├── LICENSE ├── PlaScope_supernova.png ├── README.md └── plaScope.sh /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. By contrast, 15 | the GNU General Public License is intended to guarantee your freedom to 16 | share and change all versions of a program--to make sure it remains free 17 | software for all its users. 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Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . -------------------------------------------------------------------------------- /PlaScope_supernova.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/labgem/PlaScope/ccf7a75fe0fc7418e4f1363e34b80a43267d34e4/PlaScope_supernova.png -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 |

2 | 3 | # PlaScope 4 | 5 | 6 | A targeted approach to assess the plasmidome of bacteria. 7 | 8 | If you use this tool, please cite : G. Royer, J.-W. Decousser, C. Branger, M. Dubois, C. Médigue, E. Denamur, D. Vallenet. PlaScope: a 9 | targeted approach to assess the plasmidome from genome assemblies at species level. Microbial 10 | Genomics, 2018 Sep;4(9). 11 | 12 | And don't forget the publications related to its dependencies : 13 | - Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 14 | - Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 15 | 2016;26:1721–1729 16 | 17 | 18 | ## Tell me more about PlaScope 19 | 20 | 21 | This method enables you to classify contigs from a WGS assembly according to their location (i.e. plasmid or chromosome). 22 | It is based on a smart tool called [Centrifuge](https://www.ccb.jhu.edu/software/centrifuge/), initially developed as a metagenomic classifier. 23 | We propose here an application on *E. coli* plasmidome, with a specific database build on one hand on completely finished genomes of *E. coli* from the NCBI, and on the other hand on a custom plasmid database. 24 | In fact 3 databases of plasmid have been merged together : 25 | 26 | * plasmids used to create `PlasmidFinder` (http://aac.asm.org/content/58/7/3895.long) 27 | * plasmids proposed by Orlek *et al.* (https://www.sciencedirect.com/science/article/pii/S2352340917301567?via%3Dihub) 28 | * plasmids from Branger *et al.*, Extended-spectrum ß-lactamase-genes are spreading on a wide range of Escherichia coli plasmids existing prior the use of third generation cephalosporins, Microbial Genomics, 2018, In press 29 | 30 | We also propose a Klebsiella database that has been evaluated on a clinical dataset of 12 *Klebsiella pneumoniae* strains. 31 | 32 | We think that this method can easily be applied to other bacterial species since you have got enough reference data (e.g. *Staphylococcus aureus*, *Enterococcus sp.* ...). 33 | 34 | ## Installation 35 | 36 | ### Dependencies 37 | 38 | You must install these dependencies before you start : 39 | 40 | * [SPAdes](http://bioinf.spbau.ru/spades) 3.10.1 or later if you want to run the assembly (= mode 1) (header of contigs must be the same as in version 3.10.1, *e.g* >NODE_1_length_506801_cov_117.065) 41 | * [Centrifuge](https://www.ccb.jhu.edu/software/centrifuge/) 1.0.3 42 | 43 | ### Installation 44 | 45 | `PlaScope` is essentially a wrapper script (called `plaScope.sh`) around SPAdes and Centrifuge. 