ! lines 
356 |              && ! fields_max
357 |              && ! fields;
358 |     }
359 |   template <typename T>
360 |     TsvOut& operator<< (const T &field)
361 |       { if (os)
362 |         { if (lines && fields >= fields_max)
363 |             throw runtime_error ("TsvOut: fields_max = " + to_string (fields_max));
364 |           if (fields)  
365 |             *os << '\t'; 
366 |           else if (! lines && usePound)
367 |             *os << '#';
368 |           *os << field; 
369 |           fields++;
370 |         }
371 |         return *this; 
372 |       }    
373 |   void newLn ()
374 |     { if (! os)
375 |         return;
376 |       *os << endl;
377 |       if (! lines)
378 |         fields_max = fields;
379 |       lines++;
380 |       if (fields != fields_max)
381 |         throw runtime_error ("TsvOut: fields_max = " + to_string (fields_max) + ", but fields = " + to_string (fields));
382 |       fields = 0;
383 |     }
384 | };
385 | 
386 | 
387 | 
388 | }
389 | 
390 | 
391 | 
392 | #endif
393 | 
394 | 


--------------------------------------------------------------------------------
/amrfinder_update.cpp:
--------------------------------------------------------------------------------
  1 | // amrfinder_update.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Updating of AMRFinder data
 31 | *
 32 | * Dependencies: libcurl
 33 | 
 34 | * Release changes: see amrfinder.cpp
 35 | *
 36 | */
 37 | 
 38 | 
 39 | 
 40 | // PAR
 41 | #undef TEST_UPDATE  
 42 | #define HTTPS 1   // 0: FTP
 43 | 
 44 | 
 45 | 
 46 | #undef NDEBUG 
 47 | 
 48 | #include "common.hpp"
 49 | using namespace Common_sp;
 50 | #include "curl_easy.hpp"
 51 | using namespace CURL_sp;
 52 | 
 53 | #include "common.inc"
 54 | 
 55 | 
 56 | 
 57 | namespace 
 58 | {
 59 | 
 60 | 
 61 | // URL
 62 | #ifdef TEST_UPDATE
 63 |   #define URL "https://ftp.ncbi.nlm.nih.gov/pathogen/Technical/AMRFinder_technical/test_database/"
 64 | #else
 65 |   #define URL_SUF "://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/"  
 66 |   #if HTTPS
 67 |     #define URL  "https" URL_SUF
 68 |   #else
 69 |     #define URL  "ftp" URL_SUF
 70 |   #endif
 71 | #endif
 72 | 
 73 | 
 74 | 
 75 | string getLatestMinor (Curl &curl)
 76 | // Return: empty() <=> failure
 77 | {
 78 |   StringVector dir (curl. read (URL), '\n', true);
 79 |   if (verbose ())
 80 |   {
 81 |     save (cout, dir, '\n'); 
 82 |     cout << endl;
 83 |   }
 84 |     
 85 |   Vector<SoftwareVersion> vers;  
 86 |   for (string& line : dir)
 87 |   #if HTTPS
 88 |     if (isLeft (line, "<a href="))
 89 |   	  try 
 90 |   	  {
 91 |         const size_t pos1 = line. find ('>');
 92 |         if (pos1 == string::npos)
 93 |           throw runtime_error ("Cannot find '>' after '<a href=' in " + string (URL));
 94 |         line. erase (0, pos1 + 1);
 95 | 
 96 |         const size_t pos2 = line. find ("/<");
 97 |         if (pos2 == string::npos)
 98 |           throw runtime_error ("Cannot find '/<' after '>' in " + string (URL));
 99 |         line. erase (pos2);
100 |         
101 |     	  istringstream iss (line);
102 |   		  SoftwareVersion ver (iss, true);
103 |   		  vers << std::move (ver);
104 |   		}
105 |   		catch (...) {}
106 |   #else
107 |     if (! contains (line, " -> "))
108 |     {
109 |       trimTrailing (line);
110 |       const size_t pos = line. rfind (' ');
111 |       if (pos != string::npos)
112 |       {
113 |     	  istringstream iss (line. substr (pos + 1));
114 |     	  try 
115 |     	  {
116 |     		  SoftwareVersion ver (iss, true);
117 |     		  vers << std::move (ver);
118 |     		}
119 |   		  catch (...) {}    		
120 |       }
121 |     }
122 |   #endif
123 |   if (vers. empty ())
124 |     return noString;
125 |     
126 |   vers. sort ();
127 |   return vers. back (). getMinor ();
128 | }
129 | 
130 | 
131 | 
132 | string getLatestDataVersion (Curl &curl,
133 |                              const string &minor)
134 | // Return: empty() <=> failure
135 | {
136 |   const string url (URL + minor + "/");
137 |   StringVector dir (curl. read (url), '\n', true);
138 |   if (verbose ())
139 |   {
140 |     save (cout, dir, '\n');
141 |     cout << endl;
142 |   }
143 |     
144 |   Vector<DataVersion> dataVersions;  
145 |   for (string& line : dir)
146 |   #if HTTPS
147 |     if (isLeft (line, "<a href="))
148 |       try
149 |       {
150 |         const size_t pos1 = line. find ('>');
151 |         if (pos1 == string::npos)
152 |           throw runtime_error ("Cannot find '>' after '<a href=' in " + url);
153 |         line. erase (0, pos1 + 1);
154 | 
155 |         const size_t pos2 = line. find ("/<");
156 |         if (pos2 == string::npos)
157 |           throw runtime_error ("Cannot find '/<' after '>' in " + url);
158 |         line. erase (pos2);
159 |         
160 |     	  istringstream iss (line);
161 |   		  DataVersion dv (iss);
162 |   		  dataVersions << std::move (dv);
163 |     	}
164 |   		catch (...) {}
165 |   #else
166 |     if (! contains (line, " -> "))
167 |     {
168 |       trimTrailing (line);
169 |       const size_t pos = line. rfind (' ');
170 |       if (pos != string::npos)
171 |       {
172 |     	  istringstream iss (line. substr (pos + 1));
173 |     	  try 
174 |     	  {
175 |     		  DataVersion dv (iss);
176 |     		  dataVersions << std::move (dv);
177 |     		}
178 |   		  catch (...) {}    		
179 |       }
180 |     }
181 |   #endif
182 |   if (dataVersions. empty ())
183 |     return noString;
184 |     
185 |   dataVersions. sort ();
186 |   return dataVersions. back (). str ();
187 | }
188 | 
189 | 
190 | 
191 | void fetchAMRFile (Curl &curl,
192 |                    const string &urlDir,
193 |                    const string &localDir,
194 |                    const string &fName) 
195 | {
196 |   ASSERT (isDirName (urlDir));
197 |   ASSERT (isDirName (localDir));
198 |   ASSERT (! fName. empty ());  
199 |   curl. download (urlDir + fName, localDir + fName);
200 | }
201 | 
202 | 
203 | 
204 | 	
205 | // ThisApplication
206 | 
207 | struct ThisApplication final : ShellApplication
208 | {
209 |   string curMinor;
210 | 
211 | 
212 |   ThisApplication ()
213 |     : ShellApplication ("Update the database for AMRFinder from " URL "\n\
214 | Requirement: the database directory contains subdirectories named by database versions.\
215 | ", false, false, true, true)
216 |     {
