├── .gitignore ├── .travis.yml ├── AUTHORS ├── Build.PL ├── Changes ├── DEPENDENCIES ├── INSTALL ├── INSTALL.PROGRAMS ├── INSTALL.SKIP ├── LICENSE ├── README.md ├── lib └── Bio │ ├── DB │ ├── ESoap.pm │ ├── ESoap │ │ └── WSDL.pm │ ├── SoapEUtilities.pm │ └── SoapEUtilities │ │ ├── DocSumAdaptor.pm │ │ ├── FetchAdaptor.pm │ │ ├── FetchAdaptor │ │ ├── seq.pm │ │ └── species.pm │ │ ├── GQueryAdaptor.pm │ │ ├── LinkAdaptor.pm │ │ └── Result.pm │ ├── Factory │ └── EMBOSS.pm │ └── Tools │ └── Run │ ├── Alignment │ ├── Amap.pm │ ├── Blat.pm │ ├── DBA.pm │ ├── Exonerate.pm │ ├── Gmap.pm │ ├── Kalign.pm │ ├── Lagan.pm │ ├── MAFFT.pm │ ├── MSAProbs.pm │ ├── Muscle.pm │ ├── Pal2Nal.pm │ ├── Probalign.pm │ ├── Probcons.pm │ ├── Proda.pm │ ├── Sim4.pm │ └── StandAloneFasta.pm │ ├── Analysis │ └── soap.pm │ ├── AnalysisFactory │ └── soap.pm │ ├── BEDTools.pm │ ├── BEDTools │ └── Config.pm │ ├── BlastPlus.pm │ ├── BlastPlus │ └── Config.pm │ ├── Coil.pm │ ├── EMBOSSApplication.pm │ ├── EMBOSSacd.pm │ ├── ERPIN.pm │ ├── Ensembl.pm │ ├── Eponine.pm │ ├── FootPrinter.pm │ ├── Genemark.pm │ ├── Genewise.pm │ ├── Genscan.pm │ ├── Glimmer.pm │ ├── Hmmer.pm │ ├── Infernal.pm │ ├── MCS.pm │ ├── Match.pm │ ├── Mdust.pm │ ├── Phylo │ ├── FastTree.pm │ ├── Gerp.pm │ ├── Hyphy │ │ ├── Base.pm │ │ ├── BatchFile.pm │ │ ├── FEL.pm │ │ ├── Modeltest.pm │ │ ├── REL.pm │ │ └── SLAC.pm │ ├── LVB.pm │ ├── Molphy │ │ └── ProtML.pm │ ├── Njtree │ │ └── Best.pm │ ├── Phast │ │ ├── PhastCons.pm │ │ └── PhyloFit.pm │ ├── Phylip │ │ ├── Base.pm │ │ ├── Consense.pm │ │ ├── DrawGram.pm │ │ ├── DrawTree.pm │ │ ├── Neighbor.pm │ │ ├── PhylipConf.pm │ │ ├── ProtDist.pm │ │ ├── ProtPars.pm │ │ └── SeqBoot.pm │ ├── Phyml.pm │ ├── QuickTree.pm │ ├── Raxml.pm │ ├── SLR.pm │ └── Semphy.pm │ ├── Primate.pm │ ├── Primer3.pm │ ├── Prints.pm │ ├── Profile.pm │ ├── Promoterwise.pm │ ├── Pseudowise.pm │ ├── RNAMotif.pm │ ├── RepeatMasker.pm │ ├── Samtools.pm │ ├── Samtools │ └── Config.pm │ ├── Seg.pm │ ├── Signalp.pm │ ├── Simprot.pm │ ├── StandAloneBlast.pm │ ├── StandAloneBlastPlus.pm │ ├── StandAloneBlastPlus │ └── BlastMethods.pm │ ├── StandAloneNCBIBlast.pm │ ├── StandAloneWUBlast.pm │ ├── Tmhmm.pm │ ├── TribeMCL.pm │ ├── Vista.pm │ └── tRNAscanSE.pm ├── packages └── install-samtools.sh ├── scripts ├── bp_blast2tree.pl ├── multi_hmmsearch.PLS ├── panalysis.PLS ├── papplmaker.PLS ├── run_neighbor.PLS └── run_protdist.PLS └── t ├── Amap.t ├── AnalysisFactory_soap.t ├── Analysis_soap.t ├── BEDTools.t ├── Blat.t ├── Coil.t ├── Consense.t ├── DBA.t ├── DrawGram.t ├── DrawTree.t ├── EMBOSS.t ├── Ensembl.t ├── Eponine.t ├── Exonerate.t ├── FastTree.t ├── FootPrinter.t ├── Genemark.hmm.prokaryotic.t ├── Genewise.t ├── Genscan.t ├── Gerp.t ├── Glimmer2.t ├── Glimmer3.t ├── Hmmer.t ├── Hyphy.t ├── Infernal.t ├── Kalign.t ├── LVB.t ├── Lagan.t ├── MAFFT.t ├── MCS.t ├── MSAProbs.t ├── Match.t ├── Mdust.t ├── Molphy.t ├── Muscle.t ├── Neighbor.t ├── Njtree.t ├── Pal2Nal.t ├── PhastCons.t ├── Phyml.t ├── Primate.t ├── Primer3.t ├── Prints.t ├── Probalign.t ├── Probcons.t ├── Profile.t ├── Promoterwise.t ├── ProtDist.t ├── ProtPars.t ├── Pseudowise.t ├── QuickTree.t ├── Raxml.t ├── RepeatMasker.t ├── SABlastPlus.t ├── SLR.t ├── Samtools.t ├── Seg.t ├── Semphy.t ├── SeqBoot.t ├── Signalp.t ├── Sim4.t ├── Simprot.t ├── SoapEU-function.t ├── SoapEU-unit.t ├── StandAloneFasta.t ├── Tmhmm.t ├── Tools └── Run │ ├── Dummy.pm │ ├── Dummy │ └── Config.pm │ ├── RemoteBlast.t │ ├── RemoteBlast_rpsblast.t │ ├── StandAloneBlast.t │ ├── WBCommandExts.t │ └── WrapperBase.t ├── TribeMCL.t ├── Vista.t ├── data ├── 1.bg ├── 2.bg ├── 219877.cdna.fasta ├── 219877.tree ├── 277523.cdna.fasta ├── 277523.tree ├── 3.bg ├── FootPrinter.seq.fa ├── Ft.bam ├── Ft.bed ├── Ft.bed12 ├── Ft.frag.fas ├── Ft.frag.fas.fai ├── Genscan.FastA ├── H_pylori_J99.fasta ├── H_pylori_J99.glimmer2.icm ├── H_pylori_J99.glimmer3.icm ├── NM_002254.gb ├── NM_002254.tfa ├── Phrap.fa ├── Primer3.fa ├── Prints_prot.FastA ├── TribeMCL.bls ├── TribeMCL.desc ├── amino.fa ├── apes.multi_fasta ├── apes.newick ├── blat_dna.fa ├── cel-cbr-fam.aln ├── coil_protein_input ├── consense.treefile ├── consensus.cns ├── cysprot.fa ├── cysprot.msf ├── cysprot.stockholm ├── cysprot1a.fa ├── cysprot1a.msf ├── cysprot1b.fa ├── cysprot1b.msf ├── dba1a.fa ├── dba1b.fa ├── dba2.fa ├── dna1.fa ├── dna2.fa ├── dna_seqs1.phy ├── e_coli.bed3 ├── e_coli_1.bedpe ├── e_coli_2.bedpe ├── ecolitst.fa ├── efetch_seq.wsdl ├── elink_result.xml ├── eponine.fa ├── esearch_result.xml ├── esum_result.xml ├── eutils.wsdl ├── exonerate_cdna.fa ├── exonerate_cdna_rev.fa ├── exonerate_genomic.fa ├── exonerate_genomic_rev.fa ├── fasta.fa ├── fastalib.fa ├── fastaprot.fa ├── fontfile ├── gb_result.xml ├── gerp │ ├── ENr111.gerp.tree │ └── ENr111.mfa.gz ├── gumby │ ├── hmrd.mfa │ ├── hmrd.tree │ ├── human.gff │ └── readme.txt ├── her2-edited.fasta ├── hmmpfam_protein_input ├── human.genomic ├── hyphy1.fasta ├── hyphy1.tree ├── lagan_dna.fa ├── longnames.aln ├── lvb.fa ├── lvb_sequential.phy ├── neighbor.dist ├── new_pep.fa ├── njtree_aln2.nucl.mfa ├── pal2nal.aln ├── pal2nal.nuc ├── pfam_sample_R11 ├── primate_query.fa ├── primate_target.fa ├── prints.dat ├── profile_prot.FastA ├── prosite.dat ├── protpars.phy ├── ps1.fa ├── purine.1.sto ├── purine.added.fa ├── purine.all.fa ├── purine.c.cm ├── purine.cm ├── repeatmasker.fa ├── road.pep ├── sample_dataset_1_aligned.fa ├── segmask_data.asn ├── semphy.seq ├── semphy.tree ├── signalp_input_protein ├── sim4_cdna.fa ├── sim4_database.fa ├── sim4_genomic.fa ├── simprot_tree.nh ├── species_tree_njtree.nh ├── taxdump │ ├── names.dmp │ └── nodes.dmp ├── test-aln.msf ├── test-query.fas ├── test-spa-p.fas ├── test-spa.fas ├── test.txt ├── test_prot.FastA ├── testaln.phylip ├── transfac.dat ├── tree_of_life ├── treefile.example ├── vista.cls ├── vista.gff └── xprt.gb ├── gmap-run.t └── tRNAscanSE.t /.gitignore: -------------------------------------------------------------------------------- 1 | *~ 2 | .tmp 3 | *# 4 | .#* 5 | .*.swp 6 | *(Autosaved)blib* 7 | Build 8 | Build.bat 9 | _build* 10 | pm_to_blib* 11 | *.tar.gz 12 | .lwpcookies 13 | cover_db 14 | pod2htm*.tmp 15 | .emacs.* 16 | blib* 17 | *.bak 18 | MYMETA.yml 19 | MYMETA.json 20 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: perl 2 | 3 | perl: 4 | - "5.24" 5 | #- "5.20" 6 | - "5.18" 7 | #- "5.16" 8 | #- "5.14" 9 | 10 | sudo: false 11 | env: PERL_CPANM_OPT="--notest --force --skip-satisfied" 12 | 13 | addons: 14 | apt: 15 | packages: 16 | - ncbi-blast+ 17 | - ncbi-blast+-legacy 18 | - clustalw 19 | - bwa 20 | - hmmer 21 | - probcons 22 | #- emboss 23 | #- wise 24 | #- samtools 25 | #- muscle 26 | #- bedtools 27 | #- mafft 28 | 29 | install: 30 | #These are recommended or required Perl libraries 31 | - "cpanm Bio::Perl 2>&1 | tail -n 1" 32 | - "cpanm Bio::FeatureIO 2>&1 | tail -n 1" 33 | - "cpanm IPC::Run XML::Twig 2>&1 | tail -n 1" 34 | - "cpanm Config::Any 2>&1 | tail -n 1" 35 | - "cpanm File::Sort 2>&1 | tail -n 1" 36 | #- "SAMTOOLS=( dirname `which samtools` ) cpanm Bio::DB::Sam 2>&1 | tail -n 1" 37 | 38 | # Install non-apt dependencies 39 | before_install: 40 | - bash ./packages/install-samtools.sh 41 | - export PATH=$PATH:$HOME/local/bin/ 42 | 43 | script: 44 | - "perl ./Build.PL --accept" 45 | - "./Build test" 46 | 47 | #after_success: 48 | # - ./travis_scripts/trigger-dockerhub.sh 49 | 50 | #TODO - send emails to bioperl-guts-l 51 | notifications: 52 | email: 53 | recipients: 54 | #- bioperl-guts-l@lists.open-bio.org 55 | - cjfields1@gmail.com 56 | on_success: change 57 | on_failure: change 58 | 59 | # whitelist branches 60 | branches: 61 | only: 62 | - master 63 | -------------------------------------------------------------------------------- /AUTHORS: -------------------------------------------------------------------------------- 1 | =head1 CONTRIBUTORS TO BIOPERL-RUN 2 | 3 | =over 4 | 5 | =item * Sendu Bala 6 | 7 | =item * Jer-Ming Chia 8 | 9 | =item * Rob Edwards 10 | 11 | =item * Mauricio Herrera Cuadra 12 | 13 | =item * Shawn Hoon 14 | 15 | =item * Donald Jackson 16 | 17 | =item * Keith James 18 | 19 | =item * Ratnapu Kiran Kumar 20 | 21 | =item * Balamurugan Kumarasamy 22 | 23 | =item * Catherine Letondal 24 | 25 | =item * Heikki Lehvaslaiho 26 | 27 | =item * Stephen Montgomery 28 | 29 | =item * Brian Osborne 30 | 31 | =item * Tania Oh 32 | 33 | =item * Peter Schattner 34 | 35 | =item * Martin Senger 36 | 37 | =item * Marc Sohrmann 38 | 39 | =item * Jason Stajich 40 | 41 | =item * Elia Stupka 42 | 43 | =item * David Vilanova 44 | 45 | =item * Albert Vilella 46 | 47 | =item * Tiequan Zhang 48 | 49 | =item * Juguang Xiao 50 | 51 | =back 52 | -------------------------------------------------------------------------------- /INSTALL: -------------------------------------------------------------------------------- 1 | bioperl-run INSTALLATION 2 | 3 | INSTALL THE RIGHT BIOPERL 4 | 5 | You need at least the corresponding version of Bioperl. Since this 6 | is BioPerl-run 1.007001, you should use BioPerl 1.007001. 7 | 8 | 9 | INSTALLATION 10 | 11 | Installation instructions at the following address apply here: 12 | http://bioperl.org/INSTALL.html 13 | The next 2 sections summarize the essential points from there. 14 | 15 | 16 | CPAN INSTALLATION 17 | 18 | To install using CPAN you will need a recent version (v1.8802 has 19 | been tested) of it and your prefer_installer conf set to 'MB': 20 | 21 | >cpan 22 | cpan>o conf prefer_installer MB 23 | cpan>o conf commit 24 | cpan>q 25 | 26 | Find the name of the bioperl-run version you want: 27 | 28 | >cpan 29 | cpan>d /bioperl-run/ 30 | Database was generated on Mon, 20 Nov 2006 05:24:36 GMT 31 | Distribution CJFIELDS/BioPerl-Run-1.007001.tar.gz 32 | 33 | Now install: 34 | 35 | cpan>install CJFIELDS/BioPerl-Run-1.007001.tar.gz 36 | 37 | If you've installed everything perfectly then you may pass all the tests 38 | run in the './Build test' phase. 