46 | It's written in `bash` and `awk` and should work on Linux and Mac OS X both with GNU awk and BSD awk. 47 | 48 | To install it, simply download the sources and decompress them. 49 | Don't forget to add the location of `plaScope.sh` to your `PATH`. 50 | 51 | ### Installation with BioConda 52 | 53 | The easiest way to install `PlaScope` and its dependencies is through [BioConda](https://bioconda.github.io/). 54 | Once you have created and activated a `conda` environment, simply type: 55 | 56 | ```bash 57 | $ conda install plascope 58 | ``` 59 | 60 | Note that several versions of `awk` are available in `conda` so you can further control the environment. 61 | 62 | ### Usage with the IFB Cloud 63 | 64 | Another way to use `PlaScope` is through the [IFB Cloud](https://biosphere.france-bioinformatique.fr/). 65 | Just create an account and launch the [PlaScope](https://biosphere.france-bioinformatique.fr/catalogue/appliance/155/) appliance. 66 | 67 | ## Usage 68 | 69 | You can choose between two modes: 70 | * Mode 1: SPAdes assembly then contig classification 71 | * Mode 2: contig classification only (if you already assembled your genome with SPAdes or Unicycler) 72 | 73 | ```bash 74 | $ ./plaScope.sh -h 75 | usage: plaScope.sh [OPTIONS] [ARGUMENTS] 76 | 77 | General options: 78 | -h, --help display this message and exit 79 | -v, --version display version number and exit 80 | -n, --no-banner don't print beautiful banners 81 | -t number of threads[OPTIONAL] [default : 8] 82 | -o output directory [OPTIONAL] [default : current directory] 83 | --sample Sample name [MANDATORY] 84 | --db_dir path to centrifuge database [MANDATORY] 85 | --db_name centrifuge database name [MANDATORY] 86 | 87 | Mode 1: SPAdes assembly + contig classification 88 | -1 forward paired-end reads [MANDATORY] 89 | -2 reverse paired-end reads [MANDATORY] 90 | 91 | 92 | Mode 2: contig classification of a fasta file (only if you already have your SPAdes or Unicycler assembly!) 93 | --fasta SPAdes assembly fasta file [MANDATORY] 94 | -a Specify the assembler used: spades or unicycler. Default=spades. 95 | 96 | 97 | Example mode 1: 98 | plaScope.sh -1 my_reads_1.fastq.gz -2 my_reads_2.fastq.gz -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample 99 | 100 | Example mode 2: 101 | plaScope.sh --fasta my_fastafile.fasta -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample -a unicycler 102 | 103 | 104 | 105 | Github: 106 | https://github.com/GuilhemRoyer/PlaScope 107 | ```` 108 | 109 | `PlaScope` uses a database (see [this section](#DB)) made of 3 files. 110 | The argument `--db_dir` is the path to the directory where these 3 files are located. 111 | The argument `--db_name` is the common part between the file names (see examples). 112 | 113 | 114 | ## Databases 115 | 116 | ### *E. coli* database 117 | 118 | To get the *E. coli* database, please download the following file on Zenodo: https://doi.org/10.5281/zenodo.1311641 119 | 120 | After extracting the tar.gz file, you will have 3 files : `chromosome_plasmid_db.1.cf`, `chromosome_plasmid_db.2.cf` and `chromosome_plasmid_db.3.cf`. 