217 |     	addKey ("database", "Directory for all versions of AMRFinder databases", "$BASE/data", 'd', "DATABASE_DIR");
218 |     	addKey ("blast_bin", "Directory for BLAST", "", '\0', "BLAST_DIR");
219 |     	addKey ("hmmer_bin", "Directory for HMMer", "", '\0', "HMMER_DIR");
220 |     	addFlag ("force_update", "Force updating the AMRFinder database");  // PD-3469
221 | 	    version = SVN_REV;
222 | 
223 |       // curMinor
224 |       {
225 |     	  istringstream versionIss (version);
226 |     		const SoftwareVersion softwareVersion (versionIss);
227 |         curMinor = softwareVersion. getMinor ();
228 |       }
229 |     }
230 | 
231 | 
232 | 
233 |   void createLatestLink (const string &mainDirS,
234 |                          const string &latestDir) const
235 |   {   
236 |     ASSERT (! mainDirS. empty ()); 
237 |     ASSERT (! latestDir. empty ()); 
238 |     const string latestLink (mainDirS + "latest");
239 |     ::remove (latestLink. c_str ());
240 |     setSymlink (latestDir, latestLink, false);
241 |   }
242 | 
243 | 
244 | 
245 |   void shellBody () const final
246 |   {
247 |     const string mainDirOrig  = getArg ("database");
248 |           string blast_bin    = getArg ("blast_bin");
249 |           string hmmer_bin    = getArg ("hmmer_bin");
250 |     const bool   force_update = getFlag ("force_update");
251 |         
252 |     addDirSlash (blast_bin);
253 |     addDirSlash (hmmer_bin);
254 |     
255 |         
256 |     const Verbose vrb (qc_on);
257 |     
258 | 
259 |     Curl curl;
260 |         
261 |     
262 |     const bool screen = ! isRedirected (cerr);
263 |     
264 |     // FTP site files
265 |     stderr << "Looking up the published databases at " << colorizeUrl (URL, screen) << '\n';    
266 |     string load_minor = curMinor;
267 |     string load_data_version;    
268 |     {
269 |       const string published_minor (getLatestMinor (curl));
270 |       if (published_minor. empty ())
271 |         throw runtime_error ("Cannot get the software minor version of the latest published database version");
272 |     //if (qc_on)
273 |       //stderr << "Latest published software minor version: " << published_minor << "\n";
274 |       // ASSERT: published_minor >= curMinor
275 | 
276 |       const string published_data_version (getLatestDataVersion (curl, published_minor));
277 |       if (published_data_version. empty ())
278 |         throw runtime_error ("Cannot get the latest published database version for the software minor version " + published_minor);
279 | 
280 |       const string cur_data_version (getLatestDataVersion (curl, curMinor));
281 |       load_data_version = cur_data_version;    
282 |       if (cur_data_version. empty ())  // Contents of (URL + curMinor) are empty ??
283 |       {
284 |         stderr << "\n";
285 |         const Warning w (stderr);
286 |         stderr << "Cannot get the latest published database version for the current software minor version " + curMinor + ".\n"
287 |                << "The latest published database version " + published_data_version + " for the latest published software minor version " + published_minor + " will be used instead";
288 |         load_minor        = published_minor;
289 |         load_data_version = published_data_version;
290 |       }
291 |       else if (cur_data_version != published_data_version)  
292 |       {   
293 |         ASSERT (cur_data_version < published_data_version);
294 |         stderr << "\n";
295 |         const Warning w (stderr);
296 |         stderr << "A newer version of the database exists (" << published_data_version << "), but it requires "
297 |                   "a newer version of the software (" << published_minor << ") to install.\n"
298 |                   "See " + colorizeUrl ("https://github.com/ncbi/amr/wiki/Upgrading", screen) + " for more information.\n";
299 |       }
300 |     }
301 |     ASSERT (! load_data_version. empty ());
302 |    
303 | 
304 |     // Users's files  
305 |     string mainDirS;
306 |     {
307 |       const Dir mainDir (mainDirOrig);
308 |       mainDirS = mainDir. get ();
309 |     }
310 |     addDirSlash (mainDirS);
311 |     
312 |     const string versionFName ("version.txt");
313 |     const string urlDir (URL + load_minor + "/" + load_data_version + "/");    
314 |     const string latestDir (mainDirS + load_data_version + "/");
315 |     
316 |     stderr << "Looking for the target directory: " << colorizeDir (latestDir, screen) << "\n";
317 |     if (directoryExists (latestDir))
318 |     {
319 |       if (force_update)
320 |         stderr << colorizeDir (latestDir, screen) << ": already exists, overwriting what was there\n";
321 |       else
322 |       {
323 |         curl. download (urlDir + versionFName, tmp + "/curl");
324 |         const StringVector version_old (latestDir + versionFName, (size_t) 100, true);
325 |         const StringVector version_new (tmp + "/curl", (size_t) 100, true);
326 |         if (   ! version_old. empty () 
327 |             && ! version_new. empty ()
328 |             && version_old. front () == version_new. front ()
329 |            )
330 |         {
331 |           const Warning w (stderr);
332 |           stderr << colorizeDir (latestDir, screen) << ": contains the latest version " << version_old. front () << '\n';
333 |           stderr << "Skipping update\nUse amrfinder --force_update to overwrite the existing database";
334 |           createLatestLink (mainDirS, /*latestDir*/ load_data_version);
335 |           return;
336 |         }
337 |       }
338 |     }
339 |     else
340 |       Dir (latestDir). create ();
341 |     
342 |     stderr << "Downloading AMRFinder database version " << load_data_version << " into: " << colorizeDir (latestDir, screen) << "\n";
343 |     // Requires: Software version >= 3.13.1
344 |     fetchAMRFile (curl, urlDir, latestDir, "AMR.LIB");
345 |     fetchAMRFile (curl, urlDir, latestDir, "AMRProt.fa");
346 |     fetchAMRFile (curl, urlDir, latestDir, "AMRProt-mutation.tsv");
347 |     fetchAMRFile (curl, urlDir, latestDir, "AMRProt-suppress.tsv");
348 |     fetchAMRFile (curl, urlDir, latestDir, "AMRProt-susceptible.fa");
349 |     fetchAMRFile (curl, urlDir, latestDir, "AMRProt-susceptible.tsv");
350 |     fetchAMRFile (curl, urlDir, latestDir, "AMR_CDS.fa");
351 |     fetchAMRFile (curl, urlDir, latestDir, "database_format_version.txt");  // PD-3051 
352 |     fetchAMRFile (curl, urlDir, latestDir, "fam.tsv");