39 | 40 | It's also possible that you may fail some tests. Possible explanations: 41 | problems with local Perl installation, previously undetected bug in 42 | Bioperl, flawed test script and so on. A few failed tests may not affect 43 | your usage of bioperl-run. 44 | 45 | If you decide that the failed tests will not affect how you intend to use 46 | bioperl-run and you'd like to install anyway do: 47 | 48 | cpan>force install CJFIELDS/BioPerl-Run-1.007001.tar.gz 49 | 50 | This is what most experienced Bioperl users would do. However, if you're 51 | concerned about a failed test and need assistance or advice then contact 52 | bioperl-l@bioperl.org. 53 | 54 | MANUAL INSTALLATION 55 | 56 | Download the bioperl-run archive, then extract its contents. Example: 57 | 58 | >gunzip bioperl-run-.tar.gz 59 | >tar xvf bioperl-run-.tar 60 | >cd bioperl-run 61 | 62 | where is the current release. 63 | 64 | Issue the following command from within bioperl-run/: 65 | 66 | >perl Build.PL 67 | 68 | You can run regression tests and install bioperl-run using the 69 | following commands: 70 | 71 | >./Build test 72 | >./Build install 73 | 74 | NOTE: many tests will be skipped without the necessary environment 75 | variables set to tell Bioperl where your programs are installed. 76 | 77 | INSTALLING bioperl-run ON WINDOWS 78 | 79 | The following page on the BioPerl website has up-to-date 80 | instructions on how to install bioperl-run on Windows: 81 | 82 | http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows 83 | 84 | (the instructions are aimed at bioperl-core, but apply 85 | equally to bioperl-run) 86 | -------------------------------------------------------------------------------- /INSTALL.SKIP: -------------------------------------------------------------------------------- 1 | ConfigData\.\S+$ 2 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Description 2 | 3 | This is the home for *bioperl-run*, which contain modules that provides a Perl 4 | interface to various bioinformatics applications. This allows various 5 | applications to be used with common BioPerl objects. 6 | 7 | See the *Changes* file for more information about what is contained in 8 | here. 9 | 10 | # Installation 11 | 12 | See the accompanying *INSTALL* file for details on installing 13 | bioperl-run. 14 | 15 | # Feedback 16 | 17 | Write down any problems or praise and send them to 18 | bioperl-l@bioperl.org. 19 | 20 | # Bugs 21 | 22 | Bug reports can be made using the GitHub Issues tracker for this distribution. 23 | -------------------------------------------------------------------------------- /lib/Bio/Tools/Run/ERPIN.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioperl/bioperl-run/f9a864a1214361f281d31e9b8baaf70f760f6687/lib/Bio/Tools/Run/ERPIN.pm -------------------------------------------------------------------------------- /packages/install-samtools.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 3 | tar -xjvf samtools-1.3.1.tar.bz2 4 | cd samtools-1.3.1 && make prefix=$HOME/local && make prefix=$HOME/local install 5 | -------------------------------------------------------------------------------- /scripts/run_neighbor.PLS: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | =head1 NAME 6 | 7 | run_neighbor - run Phylip's 'neighbor' program through Bioperl 8 | 9 | =head1 SYNOPSIS 10 | 11 | run_neighbor [-i inputfile] [-o outfilename] 12 | 13 | =head1 DESCRIPTION 14 | 15 | Provide an matrix file to run neighbor on. File should be named of 16 | the forma file.matrix or file.protdist (the ending doesn't matter, but 17 | the program expects a file in the form of (\S+)\.(\S+). 18 | 19 | This will run the application 'neighbor' to build a 20 | Neighbor-Joining tree from a protein distance matrix. 21 | 22 | =head1 AUTHOR 23 | 24 | Jason Stajich, jason-AT-open-bio-DOT-org 25 | 26 | =cut 27 | 28 | use Bio::TreeIO; 29 | use Bio::Tools::Run::Phylo::Phylip::Neighbor; 30 | use Getopt::Long; 31 | 32 | my @params = ('type'=>'NJ', 'quiet' => 1); 33 | 34 | my $matrixfile; 35 | my $out; 36 | GetOptions( 37 | 'i|input:s' => \$matrixfile, 38 | 'o|out:s' => \$out, 39 | 'h|help' => sub { exec('perldoc',$0); exit(0) } 40 | ); 41 | ($matrixfile) ||= shift @ARGV; 42 | 43 | my ($stem,$ext) = ($matrixfile =~ /(\S+)\.