121 | All these files are required for `PlaScope`. 122 | In this case, the `--db_name` to use is "chromosome_plasmid_db". 123 | 124 | 125 | ### Klebsiella database 126 | 127 | To get the Klebsiella database, please download the following file on Zenodo: https://doi.org/10.5281/zenodo.1311647 128 | 129 | After extracting the tar.gz file, you will have 3 files : `Klebsiella_PlaScope.1.cf`, `Klebsiella_PlaScope.2.cf` and `Klebsiella_PlaScope.3.cf`. 130 | All these files are required for `PlaScope`. 131 | In this case, the `--db_name` to use is "Klebsiella_PlaScope". 132 | 133 | This database has not been extensively benchmarked. 134 | We only have assessed its performances by searching for plasmids and resistance genes location on a set of 12 *Klebsiella pneumoniae* strains from https://academic.oup.com/jac/article/73/7/1796/4966148. 135 | 136 | ### Create your own database 137 | 138 | You can also design your own database as explained on [this page](https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database). 139 | 140 | You need to prepare four files: 141 | 142 | * database.fna : a multifasta file of your database 143 | ``` 144 | >Chromosome_1 145 | ATGGATAAGTTGCTGAACAAAAAGAT...... 146 | >Chromosome_2 147 | GAGTGAACGGATGAAACAGAAAGACC...... 148 | >Plasmid_1 149 | TCTCGAATGATAAAGGCTATGATGGC...... 150 | ``` 151 | 152 | * nodes.dmp : an artificial taxonomy (*i.e.* root, chromosome, plasmid) 153 | ``` 154 | 1 | 1 | root 155 | 2 | 1 | chromosome 156 | 3 | 1 | plasmid 157 | ``` 158 | 159 | * seqid_to_taxid.map : a mapping file between the sequences and their taxonomic assignment 160 | ``` 161 | Chromosome_1 2 162 | Chromosome_2 2 163 | Plasmid_1 3 164 | ``` 165 | 166 | * names.dmp : a file mapping taxonomy IDs to a name 167 | ``` 168 | 1 | root | | | 169 | 2 | chromosome | | | 170 | 3 | plasmide | | | 171 | ``` 172 | Then, build your database as follow: 173 | 174 | ``` 175 | centrifuge-build -p 10 --conversion-table seqid_to_taxid.map --taxonomy-tree nodes.dmp --name-table names.dmp database.fna chromosome_plasmid_db 176 | ``` 177 | 178 | # Contributors 179 | 180 | - Guilhem Royer (CEA-Genoscope, now at Pasteur): design, implementation, evaluation 181 | - David Valllenet (CEA-Genoscope): design 182 | - Julian Paganini (UMC Utrecht): new feature: accept unicycler assemblies 183 | -------------------------------------------------------------------------------- /plaScope.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | 4 | # Copyright 2018, Guilhem Royer 5 | # 6 | # This file is part of PlaScope. 7 | # 8 | # PlaScope is free software: you can redistribute it and/or modify 9 | # it under the terms of the GNU General Public License as published by 10 | # the Free Software Foundation, either version 3 of the License, or 11 | # (at your option) any later version. 12 | # 13 | # PlaScope is distributed in the hope that it will be useful, 14 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 15 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 16 | # GNU General Public License for more details. 17 | # 18 | # You should have received a copy of the GNU General Public License 19 | # along with PlaScope. If not, see . 