353 |     fetchAMRFile (curl, urlDir, latestDir, "taxgroup.tsv");
354 |     fetchAMRFile (curl, urlDir, latestDir, versionFName);
355 |     
356 |     StringVector dnaPointMuts;
357 |     {
358 |       LineInput f (latestDir + "taxgroup.tsv");
359 |       while (f. nextLine ())
360 |       {
361 |    	    if (isLeft (f. line, "#"))
362 | 	 	      continue;
363 |         string taxgroup, gpipe;
364 |         int n = -1;
365 |         istringstream iss (f. line);
366 |         iss >> taxgroup >> gpipe >> n;
367 |         if (n < 0)
368 |           throw runtime_error ("Bad " + latestDir + "taxgroup.tsv");
369 |         if (n)
370 |           dnaPointMuts << taxgroup;
371 |       }
372 |     }
373 |     
374 |     for (const string& dnaPointMut : dnaPointMuts)
375 |     {
376 |       fetchAMRFile (curl, urlDir, latestDir, "AMR_DNA-" + dnaPointMut + ".fa");
377 |       fetchAMRFile (curl, urlDir, latestDir, "AMR_DNA-" + dnaPointMut + ".tsv");
378 |     }
379 | 
380 |     fetchAMRFile (curl, urlDir, latestDir, "changes.txt");
381 | 
382 |     createLatestLink (mainDirS, load_data_version);
383 |   
384 | 
385 |     prog2dir ["amrfinder_index"] = execDir;
386 | 	  exec (fullProg ("amrfinder_index") + shellQuote (latestDir) 
387 | 	          + makeKey ("blast_bin", blast_bin)   
388 | 	          + makeKey ("hmmer_bin", hmmer_bin)  
389 | 	          + ifS (getQuiet (), " -q") + ifS (qc_on, " --debug") + " > " + tmp + "/amrfinder_index.err", tmp + "/amrfinder_index.err"); 
390 |   }
391 | };
392 | 
393 | 
394 | 
395 | }  // namespace
396 | 
397 | 
398 | 
399 | int main (int argc, 
400 |           const char* argv[])
401 | {
402 |   ThisApplication app;
403 |   return app. run (argc, argv);  
404 | }
405 | 
406 | 
407 | 
408 | 


--------------------------------------------------------------------------------
/dna_mutation.cpp:
--------------------------------------------------------------------------------
  1 | // dna_mutation.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   Identification of mutations at DNA level
 31 | *
 32 | * Release changes: see amrfinder.cpp
 33 | *
 34 | */
 35 |    
 36 |    
 37 | #undef NDEBUG 
 38 | 
 39 | #include "common.hpp"
 40 | #include "tsv.hpp"
 41 | using namespace Common_sp;
 42 | #include "alignment.hpp"
 43 | using namespace Alignment_sp;
 44 | #include "columns.hpp"
 45 | 
 46 | #include "common.inc"
 47 | 
 48 | 
 49 | 
 50 | namespace
 51 | {  
 52 | 
 53 | map <string/*accession*/, Vector<AmrMutation>>  accession2mutations;
 54 | string input_name;
 55 | bool print_node = false;
 56 | 
 57 | 
 58 | 
 59 | struct BlastnAlignment final : Alignment
 60 | {
 61 | 	// PD-2001
 62 |  	static constexpr const size_t flankingLen = 200;  // PAR  
 63 |   string organism;
 64 |   string refAccessionFrag;
 65 |   string product;
 66 |   string gene;
 67 |   
 68 | 
 69 |   BlastnAlignment (const string &line,
 70 |                    const string &organism_arg)
 71 |     : Alignment (line, false, false)
 72 |     , organism (organism_arg)
 73 |     {
 74 |       // To match AmrMutation
 75 |       strUpper (qseq);
 76 |       strUpper (sseq);
 77 |       
 78 | 	    replace (organism, '_', ' ');
 79 |       try
 80 |       {
 81 |         // qseqid =      NC_022347.1@23S_ribosomal_RNA@23S@-159:1040292-1037381
 82 |         //           accesion_version@gene_name@gene_symbol@offset:start-stop
 83 | 	      ASSERT (! qseqid. empty ());
 84 | 	      // PD-3419
 85 | 	      {
 86 |   	      string s (qseqid);
 87 |   	      refAccessionFrag =       findSplit (s, '@');
 88 |   	      product          =       findSplit (s, '@');
 89 |   	      gene             =       findSplit (s, ':');
 90 |   	    //ref_offset       = stoi (findSplit (s, ':'));
 91 |   	      refAccessionFrag += ":" + s;
 92 |   	    }
 93 | 	      replace (product, '_', ' ');
 94 |   	    if (const Vector<AmrMutation>* refMutations = findPtr (accession2mutations, qseqid))
 95 |   	      setSeqChanges (*refMutations, flankingLen);
 96 | 		  }
 97 | 		  catch (const exception &e)
 98 | 		  {
 99 | 		  	throw runtime_error (line + "\n" + e. what ());;
100 | 		  }
101 |     }
102 |   void qc () const override
103 |     { if (! qc_on)
104 |         return;
105 |       Alignment::qc ();
106 |       QC_ASSERT (! aProt);
107 |       QC_ASSERT (! refAccessionFrag. empty ());
108 |       QC_ASSERT (! product. empty ());
109 |       QC_ASSERT (! gene. empty ());
110 |       QC_ASSERT (! organism. empty ());
111 |     }
112 |   void report (TsvOut& td,
113 |                bool mutationAll) const 
114 |     { for (const SeqChange& seqChange : seqChanges)
115 |       {
116 |         VectorPtr<AmrMutation> mutations (seqChange. mutations);
117 |         if (mutations. empty ())
118 |           mutations << nullptr;
119 |         for (const AmrMutation* mutation : mutations)
120 |         {
121 |           {
122 |             bool skip = true;
123 |             if (mutationAll)
124 |               skip = false;
125 |             if (! seqChange. empty () && mutation && ! seqChange. replacement)  // resistant mutation
126 |               skip = false;
127 |             if (skip)
128 |               continue;
129 |           }
130 |           ASSERT (! (seqChange. empty () && ! mutation));
131 |     	    if (! input_name. empty ())
132 |     	      td << input_name;;
133 |           td << na  // PD-2534
134 |              << nvl (sseqid, na)
135 |              << (empty () ? 0 : sInt. start + 1)
136 |              << (empty () ? 0 : sInt. stop)
137 |              << (empty () ? string (na) : string (1, strand2char (sInt. strand)))
138 |              << (mutation
139 |                    ? seqChange. empty ()
140 |                      ? mutation->wildtype ()
141 |                      : mutation->geneMutation
142 |                    : gene + "_" + seqChange. getMutationStr ()
143 |                 )
144 |              << (mutation
145 |                    ? seqChange. empty ()
146 |                        ? organism + " " + product + " [WILDTYPE]"
147 |                        : mutation->name
148 |                    : organism + " " + product + " [UNKNOWN]"
149 |                 )
150 |              << "core"  // PD-2825
151 |              // PD-1856
152 |              << "AMR"
153 |              << "POINT"
154 |              << (mutation ? nvl (mutation->classS,   na) : na)
155 |              << (mutation ? nvl (mutation->subclass, na) : na);
156 |            if (empty ())