(\S+)$/) ; 44 | $stem ||= $matrixfile; 45 | 46 | my $outfh; 47 | if( $out ) { 48 | open($outfh, ">$out") || die($!); 49 | } else { 50 | open($outfh, ">$stem.tree") || die($!); 51 | } 52 | 53 | my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params); 54 | my (@trees) = $tree_factory->create_tree($matrixfile); 55 | 56 | my $outtree = new Bio::TreeIO(-fh => $outfh); 57 | foreach my $tree ( @trees ){ 58 | $outtree->write_tree($tree); 59 | } 60 | -------------------------------------------------------------------------------- /scripts/run_protdist.PLS: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | =head1 NAME 6 | 7 | run_neighbor - run Phylip's 'protdist' program through Bioperl 8 | 9 | =head1 SYNOPSIS 10 | 11 | run_protdist [-i inputfile] [-o outfilename] 12 | 13 | =head1 DESCRIPTION 14 | 15 | Provide an alignment file to run protdist on. File should be named 16 | either .aln or .phy. This is required so that we can determine if we 17 | need to convert a clustalw alignment into phylip. You are welcome to 18 | extend the script to work on other MSA formats which bioperl supports. 19 | This is intended to be used in very simple manual pipelines. 20 | 21 | The input file should be named in the form of file.phy or file.aln 22 | the program expects a file in the form of (\S+)\.(\S+). 23 | 24 | This will run the application 'protdist' using the 'KIMURA' formula to 25 | build a a protein distance matrix. Those with phylip3.6 will want to 26 | make some changes if they want to use JTT. I'm happy to help add this 27 | in as a cmd-line argument if it is requested. 28 | 29 | =head1 AUTHOR 30 | 31 | Jason Stajich, jason-AT-open-bio-DOT-org 32 | 33 | =cut 34 | 35 | use Bio::AlignIO; 36 | use Bio::Tools::Run::Phylo::Phylip::ProtDist; 37 | use Getopt::Long; 38 | 39 | my @params = ( 'MODEL' => 'KIMURA', 40 | 'quiet' => 1, 41 | ); 42 | 43 | my ($out,$file); 44 | 45 | GetOptions( 46 | 'o|out:s' => \$out, 47 | 'i|in:s' => \$file, 48 | 'h|help' => sub { exec('perldoc',$0); exit(0) } 49 | ); 50 | 51 | ($file) ||= shift @ARGV; 52 | 53 | my ($stem,$ext) = ($file =~ /(\S+)\.(\S+)$/); 54 | $stem ||= $file; 55 | 56 | my $outfh; 57 | if( $out ) { 58 | open($outfh, ">$out") || die($!); 59 | } else { 60 | open($outfh, ">$stem.matrix") || die($!); 61 | } 62 | 63 | if( $ext eq 'aln' ) { 64 | my $inaln = new Bio::AlignIO(-file => $file, 65 | -format => 'clustalw'); 66 | $file = "$stem.phy"; 67 | 68 | my $outreformat = new Bio::AlignIO(-file => ">$file", 69 | -interleaved => 1, 70 | -format => 'phylip'); 71 | while( my $aln = $inaln->next_aln ) { 72 | $outreformat->write_aln($aln); 73 | } 74 | $outreformat->close(); 75 | $outreformat = undef; 76 | $inaln = undef; 77 | } 78 | 79 | my $factory = new Bio::Tools::Run::Phylo::Phylip::ProtDist(@params); 80 | my (@matrix) = $factory->create_distance_matrix($file); 81 | 82 | foreach my $mat ( @matrix ) { 83 | print $outfh $mat->print_matrix; 84 | } 85 | 86 | -------------------------------------------------------------------------------- /t/Amap.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 18); 9 | 10 | use_ok('Bio::Tools::Run::Alignment::Amap'); 11 | use_ok('Bio::SeqIO'); 12 | use_ok('File::Spec'); 13 | } 14 | 15 | END { 16 | # Things to do right at the very end, just 17 | # when the interpreter finishes/exits 18 | # E.g. deleting intermediate files produced during the test 19 | foreach my $file ( qw(cysprot.dnd cysprot1a.dnd mlc) ) { 20 | unlink $file; 21 | } 22 | } 23 | 24 | # if we got to here, thats OK! 25 | # is this really needed? 26 | #ok( 1, 'All the required modules are present'); 27 | 28 | # setup input files etc 29 | my $inputfilename = test_input_file("cysprot.fa"); 30 | ok( -e $inputfilename, 'Found input file' ); 31 | 32 | # setup output files etc 33 | # none in this test 34 | 35 | # setup global objects that are to be used in more than one test 36 | # Also test they were initialised correctly 37 | my @params = (); 38 | my $factory = Bio::Tools::Run::Alignment::Amap->new(@params); 39 | isa_ok( $factory, 'Bio::Tools::Run::Alignment::Amap'); 40 | 41 | # test factory default values 42 | is( $factory->program_dir, undef, 'program_dir returned correct default' ); 43 | is( $factory->error_string, '', 'error_string returned correct default' ); 44 | is( $factory->aformat, 'fasta', 'aformat returned correct default' ); 45 | is( $factory->outfile_name, 'mlc', 'outfile_name returned correct default' ); 46 | 47 | # Now onto the nitty gritty tests of the modules methods 48 | is( $factory->program_name(), 'amap', 'Correct exe default name' ); 49 | 50 | # block of tests to skip if you know the tests will fail 51 | # under some condition. E.g.: 52 | # Need network access, 53 | # Wont work on particular OS, 54 | # Cant find the exectuable 55 | # DO NOT just skip tests that seem to fail for an unknown reason 56 | 57 | SKIP: { 58 | # condition used to skip this block of tests 59 | #skip($why, $how_many_in_block); 60 | test_skip(-requires_executable => $factory, 61 | -tests => 8); 62 | 63 | # test all factory methods that depend on the executable 64 | # TODO: isnt( $factory->program_dir, undef, 