20 | 21 | ############################################################## 22 | # Author Guilhem ROYER groyer@genoscope.cns.fr | 06/04/2018 # 23 | ############################################################## 24 | 25 | VERSION=1.3.1 26 | 27 | set -e 28 | set -u 29 | set -o pipefail 30 | 31 | 32 | ############# 33 | # Help # 34 | ############# 35 | 36 | version() 37 | { 38 | cat << EOF 39 | $VERSION 40 | EOF 41 | } 42 | 43 | usage() 44 | { 45 | cat << EOF 46 | usage: plaScope.sh [OPTIONS] [ARGUMENTS] 47 | 48 | General options: 49 | -h, --help display this message and exit 50 | -v, --version display version number and exit 51 | -n, --no-banner don't print beautiful banners 52 | -t number of threads[OPTIONAL] [default : 8] 53 | -o output directory [OPTIONAL] [default : current directory] 54 | --sample Sample name [MANDATORY] 55 | --db_dir path to centrifuge database [MANDATORY] 56 | --db_name centrifuge database name [MANDATORY] 57 | 58 | Mode 1: SPAdes assembly + contig classification 59 | -1 forward paired-end reads [MANDATORY] 60 | -2 reverse paired-end reads [MANDATORY] 61 | 62 | 63 | Mode 2: contig classification of a fasta file (only if you already have your SPAdes or Unicycler assembly!) 64 | --fasta SPAdes or Unicycler assembly fasta file [MANDATORY] 65 | -a Specify the assembler used: spades or unicycler. Default=spades. 66 | 67 | 68 | Example mode 1: 69 | plaScope.sh -1 my_reads_1.fastq.gz -2 my_reads_2.fastq.gz -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample 70 | 71 | Example mode 2: 72 | plaScope.sh --fasta my_fastafile.fasta -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample -a unicycler 73 | 74 | 75 | 76 | Github: 77 | https://github.com/GuilhemRoyer/PlaScope 78 | 79 | EOF 80 | } 81 | 82 | 83 | ################################ 84 | # Just a little bit of art # 85 | ################################ 86 | 87 | 88 | plascope() 89 | { 90 | 91 | if [[ ${NO_BANNER} -eq 1 ]] 92 | then 93 | return 94 | fi 95 | 96 | cat << "EOF" 97 | 98 | # MNXXXXXXXXXXXXNWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWXXXXXXXXXXXXXXXXNMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 99 | No'''''''''''''cOWMMWKOOOXWMMMMMMMMMMMMMMWKO0OO0000O0XMMMMNk;''''''''''''',:dXMWX00000000OO0O0NMMMN0O000000OOKNMMWX0000000000OKWMMMN0O000000000000O0NM 100 | N: .:0W0, cNMMMMMMMMMMMMWO:. 'dXM0; ,xKNWKl. .,xNMNx,. .;kNNc .:0WMO' .'dXM 101 | N: .:lllll; ,00' :NMMMMMMMMMMMWd. ;0d ,llllllllokNMMMO' 'dXMMX: oX: .lXk. .lKWMM 102 | N: ,KMWWKl. .c0W0' :NMMMMMMMMMMMN: .okkkkkk; .kd .xMMMMMMMMMMMMMMd. :kkkkkkOXMMMM0' ,xkkkkkd. ;K: .okd; ,kNk. ;kkkkkkkKWMMMM 103 | N: ,KWKl. .c0WMM0' :NMMMMMMMMMMMN: 'OOxxxxx; .kd cOkkkkkkOkOXMMMd. .xMMMMMMMMMMMM0' cWMMMMMX; ;K: ,Ox, ,xNMMk. ;xxxxxxONMMMMM 104 | N: 'ko. .c0WMMMM0' :NMMMMMMMMMMMN: .:. .kO. 'dOXd .xMMMMMMMMMMMM0' cWMMMMMX; ;K: .:. ,xNMMMMk. .OMMMMM 105 | N: .:. .:OWMMMMMM0' :NMMMMMMMMMMMN: 'kOxxxxx; .kWKl. :l. .xMMMMMMMMMMMM0' cWMMMMMX; ;K: ,kd,,xNMMMMMMk. ,xxxxxxONMMMMM 106 | N: ,0O:cOWMMMMMMMM0' ,k0O0000OO0OKN: '0MMMMMMo .kMMWXOOOOOOOOOk, ':. c0OO000000O0X0' ,k0O0OOx' ;K: ,KWNNMMMMMMMMk. :O000000O00OXM 107 | N: ,KMWWMMMMMMMMMM0' :Kc '0MMMMMMo .kMMMMMMMMMMMMMNc 'o' .dK; lK: ,KMMMMMMMMMMMk. cN 108 | N: ,KMMMMMMMMMMMMM0, ;Kc ,0MMMMMWo .k0lcccccccccccc. 