157 |              td << na
158 |                 << na
159 |                 << na
160 |                 << na
161 |                 << na
162 |                 << na
163 |                 << na
164 |                 << na;
165 |            else
166 |              td << "POINTN"  // PD-2088
167 |                 << sInt. len ()  // was: targetLen  // PD-3796
168 |                 << qlen
169 |                 << qRelCoverage () * 100  
170 |                 << relIdentity () * 100  
171 |                 << sseq. size ()
172 |                 << refAccessionFrag  // qseqid
173 |                 << product;  // pm.gene
174 |           // HMM
175 |           td << na
176 |              << na;
177 | 	        if (print_node)
178 | 	          td << na;
179 | 	        td. newLn ();
180 | 	      #if 0
181 |           if (! seqChange. empty () && mutation && ! seqChange. replacement)  // resistant mutation
182 |             os << td. str () << endl;
183 |           if (mutation_all. get ())
184 |   	        *mutation_all << td. str () << endl;
185 |   	    #endif
186 |   	    }
187 |       }
188 |     }
189 |     
190 | 
191 |   bool good () const
192 |     { return sseq. size () >= min (qlen, 2 * flankingLen + 1); }
193 | #if 0
194 |   bool operator< (const BlastnAlignment &other) const
195 |     { LESS_PART (*this, other, sseqid);
196 |       LESS_PART (other, *this, relIdentity ());
197 |       LESS_PART (*this, other, sstart);
198 |       LESS_PART (*this, other, qseqid);
199 |       return false;
200 |     }
201 | #endif
202 | };
203 | 
204 | 
205 | 
206 | 
207 | struct Batch
208 | {
209 |   VectorOwn<BlastnAlignment> blastAls;   
210 |   
211 |   
212 |   explicit Batch (const string &mutation_tab)
213 | 	  {
214 | 	    {
215 |         LineInput f (mutation_tab);
216 |    	  	Istringstream iss;
217 |     	  while (f. nextLine ())
218 |     	  {
219 | 	  	    if (isLeft (f. line, "#"))
220 | 	  	      continue;
221 |      	  	iss. reset (f. line);
222 |     	  	string accession, geneMutation_std, geneMutation_report, classS, subclass, name;
223 |     			int pos;
224 |     	  	iss >> accession >> pos >> geneMutation_std >> geneMutation_report >> classS >> subclass >> name;
225 |     	  	QC_ASSERT (pos > 0);
226 |     	  	QC_ASSERT (! name. empty ());
227 |    	  		accession2mutations [accession] << std::move (AmrMutation ((size_t) pos, geneMutation_std, geneMutation_report, classS, subclass, name));
228 |     	  }	    
229 |     	}
230 |   	  for (auto& it : accession2mutations)
231 |   	  {
232 |   	  	it. second. sort ();
233 |   	    if (! it. second. isUniq ())
234 |   	  	  throw runtime_error ("Duplicate reference mutations for " + it. first);
235 |   	  }
236 | 	  }
237 | 	  	  
238 | 
239 | 	void report (TsvOut &td,
240 | 	             bool mutationAll) const
241 | 	{
242 | 	  ASSERT (td. empty ());
243 | 	  
244 |   	// Cf. BlastnAlignment::report()
245 |     if (! input_name. empty ())
246 |       td << "Name";
247 |     td << prot_colName   // sseqid 
248 |        // Contig
249 |        << contig_colName
250 |        // target
251 |        << start_colName  
252 |        << stop_colName
253 |        << strand_colName
254 |        //
255 |        << genesymbol_colName
256 |        << elemName_colName  // was: "AmrMutation name"
257 |        << scope_colName
258 |        << type_colName
259 |        << subtype_colName
260 |        << class_colName
261 |        << subclass_colName
262 |        //
263 |        << method_colName
264 |        << targetLen_colName
265 |        //
266 |        << refLen_colName  // qlen
267 |        << refCov_colName  // queryCoverage
268 |        << refIdent_colName
269 |        << alignLen_colName  // length
270 |        << closestRefAccession_colName 
271 |        << closestRefName_colName
272 |        //
273 |        << hmmAccession_colName
274 |        << hmmDescr_colName
275 |        ;
276 |     if (print_node)
277 |       td << hierarchyNode_colName; 	      
278 |     td. newLn ();
279 | 
280 |   	for (const BlastnAlignment* blastAl : blastAls)
281 |   	{
282 |   	  ASSERT (blastAl);
283 |    	  blastAl->report (td, mutationAll);
284 |    	  blastAl->qc ();
285 |     }
286 | 	}
287 | };
288 | 
289 | 
290 | 
291 | 
292 | // ThisApplication
293 | 
294 | struct ThisApplication final : Application
295 | {
296 |   ThisApplication ()
297 |     : Application ("Find mutations at DNA level and report in the format of amr_report.cpp")
298 |     {
299 |       addPositional ("blastn", string ("blastn output in the format: ") + Hsp::format [true] + ". qseqid is the 1st column of <mutation> table");
300 |       addPositional ("mutation", "Mutations table");
301 |       addPositional ("organism", "Organism name");
302 |       addKey ("mutation_all", "File to report all mutations");
303 |       addKey ("name", "Text to be added as the first column \"name\" to all rows of the report");
304 |       addFlag ("print_node", "Print FAM.id"); 
305 | 	    version = SVN_REV;
306 |     }
307 | 
308 | 
309 | 
310 |   void body () const final
311 |   {
312 |     const string blastnFName        = getArg ("blastn");
313 |     const string mutation_tab       = getArg ("mutation");  
314 |     const string organism           = getArg ("organism");  
315 |     const string mutation_all_FName = getArg ("mutation_all");
316 |                  input_name         = getArg ("name");
317 |                  print_node         = getFlag ("print_node");
318 |     
319 | 
320 |     Batch batch (mutation_tab);  
321 |   
322 |   
323 |     // Input 
324 |     {
325 |       LineInput f (blastnFName);
326 |   	  while (f. nextLine ())
327 |   	  {
328 |   	    { 
329 |   	      Unverbose unv;
330 |   	      if (verbose ())
331 |   	        cout << f. line << endl;  
332 |   	    }
333 |   	    unique_ptr<BlastnAlignment> al (new BlastnAlignment (f. line, organism));
334 |   	    al->qc ();  
335 |   	    if (al->good ())
336 |   	      batch. blastAls << al. release ();
337 |   	  }
338 |   	}
339 |   	if (verbose ())
340 |   	{
341 |   	  cout << "# Good Blasts: " << batch. blastAls. size () << endl;
342 | 		  for (const BlastnAlignment* blastAl : batch. blastAls)
343 | 		  {
344 | 		    ASSERT (blastAl);
345 | 		    blastAl->saveText (cout);
346 | 		    cout << ' ' << blastAl->seqChanges. size () << endl;
347 | 		  }
348 | 		}
349 | 		
350 |     
351 |     // Group by sseqid and process each sseqid separately for speed ??    