'program found in ENV variable' ); 65 | ok( $factory->version >= 2.0, 'Correct minimum program version' ); 66 | 67 | # test execution using filename 68 | my $aln = $factory->align($inputfilename); 69 | 70 | # now test the factory error methods etc 71 | is( $factory->error_string, '', 'No error occured' ); 72 | isnt( $factory->outfile_name, undef, 'outfile_name returned something' ); 73 | 74 | # now test its output 75 | isa_ok( $aln, 'Bio::SimpleAlign'); 76 | is( $aln->num_sequences, 7, 'Correct number of seqs returned' ); 77 | 78 | # test execution using an array of Seq objects 79 | my $str = Bio::SeqIO->new( 80 | '-file' => $inputfilename, 81 | '-format' => 'Fasta', 82 | ); 83 | my @seq_array =(); 84 | while ( my $seq = $str->next_seq() ) { 85 | push (@seq_array, $seq) ; 86 | } 87 | $aln = $factory->align(\@seq_array); 88 | # now test its output 89 | isa_ok( $aln, 'Bio::SimpleAlign'); 90 | is( $aln->num_sequences, 7, 'Correct number of seqs returned' ); 91 | 92 | # Use this alignment to fully test the methods 93 | is( int($aln->average_percentage_identity), 45, 'Got the correct ave % identity' ); 94 | 95 | } 96 | 97 | # TODO: test factory methods that change parameters 98 | #TODO: { 99 | # local $TODO = 'program_name setting is unfinished'; 100 | # $factory->program_name('something_silly'); 101 | # is( $factory->program_name, 'something_silly', 'Set and got program_name correctly') ; 102 | #} 103 | 104 | -------------------------------------------------------------------------------- /t/AnalysisFactory_soap.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | # $id$ 3 | ## Bioperl Test Harness Script for Modules 4 | 5 | use strict; 6 | 7 | BEGIN { 8 | use Bio::Root::Test; 9 | 10 | # The EMBL-EBI Soaplab server has been decommissioned on 1st February 2013 11 | # (https://www.ebi.ac.uk/Tools/webservices/about/news). 12 | # Website "http://www.ebi.ac.uk/soaplab/services" dont exists anymore, 13 | # so tests will fail with "404 Not Found" if executed 14 | test_begin(-tests => 0, 15 | -requires_networking => 1); 16 | use_ok('Bio::Tools::Run::AnalysisFactory'); 17 | } 18 | 19 | 20 | # setup global objects that are to be used in more than one test 21 | # Also test they were initialised correctly 22 | # test new with default access 23 | my $factory = Bio::Tools::Run::AnalysisFactory->new(); 24 | isa_ok( $factory, 'Bio::Tools::Run::AnalysisFactory'); 25 | 26 | # test new with explicit access 27 | $factory = Bio::Tools::Run::AnalysisFactory->new(-access=>'soap'); 28 | isa_ok( $factory, 'Bio::Tools::Run::AnalysisFactory'); 29 | 30 | # test new with non-existing access 31 | throws_ok { Bio::Tools::Run::AnalysisFactory->new(-access=>'non_existing') } qr/cannot be found or loaded/, 'Non existant access method threw an error'; 32 | 33 | # test default factory values 34 | 35 | # Now onto the nitty gritty tests of the modules methods 36 | SKIP: { 37 | test_skip(-tests => 9, -requires_module => 'SOAP::Lite'); 38 | use_ok('SOAP::Lite'); 39 | 40 | my $array_ref = $factory->available_categories; 41 | isa_ok( $array_ref, 'ARRAY' ); 42 | ok( grep(/protein/i, @$array_ref), 'available_categories returned category with protein' ); 43 | 44 | $array_ref = $factory->available_analyses; 45 | isa_ok( $array_ref, 'ARRAY' ); 46 | ok( grep(/seqret/i, @$array_ref), 'available_analyses returned category with seqret' ); 47 | 48 | $array_ref = $factory->available_analyses('edit'); 49 | isa_ok( $array_ref, 'ARRAY' ); 50 | ok( grep(/seqret/i, @$array_ref), 'available_analyses("edit") returned something' ); 51 | 52 | my $service; 53 | lives_ok {$service = $factory->create_analysis('edit.seqret')}; 54 | skip ("create_analysis failed :$@", 1) if $@; 55 | isa_ok( $service, 'Bio::Tools::Run::Analysis::soap' ); 56 | } 57 | -------------------------------------------------------------------------------- /t/Analysis_soap.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | # $id$ 3 | ## Bioperl Test Harness Script for Modules 4 | 5 | use strict; 6 | 7 | BEGIN { 8 | use Bio::Root::Test; 9 | 10 | # The EMBL-EBI Soaplab server has been decommissioned on 1st February 2013 11 | # (https://www.ebi.ac.uk/Tools/webservices/about/news). 