'O0c. oWXo. ,xNN: ,KMMMMMMMMMMMk. cN 109 | N: ,KMMMMMMMMMMMMMN0kkkkkkkkkkkkkkk0WKkkk0WMMMMMMXOkkONd .;dNMWKkkkkkkkkkkkkkXMMMXOkkkkkkkkkONMMWKkkk0WMMMMMMMMMMMNOkkkkkkkkkkkkkkkKW 110 | No',,lXMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMO;,,,',,,,,,,,,,lKWWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 111 | MWNWNWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWWWWWWWWWWWWWWWWWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 112 | 113 | EOF 114 | } 115 | 116 | mode_1() 117 | { 118 | 119 | if [[ ${NO_BANNER} -eq 1 ]] 120 | then 121 | echo "Mode 1" 122 | return 123 | fi 124 | 125 | cat << "EOF" 126 | 127 | MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 128 | MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 129 | MMMMMWKkkkONMMMMMN0kkk0WMMMMMMMMMMMMMMMMMMMMMMMMMMMW0kkkKWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWKkkk0NMMMMMMMMM 130 | MMMMMWl .oOXWXOd. ;KMMMMMMMMMMMMMMMMMMMMMMMMMMMX; cNMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWXk; ,0MMMMMMMMM 131 | MMMMMWl .oKo. ;KMMMMWXXXXXXNWMMMMMMMMMMMMMMK; :NMMMMMMMMNXXXXXXNMMMMMMMMMMMMMMMMMMMMMMMMMMMMXl.. '0MMMMMMMMM 132 | MMMMMWl ... ;KMMMWO;.....:KMMMMMMMMMMWWWW0; :XMMMMMMMNo.....'xWMMMMMMMMMMMMMMMMMMMMMMMMMMMWXO; '0MMMMMMMMM 133 | MMMMMWl ;KMM0l' ;xc..,ckWMMMMMMWk;,,' :NMMMMMNx;. .lxxxl:oXMMMMMMMMMMMMMMMMMMMMMMMMMMMNl '0MMMMMMMMM 134 | MMMMMWl .:l. .lc. ;KMMx. oWk. lNMMMMNko, 'll. :NMMMMMX: .,cc:. '0MMMMMMMMMMMMMMMMMMMMMMMMMMMNc '0MMMMMMMMM 135 | MMMMMWl .ONxcxWK, ;KMMx. oWk. lNMMMM0, cNK; :NMMMMMX: .;cccccdXMMMMMMMMMMMMMMMMMMMMMMMMMMMNc ,0MMMMMMMMM 136 | MMMMMWl .OMMMMM0, ;KMM0:. :kl. .;xWMMMMK:.. ,xx;. ,xKWMMMNd'. .okkOXWMMMMMMMMMMMMMMMMMMMMMMMMMN0OOx, .oOOOKWMMMM 137 | MMMMMWd...;0MMMMMKc...cXMMWNO;.....:0WWMMMMMWNKo...;xOc..'lXMMMMWXl...'.,xWMMMMMMMMMMMMMMMMMMMMMMMMWO;''.......'.'dNMMMM 138 | MMMMMMNXXXXWMMMMMWNXXXNWMMMMWXXXXXXNWMMMMMMMMMMNXXXXWWNXXXNWMMMMMMNXKXXXXNMMMMMMMMMMMMMMMMMMMMMMMMMMWXXXXXXXXXXXXXNMMMMM 139 | MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 140 | MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 141 | 142 | EOF 143 | } 144 | 145 | 146 | mode_2() 147 | { 148 | 149 | if [[ ${NO_BANNER} -eq 1 ]] 150 | then 151 | echo "Mode 2" 152 | return 153 | fi 154 | 155 | cat << "EOF" 156 | 157 | 158 | MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 159 | MMMMWNNNNWMMMMMWNNNNWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWNNNWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWNNNNNNNNNNWMMMMMMMMM 160 | MMMWx'..:OWWMWN0c..'oNMMMMMMMMMMMMMMMMMMMMMMMMMMMXl..'oNMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWWXo''''''''''dXWWMMMMMM 161 | MMMWl .;kWk,. :NMMMMMMMMMMMMMMMMMMMMMMMMMMMK, ;XMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM0:'. ;xxxxxd, .'cKMMMMMM 162 | MMMWl ':' :XMMMMKocccccdXMMMMMMMMMMMMMMK, ;XMMMMMMMWOccccclOWMMMMMMMMMMMMMMMMMMMMMMMXkddxKMMMNx:. .OMMMMMM 163 | MMMWl :XMMXk:. .c, .cxKMMMMMMMM0ooo:. ;XMMMMMW0d' .;cccodkNMMMMMMMMMMMMMMMMMMMMMMMMMW0xddl. 