352 |   //Common_sp::sort (batch. blastAls);
353 |     for (const BlastnAlignment* blastAl1 : batch. blastAls)
354 |       for (const SeqChange& seqChange1 : blastAl1->seqChanges)
355 |       {
356 |         ASSERT (seqChange1. al == blastAl1);
357 |       //ASSERT (seqChange1. mutation);
358 |         for (const BlastnAlignment* blastAl2 : batch. blastAls)
359 |           if (   blastAl2->sseqid  == blastAl1->sseqid
360 |               && blastAl2->sInt. strand == blastAl1->sInt. strand
361 |               && blastAl2 != blastAl1
362 |              )  
363 |           //for (Iter<Vector<SeqChange>> iter (var_cast (blastAl2) -> seqChanges); iter. next (); )
364 |             for (SeqChange& seqChange2 : var_cast (blastAl2) -> seqChanges)
365 |             {
366 |             //SeqChange& seqChange2 = *iter;
367 |               ASSERT (seqChange2. al == blastAl2);
368 |             //ASSERT (seqChange2. mutation);
369 |               if (   seqChange1. start_target == seqChange2. start_target 
370 |                   && seqChange1. better (seqChange2)                
371 |                  )
372 |               //iter. erase ();
373 |                 seqChange2. replacement = & seqChange1;
374 |             }
375 |       }
376 | 		
377 |   #if 0
378 |   	// [UNKNOWN]
379 |   	{
380 |     	map<AmrMutation, const AmrMutation*> mutation2ptr;
381 |     	for (const auto& it : accession2mutations)
382 |     	  for (const AmrMutation& mut : it. second)
383 |     	    mutation2ptr [mut] = & mut;
384 |     	for (const BlastnAlignment* al : batch. blastAls)
385 |     	  for (const SeqChange& seqChange : al->seqChanges)
386 |     	    if (const AmrMutation* mut = seqChange. mutation)
387 |     	      mutation2ptr. erase (*mut);
388 |     	for (const auto& it : mutation2ptr)
389 |     	{
390 |     	  const auto al = new BlastnAlignment (* it. second);
391 |     	  batch. blastAls << al;
392 |     	}
393 |     }
394 |   #endif
395 | 
396 | 
397 |     // Output
398 |     {
399 |       TsvOut td (cout, 2, false);
400 |       td. usePound = false;
401 |       batch. report (td, false);
402 |     }
403 |     if (! mutation_all_FName. empty ())
404 |     {
405 |       OFStream f (mutation_all_FName);
406 |       TsvOut td (f, 2, false);
407 |       td. usePound = false;
408 |       batch. report (td, true);
409 |     }
410 |   }
411 | };
412 | 
413 | 
414 | 
415 | }  // namespace
416 | 
417 | 
418 | 
419 | int main (int argc, 
420 |           const char* argv[])
421 | {
422 |   ThisApplication app;
423 |   return app. run (argc, argv);  
424 | }
425 | 
426 | 
427 | 
428 | 


--------------------------------------------------------------------------------
/test_dna_mut_all.expected:
--------------------------------------------------------------------------------
 1 | Protein identifier	Contig id	Start	Stop	Strand	Gene symbol	Sequence name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	HMM description
 2 | NA	contig05	237	1224	-	23S_A2058A	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN	POINTN	988	2905	34.01	81.08	1004	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
 3 | NA	contig05	237	1224	-	23S_C2611C	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	ERYTHROMYCIN/TELITHROMYCIN	POINTN	988	2905	34.01	81.08	1004	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
 4 | NA	contig05	237	1224	-	23S_G2057G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MULTIDRUG	CHLORAMPHENICOL/ERYTHROMYCIN/TELITHROMYCIN	POINTN	988	2905	34.01	81.08	1004	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
 5 | NA	contig05	237	1224	-	23S_G2447G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	OXAZOLIDINONE	LINEZOLID	POINTN	988	2905	34.01	81.08	1004	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
 6 | NA	contig05	237	1224	-	23S_T2609T	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	TELITHROMYCIN	POINTN	988	2905	34.01	81.08	1004	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
 7 | NA	contig14	1	1089	+	pmrB_A159A	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
 8 | NA	contig14	1	1089	+	pmrB_C84R	Escherichia colistin resistant PmrB	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
 9 | NA	contig14	1	1089	+	pmrB_E121E	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
10 | NA	contig14	1	1089	+	pmrB_E166E	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
11 | NA	contig14	1	1089	+	pmrB_G206G	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
12 | NA	contig14	1	1089	+	pmrB_L10L	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
13 | NA	contig14	1	1089	+	pmrB_L14L	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
14 | NA	contig14	1	1089	+	pmrB_P94P	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
15 | NA	contig14	1	1089	+	pmrB_T147T	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
16 | NA	contig14	1	1089	+	pmrB_T156T	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
17 | NA	contig14	1	1089	+	pmrB_V161V	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
18 | NA	contig14	1093	2181	+	pmrB_A159A	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
19 | NA	contig14	1093	2181	+	pmrB_C84R	Escherichia colistin resistant PmrB	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
20 | NA	contig14	1093	2181	+	pmrB_E121E	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
21 | NA	contig14	1093	2181	+	pmrB_E166E	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
22 | NA	contig14	1093	2181	+	pmrB_G206G	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
23 | NA	contig14	1093	2181	+	pmrB_L10L	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
24 | NA	contig14	1093	2181	+	pmrB_L14L	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
25 | NA	contig14	1093	2181	+	pmrB_P94P	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
26 | NA	contig14	1093	2181	+	pmrB_T147T	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
27 | NA	contig14	1093	2181	+	pmrB_T156T	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
28 | NA	contig14	1093	2181	+	pmrB_V161V	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	POINTX	363	363	100.00	99.72	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
29 | NA	contig14	2185	3273	+	pmrB_A159A	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
30 | NA	contig14	2185	3273	+	pmrB_C84C	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
31 | NA	contig14	2185	3273	+	pmrB_E121E	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
32 | NA	contig14	2185	3273	+	pmrB_E166E	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
33 | NA	contig14	2185	3273	+	pmrB_G206G	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
34 | NA	contig14	2185	3273	+	pmrB_L10L	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
35 | NA	contig14	2185	3273	+	pmrB_L14L	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
36 | NA	contig14	2185	3273	+	pmrB_P94P	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
37 | NA	contig14	2185	3273	+	pmrB_T147T	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
38 | NA	contig14	2185	3273	+	pmrB_T156T	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
39 | NA	contig14	2185	3273	+	pmrB_V161V	two-component system sensor histidine kinase PmrB [WILDTYPE]	core	AMR	POINT	COLISTIN	COLISTIN	EXACTX	363	363	100.00	100.00	363	WP_001300761.1	two-component system sensor histidine kinase PmrB	NA	NA
40 | NA	contig15	1	2905	+	23S_A2058T	Escherichia azithromycin/erythromycin/telithromycin resistant 23S	core	AMR	POINT	MACROLIDE	AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