12 | # Website "http://www.ebi.ac.uk/soaplab/services" dont exists anymore, 13 | # so tests will fail with "404 Not Found" if executed 14 | test_begin(-tests => 0, 15 | -requires_networking => 1); 16 | use_ok('Bio::Tools::Run::Analysis'); 17 | use_ok('File::Spec'); 18 | } 19 | 20 | SKIP: { 21 | test_skip(-tests => 15, -requires_module => 'SOAP::Lite'); 22 | use_ok('SOAP::Lite'); 23 | 24 | my $seqret = Bio::Tools::Run::Analysis->new(-name=>'edit.seqret'); 25 | my $seq = 'tatacga'; 26 | 27 | SKIP: { 28 | # condition used to skip this block of tests 29 | #skip($why, $how_many_in_block); 30 | skip("Failed to create the analysis object", 1) 31 | unless isa_ok( $seqret, 'Bio::Tools::Run::Analysis::soap'); 32 | 33 | # test seqret service with some testing data 34 | # TODO: use BIOPERLDEBUG to skip these tests 35 | my %input = ( 36 | 'sequence_direct_data' => $seq, 37 | 'osformat' => 'raw', 38 | ); 39 | is( $seqret->analysis_name, 'seqret', 'analysis_name returned seqret' ); 40 | isa_ok( $seqret->analysis_spec, 'HASH'); 41 | 42 | my $input_spec = $seqret->input_spec; 43 | isa_ok( $input_spec, 'ARRAY' ); 44 | ok( @$input_spec > 0, 'input_spec returned an array with something in it' ); 45 | isa_ok( $input_spec->[0], 'HASH' ); 46 | my $result_spec = $seqret->result_spec; 47 | isa_ok( $result_spec, 'ARRAY' ); 48 | ok( @$result_spec > 0, 'result_spec returned an array with something in it' ); 49 | like( $seqret->describe, '/^<\?xml /', 'describe seems to have returned the correct thing' ); 50 | my $job = $seqret->create_job (\%input); 51 | SKIP: { 52 | skip("Object not created correctly", 6) unless isa_ok( $job, 'Bio::Tools::Run::Analysis::Job' ); 53 | 54 | is( $job->status, 'CREATED', 'Job status correct' ); 55 | # TODO: not goot to use private methods 56 | my $cloned_job = $seqret->create_job ($job->{'_id'}); 57 | 58 | SKIP: { 59 | skip( "Couldn't clone the job", 2 ) 60 | unless isa_ok( $cloned_job, 'Bio::Tools::Run::Analysis::Job', 61 | 'Job cloned successfully' ); 62 | 63 | like( $cloned_job->last_event, '/^<\?xml /', 64 | 'last_event seems to have returned the correct thing' ); 65 | $cloned_job->remove; 66 | # TODO: not good to use private methods 67 | is( $cloned_job->{'_destroy_on_exit'}, 1, 68 | 'Cloned job removed successfully' ); 69 | } 70 | } 71 | } 72 | } 73 | -------------------------------------------------------------------------------- /t/Coil.t: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | #-*-Perl-*- 3 | # ## Bioperl Test Harness Script for Modules 4 | # # 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 6); 9 | 10 | use_ok('Bio::Tools::Run::Coil'); 11 | use_ok('Bio::SeqIO'); 12 | } 13 | 14 | SKIP: { 15 | my $factory = Bio::Tools::Run::Coil->new(); 16 | test_skip(-requires_executable => $factory, 17 | -requires_env => 'COILSDIR', 18 | -tests => 4); 19 | ok $factory->isa('Bio::Tools::Run::Coil'); 20 | 21 | my $prot_file= test_input_file("coil_protein_input"); 22 | 23 | my $seq1 = Bio::Seq->new(); 24 | my $seqstream = Bio::SeqIO->new(-file => $prot_file, -fmt => 'Fasta'); 25 | $seq1 = $seqstream->next_seq(); 26 | 27 | my $coil_present = $factory->executable(); 28 | unless ($coil_present) { 29 | skip("coil program not found", 3); 30 | } 31 | 32 | $factory->quiet(1); 33 | my @feat = $factory->predict_protein_features($seq1); 34 | 35 | ok $feat[0]->isa('Bio::SeqFeatureI'); 36 | ok ($feat[0]->start,71); 37 | ok ($feat[0]->end,91); 38 | } -------------------------------------------------------------------------------- /t/Consense.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 8, 9 | -requires_module => 'IO::String'); 10 | use_ok('Bio::Tools::Run::Phylo::Phylip::Consense'); 11 | use_ok('Bio::AlignIO'); 12 | } 13 | 14 | my $verbose = test_debug(); 15 | 16 | my $sb_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new(-verbose => $verbose); 17 | 18 | SKIP: { 19 | test_skip(-requires_executable => $sb_factory, 20 | -tests => 6); 21 | 22 | isa_ok($sb_factory,'Bio::Tools::Run::Phylo::Phylip::Consense'); 23 | 24 | $sb_factory->rooted(1); 25 | 26 | is $sb_factory->rooted, 1, "could not set rooted option"; 27 | 28 | $sb_factory->quiet($verbose); # Suppress protpars messages to terminal 29 | 30 | my $inputfilename = test_input_file("consense.treefile"); 31 | my $tree = $sb_factory->run($inputfilename); 32 | 33 | is $tree->number_nodes, 13; 34 | 35 | my $node = $tree->find_node('CATH_RAT'); 36 | is $node->branch_length, "10.0"; 37 | is $node->id, 'CATH_RAT'; 38 | 39 | my @nodes = $tree->get_nodes; 40 | 41 | is scalar(@nodes),13; 42 | } 43 | -------------------------------------------------------------------------------- /t/DBA.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 18); 9 | use_ok('Bio::Tools::Run::Alignment::DBA'); 10 | use_ok('Bio::SimpleAlign'); 11 | use_ok('Bio::AlignIO'); 12 | use_ok('Bio::SeqIO'); 13 | } 14 | 15 | my $verbose = -1; 16 | my @params = ('matchA' => 0.75, 'matchB' => '0.55','dymem'=>'linear'); 17 | my $factory = Bio::Tools::Run::Alignment::DBA->new(@params); 18 | 19 | SKIP: { 20 | test_skip(-requires_executable => $factory, 21 | -tests => 14); 22 | 23 | isa_ok $factory,'Bio::Tools::Run::Alignment::DBA'; 24 | my $bequiet = 1; 25 | $factory->quiet($bequiet); # Suppress clustal messages to terminal 26 | 27 | #test with one file with 2 sequences 28 | my $inputfilename_1a = test_input_file("dba1a.fa"); 29 | my $inputfilename_1b = test_input_file("dba1b.fa"); 30 | my $inputfilename2 = test_input_file("dba2.fa"); 31 | my $aln; 32 | my @hsps = $factory->align($inputfilename2); 33 | isa_ok($hsps[0],"Bio::Search::HSP::GenericHSP"); 34 | is($hsps[0]->query->start,4); 35 | is($hsps[0]->query->end,209); 36 | is($hsps[0]->gaps,6); 37 | 38 | #test with 2 files of 1 sequence each 39 | my @files = ($inputfilename_1a,$inputfilename_1b); 40 | @hsps = $factory->align(\@files); 41 | is($hsps[0]->query->start,3); 42 | is($hsps[0]->query->end,88); 43 | is($hsps[0]->gaps,0); 44 | is($hsps[1]->hit->start,90); 45 | is($hsps[1]->hit->end,195); 46 | is($hsps[1]->gaps,0); 47 | 48 | #test with an array of 2 PrimarySeqI objects 49 | 50 | my $str = Bio::SeqIO->new(-file=> test_input_file("dba2.fa"), '-format' => 'Fasta'); 51 | my @seq_array =(); 52 | 53 | while ( my $seq = $str->next_seq() ) { 54 | push (@seq_array, $seq) ; 55 | } 56 | @hsps = $factory->align(\@seq_array); 57 | is($hsps[0]->query->start,4); 58 | is($hsps[0]->query->end,209); 59 | is($hsps[0]->gaps,6); 60 | } 61 | -------------------------------------------------------------------------------- /t/DrawGram.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | # 4 | 5 | use strict; 6 | 7 | BEGIN { 8 | use Bio::Root::Test; 9 | test_begin(-tests => 6); 10 | use_ok('Bio::Tools::Run::Phylo::Phylip::DrawGram'); 11 | use_ok('Bio::TreeIO'); 12 | } 13 | 14 | SKIP: { 15 | my @params = ('-verbose' => test_debug(), 16 | 'quiet' => 1); 17 | my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawGram->new(@params); 18 | test_skip(-requires_executable => $treedraw, 19 | -tests => 4); 20 | 21 | $treedraw->fontfile(test_input_file('fontfile')); 22 | 23 | my $file = $treedraw->draw_tree(test_input_file('treefile.example')); 24 | ok($file); 25 | ok(-e $file); 26 | 27 | if( test_debug() ) { 28 | `gs $file`; 29 | } 30 | unlink($file); 31 | 32 | my $intree = Bio::TreeIO->new(-file => test_input_file('treefile.example')); 33 | 34 | $treedraw->HORIZMARGINS(['2.00','2.5']); 35 | $treedraw->ANCESTRALNODES('C'); 36 | $treedraw->TREESTYLE('PHEN'); 37 | $treedraw->USEBRANCHLENS('N'); 38 | 39 | $file = $treedraw->draw_tree(test_input_file('treefile.example')); 40 | 41 | ok($file); 42 | ok(-e $file); 43 | 44 | if( test_debug() ) { 45 | `gs $file`; 46 | } 47 | unlink($file); 48 | } 49 | -------------------------------------------------------------------------------- /t/DrawTree.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | # 4 | 5 | use strict; 6 | 7 | BEGIN { 8 | use Bio::Root::Test; 9 | test_begin(-tests => 6); 10 | use_ok('Bio::Tools::Run::Phylo::Phylip::DrawTree'); 11 | use_ok('Bio::TreeIO'); 12 | } 13 | 14 | SKIP: { 15 | my @params = ('-verbose' => 0, 16 | 'quiet' => 1); 17 | my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawTree->new(@params); 18 | test_skip(-requires_executable => $treedraw, 19 | -tests => 4); 20 | 21 | $treedraw->fontfile(test_input_file('fontfile')); 22 | my $file = $treedraw->draw_tree(test_input_file('treefile.example')); 23 | ok($file); 24 | ok(-e $file); 25 | 26 | if( test_debug() ) { 27 | `gs $file`; 28 | } else { 29 | unlink($file); 30 | } 31 | 32 | my $intree = Bio::TreeIO->new(-file => test_input_file('treefile.example')); 33 | 34 | $file = $treedraw->draw_tree(test_input_file('treefile.example')); 35 | ok($file); 36 | ok(-e $file); 37 | 38 | if( test_debug() ) { 39 | `gs $file`; 40 | } else { 41 | unlink($file); 42 | } 43 | } -------------------------------------------------------------------------------- /t/Ensembl.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 7, 9 | -requires_networking => 1); 10 | use_ok('Bio::Tools::Run::Ensembl'); 11 | } 12 | 13 | my $setup_ok = Bio::Tools::Run::Ensembl->registry_setup(); 14 | 15 | # test database access 16 | SKIP: { 17 | test_skip(-tests => 6, -requires_module => 'Bio::EnsEMBL::Registry'); 18 | skip("There was some problem contacting the EnsEMBL database?", 6) unless $setup_ok; 19 | 20 | # get an adaptor 21 | ok my $adaptor = Bio::Tools::Run::Ensembl->get_adaptor('human', 'Exon'); 22 | isa_ok $adaptor, 'Bio::EnsEMBL::DBSQL::ExonAdaptor'; 23 | if ($adaptor->can('species_id')) { 24 | is $adaptor->species_id, 1; 25 | } 26 | else { 27 | ok 1; 28 | } 29 | 30 | # get an 'easy' gene - one that is in Ensembl 31 | ok my $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human', 32 | -name => 'BRCA2'); 33 | isa_ok $gene, 'Bio::EnsEMBL::Gene'; 34 | is $gene->external_name, 'BRCA2'; 35 | 36 | 37 | #*** don't know suitable gene names to test the following, to be completed... 