'lxXMMMMMM 164 | MMMWl ',. .,,. :XMMk. oWk. oWMMMMWX0: .,,. ;XMMMMMNc .lxxd, '0MMMMMMMMMMMMMMMMMMMMMMMWKx, .,xWMMMMMMMM 165 | MMMWl .OXl.oN0, :XMMk. oWk. oWMMMMK;. :XK, ;XMMMMMN: .''''.cKMMMMMMMMMMMMMMMMMMMMMNKk; ...'dNWMMMMMMMMM 166 | MMMWl .OMNXNMK, :XMMO' lXx. .dWMMMMK, ;0O, ,0NMMMMNl. .d000KNNWMMMMMMMMMMMMMMMMMMMMMO' .d000KXXXNWMMMMMM 167 | MMMWl 'OMMMMMK, :NMMNKo. ... .dKNMMMMMW0k: ..,od' ..lXMMMWXO; .'',xWMMMMMMMMMMMMMMMMMMMMMMMk. .''''''..cKMMMMM 168 | MMMMKkkkONMMMMMW0kkkKWMMMMNOkkkkk0NMMMMMMMMMMXkkkOXW0kkk0WMMMMMWKkkkkkkKMMMMMMMMMMMMMMMMMMMMMMMMNOkkkkkkkkkkkkkkONMMMMMM 169 | MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 170 | MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM 171 | 172 | EOF 173 | } 174 | 175 | #print on stderr 176 | echoerr() { printf "Error: %s\n" "$*" >&2; } 177 | 178 | #testfile 179 | testfile() 180 | { 181 | if [[ ! -f "$1" ]] 182 | then 183 | echoerr "File $1 not found." 184 | exit 1 185 | fi 186 | 187 | if [[ ! -s "$1" ]] 188 | then 189 | echoerr "File $1 empty." 190 | exit 1 191 | fi 192 | 193 | } 194 | 195 | ######################## 196 | ### Contig sorting ## 197 | ######################## 198 | 199 | 200 | contig_sorting_unicycler() 201 | { 202 | 203 | local plascopeextendres="$1" 204 | 205 | local contigcov=${CONTIGCOV} 206 | local contiglength=${CONTIGLENGTH} 207 | local hitlength=${HITLENGTH} 208 | 209 | awk -F'\t' -v contigcov=${contigcov} -v contiglength=${contiglength} -v hitlength=${hitlength} ' 210 | BEGIN { 211 | TPLASCOPERES[0]="unclassified" 212 | TPLASCOPERES[1]="unclassified" 213 | TPLASCOPERES[2]="chromosome" 214 | TPLASCOPERES[3]="plasmid" 215 | OFS="\t" 216 | 217 | #skip first line 218 | getline 219 | } 220 | 221 | {clab=$1; split(clab,T,":") ; ccov=T[5]; 222 | 223 | if ( $7>=contiglength && $6>=hitlength && ccov>contigcov ) print $1,TPLASCOPERES[$3] 224 | 225 | else print $1,TPLASCOPERES[0] 226 | 227 | }' $plascopeextendres 228 | 229 | } 230 | 231 | contig_sorting_spades() 232 | { 233 | 234 | local plascopeextendres="$1" 235 | 236 | local contigcov=${CONTIGCOV} 237 | local contiglength=${CONTIGLENGTH} 238 | local hitlength=${HITLENGTH} 239 | 240 | awk -F'\t' -v contigcov=${contigcov} -v contiglength=${contiglength} -v hitlength=${hitlength} ' 241 | BEGIN { 242 | TPLASCOPERES[0]="unclassified" 243 | TPLASCOPERES[1]="unclassified" 244 | TPLASCOPERES[2]="chromosome" 245 | TPLASCOPERES[3]="plasmid" 246 | OFS="\t" 247 | 248 | #skip first line 249 | getline 250 | } 251 | 252 | {clab=$1; split(clab,T,"_") ; ccov=T[6]; 253 | 254 | if ( $7>=contiglength && $6>=hitlength && ccov>contigcov ) print $1,TPLASCOPERES[$3] 255 | 256 | else print $1,TPLASCOPERES[0] 257 | 258 | }' $plascopeextendres 259 | 260 | } 261 | 262 | 263 | ######################################### 264 | ###### Awk fasta extraction ####### 265 | ######################################### 266 | 267 | contig_extraction() 268 | { 269 | 270 | local contigfile="$1" 271 | local contigsortingfile="$2" 272 | local contigfileprefix="$3" 273 | 274 | awk -F'\t' -v contigfileprefix=${contigfileprefix} ' 275 | NR==FNR{Tcontig[">"$1]=$2;next} 276 | 277 | /^>/ { 278 | if ($1 in Tcontig) output=contigfileprefix"_"Tcontig[$1]".fasta" 279 | else 280 | { 281 | print "Warning:", $1, "not classified." > "/dev/stderr" 282 | output="" 283 | } 284 | 285 | } 286 | 287 | output { print > output }' $contigsortingfile $contigfile 288 | 289 | } 290 | 291 | 292 | #################################### 293 | #### Get argument with getopts ##### 294 | #################################### 295 | 296 | #Establish default value for assembler 297 | assembler='spades' 298 | 299 | while getopts ":1:2:o:t:-:h:v:n:a:" optchar; do 300 | case "${optchar}" in 301 | -) 302 | case "${OPTARG}" in 303 | help) 304 | usage 305 | exit 306 | ;; 307 | version) 308 | version 309 | exit;; 310 | no-banner) 311 | NO_BANNER=1 312 | ;; 313 | db_dir) 314 | CENTRI_DIR="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 )) 315 | ;; 316 | db_name) 317 | DB_NAME="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 )) 318 | ;; 319 | fasta) 320 | FASTA="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 )) 321 | ;; 322 | sample) 323 | PREFIX="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 )) 324 | ;; 325 | esac;; 326 | h) 327 | usage 328 | exit 329 | ;; 330 | v) 331 | version 332 | exit 333 | ;; 334 | n) 335 | NO_BANNER=1 336 | ;; 337 | 1) 338 | READ1=${OPTARG} 339 | ;; 340 | 2) 341 | READ2=${OPTARG} 342 | ;; 343 | t) 344 | THREADS=${OPTARG} 345 | ;; 346 | o) 347 | O_DIR=${OPTARG} 348 | ;; 349 | a) 350 | assembler=${OPTARG} 351 | ;; 352 | ?) 353 | usage 354 | exit 1 355 | ;; 356 | esac 357 | done 358 | 359 | 360 | #MODE 1 or 2 361 | MODE="" 362 | 363 | #Check that mandatory options are not empty 364 | 365 | if [[ -z "${CENTRI_DIR:-}" ]] || [[ -z "${DB_NAME:-}" ]] || [[ -z "${PREFIX:-}" ]] 366 | then 367 | usage 368 | exit 1 369 | fi 370 | 371 | 372 | if [[ ( -z "${FASTA:-}" ) && ( ( -z "${READ1:-}" ) || ( -z "${READ2:-}" ) ) ]] 373 | then 374 | usage 375 | exit 1 376 | fi 377 | 378 | 379 | #Check that "mode 1" and "mode 2" are not used at the same time 380 | 381 | if [[ "${FASTA:-}" && ( "${READ1:-}" || "${READ2:-}" ) ]] 382 | then 383 | echoerr "Mode 1 and mode 2 can't be run at the same time. Please provide fastq files (mode 1) OR a fasta file (mode 2)" 384 | usage 385 | exit 1 386 | fi 387 | 388 | if [[ "${FASTA:-}" ]] 389 | then 390 | MODE=2 391 | 392 | testfile "${FASTA}" 393 | 394 | elif [[ "${READ1:-}" && "${READ2:-}" ]] 395 | then 396 | MODE=1 397 | 398 | testfile "${READ1}" 399 | testfile "${READ2}" 400 | else 401 | usage 402 | exit 1 403 | fi 404 | 405 | # default value: use banner 406 | NO_BANNER=${NO_BANNER-0} 407 | 408 | # Set default values of optional parameters 409 | if [[ -z "${THREADS:-}" ]] 410 | then 411 | # default value: 8 412 | THREADS=8 413 | fi 414 | 415 | if [[ -z "${O_DIR:-}" ]] 416 | then 417 | # default value: current directory 418 | O_DIR="." 