41 | NA	contig15	1	2905	+	23S_C2611C	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
42 | NA	contig15	1	2905	+	23S_G2032G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	LINCOSAMIDE/OXAZOLIDINONE	CLINDAMYCIN/LINEZOLID	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
43 | NA	contig15	1	2905	+	23S_G2032G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE/OXAZOLIDINONE	CLARITHROMYCIN/LINEZOLID	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
44 | NA	contig15	1	2905	+	23S_G2032G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	OXAZOLIDINONE	LINEZOLID	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
45 | NA	contig15	1	2905	+	23S_G2057G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MULTIDRUG	CHLORAMPHENICOL/ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
46 | NA	contig15	1	2905	+	23S_G2447G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	OXAZOLIDINONE	LINEZOLID	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
47 | NA	contig15	1	2905	+	23S_T2609T	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	TELITHROMYCIN	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
48 | NA	contig15	1	2905	+	23S_T754T	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	99.97	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
49 | NA	contig15	2906	5810	+	23S_A2058A	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	AZITHROMYCIN/ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
50 | NA	contig15	2906	5810	+	23S_C2611C	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
51 | NA	contig15	2906	5810	+	23S_G2032G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	LINCOSAMIDE/OXAZOLIDINONE	CLINDAMYCIN/LINEZOLID	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
52 | NA	contig15	2906	5810	+	23S_G2032G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE/OXAZOLIDINONE	CLARITHROMYCIN/LINEZOLID	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
53 | NA	contig15	2906	5810	+	23S_G2032G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	OXAZOLIDINONE	LINEZOLID	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
54 | NA	contig15	2906	5810	+	23S_G2057G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MULTIDRUG	CHLORAMPHENICOL/ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
55 | NA	contig15	2906	5810	+	23S_G2447G	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	OXAZOLIDINONE	LINEZOLID	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
56 | NA	contig15	2906	5810	+	23S_T2609T	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	TELITHROMYCIN	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
57 | NA	contig15	2906	5810	+	23S_T754T	Escherichia 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	ERYTHROMYCIN/TELITHROMYCIN	POINTN	2905	2905	100.00	100.00	2905	NC_004431.1:237160-240064	23S ribosomal RNA	NA	NA
58 | NA	contig16	1	720	+	nfsA_E223E	nitroreductase NfsA [WILDTYPE]	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA
59 | NA	contig16	1	720	+	nfsA_G131G	nitroreductase NfsA [WILDTYPE]	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA
60 | NA	contig16	1	720	+	nfsA_K141STOP	Escherichia nitrofurantoin resistant NfsA	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA
61 | NA	contig16	1	720	+	nfsA_Q44Q	nitroreductase NfsA [WILDTYPE]	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA
62 | NA	contig16	1	720	+	nfsA_R133R	nitroreductase NfsA [WILDTYPE]	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA
63 | NA	contig16	1	720	+	nfsA_R15C	Escherichia nitrofurantoin resistant NfsA	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA
64 | NA	contig16	1	720	+	nfsA_R203R	nitroreductase NfsA [WILDTYPE]	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA
65 | NA	contig16	1	720	+	nfsA_S33S	nitroreductase NfsA [WILDTYPE]	core	AMR	POINT	NITROFURAN	NITROFURANTOIN	POINTX	240	240	100.00	99.17	240	WP_089631889.1	nitroreductase NfsA	NA	NA
66 | NA	contig17	1	247	+	ampC_C-11C	Escherichia ampC/blaEC promoter region [WILDTYPE]	core	AMR	POINT	BETA-LACTAM	CEPHALOSPORIN	POINTN	247	245	100.00	99.19	247	NZ_CP041538.1:1149245-1149489	ampC/blaEC promoter region	NA	NA
67 | NA	contig17	1	247	+	ampC_C-42C	Escherichia ampC/blaEC promoter region [WILDTYPE]	core	AMR	POINT	BETA-LACTAM	CEPHALOSPORIN	POINTN	247	245	100.00	99.19	247	NZ_CP041538.1:1149245-1149489	ampC/blaEC promoter region	NA	NA
68 | NA	contig17	1	247	+	ampC_G-15G	Escherichia ampC/blaEC promoter region [WILDTYPE]	core	AMR	POINT	BETA-LACTAM	CEPHALOSPORIN	POINTN	247	245	100.00	99.19	247	NZ_CP041538.1:1149245-1149489	ampC/blaEC promoter region	NA	NA
69 | NA	contig17	1	247	+	ampC_T-14T	Escherichia ampC/blaEC promoter region [WILDTYPE]	core	AMR	POINT	BETA-LACTAM	CEPHALOSPORIN	POINTN	247	245	100.00	99.19	247	NZ_CP041538.1:1149245-1149489	ampC/blaEC promoter region	NA	NA
70 | NA	contig17	1	247	+	ampC_T-14TGT	Escherichia cephalosporin resistant ampC	core	AMR	POINT	BETA-LACTAM	CEPHALOSPORIN	POINTN	247	245	100.00	99.19	247	NZ_CP041538.1:1149245-1149489	ampC/blaEC promoter region	NA	NA
71 | NA	contig17	1	247	+	ampC_T-32T	Escherichia ampC/blaEC promoter region [WILDTYPE]	core	AMR	POINT	BETA-LACTAM	CEPHALOSPORIN	POINTN	247	245	100.00	99.19	247	NZ_CP041538.1:1149245-1149489	ampC/blaEC promoter region	NA	NA
72 | 


--------------------------------------------------------------------------------
/gff.cpp:
--------------------------------------------------------------------------------
  1 | // gff.cpp
  2 | 
  3 | /*===========================================================================
  4 | *
  5 | *                            PUBLIC DOMAIN NOTICE                          
  6 | *               National Center for Biotechnology Information
  7 | *                                                                          
  8 | *  This software/database is a "United States Government Work" under the   
  9 | *  terms of the United States Copyright Act.  It was written as part of    
 10 | *  the author's official duties as a United States Government employee and 
 11 | *  thus cannot be copyrighted.  This software/database is freely available 
 12 | *  to the public for use. The National Library of Medicine and the U.S.    
 13 | *  Government have not placed any restriction on its use or reproduction.  
 14 | *                                                                          
 15 | *  Although all reasonable efforts have been taken to ensure the accuracy  
 16 | *  and reliability of the software and data, the NLM and the U.S.          
 17 | *  Government do not and cannot warrant the performance or results that    
 18 | *  may be obtained by using this software or data. The NLM and the U.S.    
 19 | *  Government disclaim all warranties, express or implied, including       
 20 | *  warranties of performance, merchantability or fitness for any particular
 21 | *  purpose.                                                                
 22 | *                                                                          
 23 | *  Please cite the author in any work or product based on this material.   
 24 | *
 25 | * ===========================================================================
 26 | *
 27 | * Author: Vyacheslav Brover
 28 | *
 29 | * File Description:
 30 | *   .gff file reader
 31 | *
 32 | */
 33 |    
 34 | 
 35 | #undef NDEBUG
 36 | 
 37 | #include "gff.hpp"
 38 | 
 39 | #include "common.inc"
 40 | 
 41 | 
 42 | 
 43 | namespace GFF_sp
 44 | {
 45 | 
 46 | 
 47 | 
 48 | // Locus
 49 | 
 50 | Locus::Locus (size_t lineNum_arg,
 51 |               const string &contig_arg,
 52 |     				  size_t start_arg,
 53 |     				  size_t stop_arg,
 54 |     				  bool strand_arg,
 55 |               bool partial_arg,
 56 |               size_t crossOriginSeqLen_arg,
 57 |               string gene_arg,
 58 |               string product_arg)
 59 | : lineNum (lineNum_arg)
 60 | , contig (contig_arg)
 61 | , start (start_arg)
 62 | , stop (stop_arg)
 63 | , strand (strand_arg)
 64 | , partial (partial_arg)
 65 | , contigLen (crossOriginSeqLen_arg)
 66 | , crossOrigin (bool (crossOriginSeqLen_arg))
 67 | , gene (gene_arg)
 68 | , product (product_arg)
 69 | { 
 70 | //QC_ASSERT (lineNum >= 1);
 71 |   trim (contig);
 72 | 	if (contig. empty ())
 73 | 		throw runtime_error ("Empty contig name");
 74 | 	if (crossOrigin)
 75 | 	{
 76 | 		swap (start, stop);
 77 | 		start--;
 78 | 		stop++;
 79 | 	  QC_ASSERT (contigLen);
 80 | 		QC_ASSERT (stop <= contigLen);
 81 | 	}
 82 |   QC_ASSERT (start < stop); 
 83 | }
 84 |   
 85 |   
 86 |     
 87 | bool Locus::operator< (const Locus& other) const
 88 | { 
 89 | 	LESS_PART (*this, other, contig)
 90 |   LESS_PART (*this, other, start)
 91 |   LESS_PART (*this, other, stop)
 92 |   LESS_PART (*this, other, strand)
 93 | //LESS_PART (*this, other, contigLen);
 94 |   LESS_PART (*this, other, crossOrigin);
 95 |   return false;
 96 | }
 97 | 
 98 | 
 99 | 
100 | 
101 | // Gff
102 | 
103 | const StringVector Gff::names {"bakta", "genbank", "microscope", "patric", "pgap", "prodigal", "prokka", "pseudomonasdb", "rast", "standard"};
104 | 
105 | 
106 | Gff::Type Gff::name2type (const string &name)
107 | {
108 |   if (name == "bakta")          return bakta;
109 |   if (name == "genbank")        return genbank;
110 |   if (name == "microscope")     return microscope;
111 |   if (name == "patric")         return patric;
112 |   if (name == "pgap")           return pgap;
113 |   if (name == "prodigal")       return prodigal;
114 |   if (name == "prokka")         return prokka;
115 |   if (name == "pseudomonasdb")  return pseudomonasdb;
116 |   if (name == "rast")           return rast;
117 |   if (name == "standard")       return standard;
118 |   throw runtime_error ("Unknown GFF type: " + strQuote (name));
119 | }
120 | 
121 | 
122 | 
123 | 
124 | // Annot
125 | 
126 | namespace
127 | {
128 |   
129 | string unescape (const string &s)
130 | {
131 |   string r (unpercent (s));
132 |   trim (r);
133 |   return r;
134 | }
135 | 
136 |   
137 |   
138 | void pgap_accession (string &accession,
139 |                      bool lcl)
140 | // Update: accession
141 | {
142 |   static const string gnlPrefix ("gnl|");
143 |   static const string lclPrefix ("lcl|");
144 |   
145 |   size_t pos = accession. rfind (':');
146 |   if (pos == string::npos)
147 |   {
148 |     if (lcl)
149 |       accession = lclPrefix + accession;
150 |   }
151 |   else 
152 |   {
153 |     if (lcl)
154 |       throw runtime_error ("Accession " + strQuote (accession) + " cannot have " + strQuote (gnlPrefix) + " and " + strQuote (lclPrefix) + " at the same time");
155 |     accession [pos] = '|';
156 |     accession = gnlPrefix + accession;
157 |   }
158 | 
159 |   QC_ASSERT (! accession. empty ());
160 | }
161 |     
162 | }
163 | 
164 | 
165 | 
166 | Annot::Annot (const string &fName,
167 |               Gff::Type gffType,
168 | 	            bool protMatch,
169 | 	            bool lcl)
170 | {
171 |   IMPLY (protMatch,    gffType == Gff::genbank 
172 |                     || gffType == Gff::microscope 
173 |                     || gffType == Gff::prodigal
174 |         );
175 |   IMPLY (gffType == Gff::microscope, protMatch);
176 | //IMPLY (trimProject, gffType == Gff::genbank);
177 |   IMPLY (lcl, gffType == Gff::pgap);
178 | 
179 | 	if (fName. empty ())
180 | 		throw runtime_error ("Empty GFF file name");
181 | 	
182 |   LineInput f (fName /*, 100 * 1024, 1*/);
183 |   while (f. nextLine ())
184 |   {
185 |     trim (f. line);
186 |     
187 |     if (   (   gffType == Gff::prokka
188 |             || gffType == Gff::bakta
189 |            )
190 |         && f. line == "##FASTA"
191 |        )
192 |       break;
193 |     
194 |     if (   f. line. empty () 
195 |         || f. line [0] == '#'
196 |        )
197 |       continue;
198 | 
199 |     try
200 |     {
201 |       /*1*/       string contig     (unescape (findSplit (f. line, '\t')));
202 |       /*2*/ const string source     (unescape (findSplit (f. line, '\t')));
203 |       /*3*/ const string type       (unescape (findSplit (f. line, '\t')));
204 |       /*4*/ const string startS     (unescape (findSplit (f. line, '\t')));
205 |       /*5*/ const string stopS      (unescape (findSplit (f. line, '\t')));
206 |       /*6*/ const string score      (unescape (findSplit (f. line, '\t')));  // real number
207 |       /*7*/ const string strand     (unescape (findSplit (f. line, '\t')));
208 |       /*8*/ const string phase      (unescape (findSplit (f. line, '\t')));  // frame
209 |       /*9*/ string attributes (f. line);  
210 |       
211 |       trim (attributes);
212 |       if (attributes. empty ())
213 |       	throw runtime_error ("9 fields are expected in each line");
214 | 
215 |     #if 0
216 |       if (trimProject)
217 |         if (contains (contig, ":"))
218 |           findSplit (contig, ':');  // = project_id
219 |     #endif
220 |       if (contig. empty ())
221 |       	throw runtime_error ("empty sequence indentifier");
222 |   	  for (const char c : contig)
223 |   	  	if (! printable (c))
224 |   	  		throw runtime_error ("Non-printable character in the sequence identifier: " + to_string (c));
225 | 
226 |       if (   type != "CDS"
227 |           && type != "gene"
228 |           && type != "pseudogene"
229 |          )
230 |         continue;
231 |         
232 |       if (gffType == Gff::pgap && type != "CDS")
233 |         continue;
234 |         
235 |       long start = -1;
236 |       if (! str2<long> (startS, start))
237 | 	    	throw runtime_error ("Cannot read start");
238 |       if (start <= 0)
239 |       	throw runtime_error ("start should be >= 1");
240 |         
241 |       long stop = -1;
242 |       if (! str2<long> (stopS, stop))
243 |  	    	throw runtime_error ("Cannot read stop");
244 |       if (stop <= 0)
245 |       	throw runtime_error ("stop should be >= 1");
246 | 
247 |       if (start > stop)
248 |       	throw runtime_error ("start cannot be greater than stop");
249 | 
250 |       start--;    	
251 |       	
252 |       if (   strand != "+" 
253 |           && strand != "-"
254 |          )
255 |       	throw runtime_error ("strand should be '+' or '-'");
256 |              
257 |       const bool pseudo =    contains (attributes, "pseudo=true")
258 |                           || contains (attributes, "gene_biotype=pseudogene")
259 |                           || type == "pseudogene";
260 |     //if (pseudo && type == "CDS")  
261 |       //continue;
262 |       
263 |       const bool partial =    contains (attributes, "partial=true")
264 |                               // Gff::prodigal
265 |                            || contains (attributes, "partial=01")
266 |                            || contains (attributes, "partial=10")
267 |                            || contains (attributes, "partial=11");
268 |       
269 |       string protAttr = "Name";
270 |       switch (gffType)
271 |       {
272 |         case Gff::bakta:         protAttr = "ID"; break;
273 |         case Gff::genbank:       protAttr = (protMatch || pseudo) ? "locus_tag" : "Name"; break;
274 |         case Gff::microscope:    protAttr = "ID"; break;