419 | fi 420 | 421 | #Remove trailing slash of paths if exist 422 | DB_DIR=${CENTRI_DIR%/} 423 | OUTPUT=${O_DIR%/} 424 | 425 | #Check if directories already exist 426 | 427 | 428 | if [[ -d "${OUTPUT}/${PREFIX}_PlaScope/PlaScope_predictions" ]] 429 | then 430 | echoerr "${OUTPUT}/${PREFIX}_PlaScope/PlaScope_predictions already exists" 431 | exit 1 432 | else 433 | mkdir -p ${OUTPUT}/${PREFIX}_PlaScope/PlaScope_predictions 434 | fi 435 | 436 | if [[ -d "${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results" ]] 437 | then 438 | echoerr "${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results already exists" 439 | exit 1 440 | else 441 | mkdir -p ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results 442 | fi 443 | 444 | 445 | ################################################################ 446 | ######################## Run functions ######################## 447 | ################################################################ 448 | 449 | 450 | #plascope variables for contig evaluation 451 | 452 | if [[ $assembler = 'unicycler' ]] 453 | then 454 | readonly CONTIGCOV=0 455 | 456 | elif [[ $assembler = 'spades' ]] 457 | then 458 | readonly CONTIGCOV=2 459 | 460 | else echo "provide valid assembler name: spades or unicycler" && exit 0 461 | fi 462 | 463 | readonly CONTIGLENGTH=500 464 | readonly HITLENGTH=100 465 | 466 | step=1 467 | 468 | plascope 469 | 470 | 471 | if [[ "${MODE}" == 1 ]] 472 | then 473 | mode_1 474 | echo "Step $step: Running assembly with SPAdes" 475 | 476 | # SPAdes automatically stores its log in ${OUTPUT}/${PREFIX}_PlaScope/SPAdes/spades.log so we redirect output to /dev/nulll 477 | echo SPAdes log can be found here: ${OUTPUT}/${PREFIX}_PlaScope/SPAdes/spades.log 478 | spades.py --careful -t ${THREADS} -1 ${READ1} -2 ${READ2} -o ${OUTPUT}/${PREFIX}_PlaScope/SPAdes &> /dev/null 479 | 480 | FASTA="${OUTPUT}/${PREFIX}_PlaScope/SPAdes/contigs.fasta" 481 | (( step++ )) 482 | else 483 | mode_2 484 | 485 | fi 486 | 487 | echo "Step $step: Contigs classification with Centrifuge and custom database" 488 | 489 | export CENTRIFUGE_INDEXES=${DB_DIR} 490 | 491 | # We don't need centrifuge output but we still redirect stdout and stderr to a file 492 | CENTRIFUGE_LOG=${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/centrifuge.log 493 | echo Centrifuge log can be found here: ${CENTRIFUGE_LOG} 494 | centrifuge -f --threads ${THREADS} -x ${DB_NAME} -U ${FASTA} -k 1 --report-file ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_summary -S ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_extendedresult &> ${CENTRIFUGE_LOG} 495 | 496 | (( step++ )) 497 | 498 | echo "Step $step: Extraction of plasmid, chromosome and unclassified predictions" 499 | 500 | if [[ "$assembler" = 'unicycler' ]]; then 501 | contig_sorting_unicycler ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_extendedresult > ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_list 502 | 503 | elif [[ "$assembler" = 'spades' ]]; then 504 | contig_sorting_spades ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_extendedresult > ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_list 505 | 506 | else 507 | echo "Please provide a valid assembler: spades or unicycler" && exit 0 508 | fi 509 | 510 | contig_extraction ${FASTA} ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_list ${OUTPUT}/${PREFIX}_PlaScope/PlaScope_predictions/${PREFIX} 511 | 512 | echo "If you use PlaScope please cite: ..." 513 | 514 | exit 0 515 | 516 | --------------------------------------------------------------------------------