275 |         case Gff::patric:        protAttr = "ID"; break;
276 |         case Gff::prodigal:      protAttr = "ID"; break;
277 |         case Gff::prokka:        protAttr = "ID"; break;
278 |         case Gff::pseudomonasdb: protAttr = "Alias"; break;  // for type = "gene", "locus" for type = "CDS"
279 |         case Gff::rast:          protAttr = "ID"; break;
280 |         default: break;
281 |       }
282 |       ASSERT (! protAttr. empty ());
283 |       protAttr += "=";
284 |           
285 |       string prot_;
286 |       string gene_;
287 |       string product_;
288 |       {
289 |         string locusTag;
290 |         while (! attributes. empty ())
291 |         {
292 |     	    string s (findSplit (attributes, ';'));
293 |       	  trim (s);
294 |     	    if (isLeft (s, protAttr))
295 |     	    {
296 |     	      prot_ = s;
297 |             findSplit (prot_, '='); 
298 |     	    }
299 |     	    else if (isLeft (s, "gene="))
300 |     	    {
301 |     	      gene_ = s;
302 |     	      findSplit (gene_, '=');
303 |     	    }
304 |     	    else if (isLeft (s, "product="))
305 |     	    {
306 |     	      product_ = s;
307 |     	      findSplit (product_, '=');
308 |     	    //replace (product, tmpSpace, ' ');
309 |     	    }
310 |     	    else if (gffType == Gff::patric && isLeft (s, "locus_tag="))
311 |     	    {
312 |     	      locusTag = s;
313 |     	      findSplit (locusTag, '=');
314 |     	    }
315 |     	  }
316 |     	  trimPrefix (prot_, "\"");
317 |     	  trimSuffix (prot_, "\"");
318 |         if (prot_. empty ())
319 |         	continue;
320 |         //throw runtime_error ("no attribute '" + protAttr + "': " + f. line);
321 |         
322 |         switch (gffType)
323 |         {
324 |           case Gff::genbank:       if (contains (prot_, ":"))  findSplit (prot_, ':');  break;
325 |           case Gff::patric:        if (! locusTag. empty ())  prot_ += "|" + locusTag;  
326 |                                    if (isLeft (contig, "accn|"))  contig. erase (0, 5);
327 |                                    break;
328 |           default:  break;
329 |         }
330 |       }
331 |   	  QC_ASSERT (! prot_. empty ());
332 |   	
333 |   	        string prot    (unescape (prot_));
334 |   	  const string gene    (unescape (gene_));
335 |   	  const string product (unescape (product_));
336 |   	
337 |   	  if (gffType == Gff::pgap)
338 |   	  {
339 |   	    pgap_accession (prot, false);
340 |   	    pgap_accession (contig, lcl);
341 |   	  }
342 |   	  QC_ASSERT (! prot. empty ());
343 |   	  
344 |   	  Locus locus ((size_t) f. lineNum, contig, (size_t) start, (size_t) stop, strand == "+", partial, 0, gene, product);
345 |   	#if 0
346 |   	  // DNA may be truncated
347 |       if (type == "CDS" && ! pseudo && locus. size () % 3 != 0)
348 |       {
349 |         cout << "Locus tag: " << prot << endl;
350 |         locus. print (cout);
351 |         ERROR;
352 |       }
353 |     #endif
354 | 
355 |       prot2loci [prot] << std::move (locus);
356 |     }
357 |     catch (const exception &e)
358 |     {
359 |       throw runtime_error ("File " + fName + ", " + f. lineStr () + ": " + e. what ());
360 |     }
361 |   }
362 | }
363 |   
364 |   
365 | 
366 | Annot::Annot (const string &fName)
367 | {
368 | 	if (fName. empty ())
369 | 		throw runtime_error ("Empty BED file name");
370 | 	
371 |   LineInput f (fName /*, 100 * 1024, 1*/);
372 |   while (f. nextLine ())
373 |   {
374 |     trim (f. line);
375 |     if (   f. line. empty () 
376 |         || f. line [0] == '#'
377 |        )
378 |       continue;
379 | 
380 |     replace (f. line, ' ', '_');  // to use '\t' as delimiter
381 | 
382 |    	const string errorS ("File " + fName + ", " + f. lineStr () + ": ");
383 | 
384 |     string contig, prot;
385 |     size_t start, stop;
386 |     double score;
387 |     char strand = ' ';
388 |     static Istringstream iss;
389 |     iss. reset (f. line);
390 |     iss >> contig >> start >> stop >> prot >> score >> strand;
391 | 
392 |     if (strand == ' ')
393 |     	throw runtime_error (errorS + "at least 5 fields are expected in each line");
394 | 
395 | 	  for (const char c : contig)
396 | 	  	if (! printable (c))
397 | 	  		throw runtime_error (errorS + "Non-printable character in the sequence identifier: " + to_string (c));
398 | 
399 |     if (start >= stop)
400 |     	throw runtime_error (errorS + "start should be less than stop");
401 | 
402 |     if (   strand != '+'
403 |         && strand != '-'
404 |        )
405 |     	throw runtime_error (errorS + "strand should be '+' or '-'");
406 |            
407 | 	  trim (prot, '_');
408 | 	  ASSERT (! prot. empty ());
409 |     prot2loci [prot] << Locus ((size_t) f. lineNum, contig, start, stop, strand == '+', false/*partial*/, 0, noString, noString);
410 |   }
411 | }
412 |   
413 |   
414 | 
415 | void Annot::load_fasta2gff_prot (const string &fName)
416 | {
417 |   ASSERT (fasta2gff_prot. empty ());
418 | 
419 |   LineInput f (fName);
420 | 	Istringstream iss;
421 | 	string fasta_prot, gff_prot;
422 |   while (f. nextLine ())
423 |   {
424 |   	iss. reset (f. line);
425 |   	fasta_prot. clear ();
426 |   	gff_prot. clear ();
427 |   	iss >> fasta_prot >> gff_prot;
428 |   	QC_ASSERT (! gff_prot. empty ());
429 |   	fasta2gff_prot [fasta_prot] = gff_prot;
430 |   }
431 |   if (fasta2gff_prot. empty ())
432 |   	throw runtime_error ("File " + fName + " is empty");
433 | }
434 | 
435 | 
436 | 
437 | void Annot::load_fasta2gff_dna (const string &fName)
438 | {
439 |   map<string/*DNA GFF id*/,string/*DNA FASTA id*/> gff2fasta;  
440 |   {
441 |     LineInput f (fName);
442 |   	Istringstream iss;
443 |   	string fasta_dna, gff_dna;
444 |     while (f. nextLine ())
445 |     {
446 |     	iss. reset (f. line);
447 |     	fasta_dna. clear ();
448 |     	gff_dna. clear ();
449 |     	iss >> fasta_dna >> gff_dna;
450 |     	QC_ASSERT (! gff_dna. empty ());
451 |     	gff2fasta [gff_dna] = fasta_dna;
452 |     }
453 |   }
454 |   if (gff2fasta. empty ())
455 |   	throw runtime_error ("File " + fName + " is empty");
456 |   
457 |   for (auto& it : prot2loci)
458 |   {
459 |     Set<Locus>& loci = it. second;
460 |     for (const Locus& locus : loci)
461 |     {
462 |     	string s;
463 |     	if (! find (gff2fasta, locus. contig, s))
464 |     	  throw runtime_error ("FASTA DNA contig " + strQuote (locus. contig) + " is not found in GFF-DNA match file " + strQuote (fName));
465 |     	var_cast (locus). contig = std::move (s);
466 |     }
467 |   }
468 | }
469 | 
470 | 
471 | 
472 | const Set<Locus>& Annot::findLoci (const string &fasta_prot) const
473 | {
474 |   ASSERT (! fasta_prot. empty ());
475 | 
476 |   string gff_prot (fasta_prot);
477 |   if (! fasta2gff_prot. empty ())
478 |   {
479 |   	string s;
480 |   	if (! find (fasta2gff_prot, gff_prot, s))
481 |   	  throw runtime_error ("FASTA protein " + strQuote (fasta_prot) + " is not found in GFF-protein match file");
482 |   	gff_prot = std::move (s);
483 |   }
484 |   ASSERT (! gff_prot. empty ());
485 |   
486 |   const Set<Locus>* loci = findPtr (prot2loci, gff_prot);
487 |   if (! loci)
488 |     throw runtime_error ("FASTA protein " + fasta_prot + (fasta_prot == gff_prot ? "" : " (converted to GFF protein " + gff_prot +")") + " is misssing in .gff-file");
489 |   ASSERT (! loci->empty ());
490 | 
491 |   return *loci;
492 | }
493 | 
494 | 
495 | 
496 | }
497 | 


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