38 | 39 | # get one that isn't in human, but is in an orthologue 40 | my $orth_only = '??'; 41 | #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human', 42 | # -name => $orth_only); 43 | #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human', 44 | # -use_orthologues => 'Mus musculus', 45 | # -name => $orth_only); 46 | #is $gene->external_name, $orth_only; 47 | 48 | # get one that isn't in Ensembl but is in Swissprot 49 | my $swiss_only = '??'; 50 | #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human', 51 | # -use_orthologues => 'Mus musculus', 52 | # -name => $swiss_only); 53 | #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human', 54 | # -use_orthologues => 'Mus musculus', 55 | # -use_swiss_lookup => 1, 56 | # -name => $swiss_only); 57 | #is $gene->external_name, $swiss_only; 58 | 59 | # get one that isn't in Swissprot either, but is in NCBI 60 | my $ncbi_only = '??'; 61 | #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human', 62 | # -use_orthologues => 'Mus musculus', 63 | # -use_swiss_lookup => 1, 64 | # -name => $ncbi_only); 65 | #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human', 66 | # -use_orthologues => 'Mus musculus', 67 | # -use_swiss_lookup => 1, 68 | # -use_entrez_lookup => 1, 69 | # -name => $ncbi_only); 70 | #is $gene->external_name, $ncbi_only; 71 | } 72 | -------------------------------------------------------------------------------- /t/Eponine.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | 3 | ## Bioperl Test Harness Script for Modules 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 7); 9 | use_ok('Bio::Tools::Run::Eponine'); 10 | use_ok('Bio::SeqIO'); 11 | } 12 | 13 | SKIP: { 14 | #Java and java version check 15 | my $v; 16 | if (-d "java") { 17 | diag("You must have java to run eponine"); 18 | skip("Skipping because no java present to run eponine",5); 19 | } 20 | open(my $PIPE,"java -version 2>&1 |") || exit; 21 | 22 | while (<$PIPE>) { 23 | if (/Java\sversion\:?\s+\"?(\d+\.\d+)\"?/i) { 24 | $v = $1; 25 | last; 26 | } 27 | } 28 | if ($v < 1.2) { 29 | diag("You need at least version 1.2 of JDK to run eponine"); 30 | skip("Skipping due to old java version",5); 31 | } 32 | 33 | test_skip( -requires_env => 'EPONINEDIR', -tests => 5); 34 | my $inputfilename= test_input_file("eponine.fa"); 35 | my $fact = Bio::Tools::Run::Eponine->new("threshold" => 0.999); 36 | 37 | is ($fact->threshold, 0.999); 38 | my @feats = $fact->run($inputfilename); 39 | is ($feats[0]->start, 69); 40 | is ($feats[0]->end, 69); 41 | is ($feats[0]->strand, 1); 42 | is ($feats[1]->start,178 ); 43 | } 44 | -------------------------------------------------------------------------------- /t/Exonerate.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 89); 9 | use_ok('Bio::Tools::Run::Alignment::Exonerate'); 10 | } 11 | 12 | my $verbose = test_debug() || -1; 13 | 14 | my $query= test_input_file("exonerate_cdna.fa"); 15 | my $target= test_input_file("exonerate_genomic.fa"); 16 | my $targetrev= test_input_file("exonerate_genomic_rev.fa"); 17 | 18 | my $run = Bio::Tools::Run::Alignment::Exonerate->new(-verbose => $verbose, 19 | arguments=>'--model est2genome --bestn 1'); 20 | SKIP: { 21 | test_skip(-requires_executable => $run, -tests => 88); 22 | 23 | isa_ok $run, 'Bio::Tools::Run::Alignment::Exonerate'; 24 | ok $run->version; 25 | 26 | my $searchio= $run->run($query,$target); 27 | isa_ok $searchio, "Bio::SearchIO"; 28 | my @expect = ( [qw(29 268 4 242)],# target-start t-end query-start q-end 29 | [qw(526 646 243 363)], 30 | [qw(964 1056 364 456)], 31 | [qw(1770 1923 457 610)], 32 | [qw(2250 2479 611 840 )], 33 | [qw(2565 2687 841 963)], 34 | [qw(2769 3074 964 1279)] ); 35 | RESULT: while(my $result = $searchio->next_result){ 36 | while( my $hit = $result->next_hit ) { 37 | # ok($hit->start('hit'), 29); 38 | # ok($hit->end('hit'), 3074); 39 | my $i = 0; 40 | while( my $hsp = $hit->next_hsp ) { 41 | is ($hsp->hit->strand, 1); 42 | is ($hsp->query->strand, 1); 43 | is ($hsp->hit->start,$expect[$i]->[0]); 44 | is ($hsp->hit->end,$expect[$i]->[1]); 45 | is ($hsp->query->start,$expect[$i]->[2]); 46 | is ($hsp->query->end,$expect[$i]->[3]); 47 | $i++; 48 | if( $verbose > 0 ) { 49 | warn("TARGET:", $hsp->hit->location->to_FTstring, "\n"); 50 | warn("QUERY: ",$hsp->query->location->to_FTstring, "\n"); 51 | } 52 | } 53 | last; # only show a single HIT 54 | } 55 | last; 56 | } 57 | 58 | 59 | $searchio= $run->run($query,$targetrev); 60 | isa_ok $searchio,"Bio::SearchIO"; 61 | my @expectrev; 62 | if ($run->version >= 2 ) { # latest 2.0.0 version 63 | @expectrev = ( # target-start t-end query-start q-end 64 | [qw(2834 3073 4 242)], 65 | [qw(2456 2576 243 363)], 66 | [qw(2046 2138 364 456)], 67 | [qw(1179 1332 457 610)], 68 | [qw(623 852 611 840)], 69 | [qw(415 537 841 963)], 70 | [qw(28 333 964 1279)] 71 | ); 72 | } else { # version 1.4.0 presumably 73 | @expectrev = ( # target-start t-end query-start q-end 74 | [qw(28 333 964 1279)], 75 | [qw(415 537 841 963)], 76 | [qw(623 852 611 840)], 77 | [qw(1179 1332 457 610)], 78 | [qw(2046 2138 364 456)], 79 | [qw(2456 2576 243 363)], 80 | [qw(2834 3073 4 242)] 81 | ); 82 | 83 | } 84 | RESULT: while(my $result = $searchio->next_result){ 85 | while( my $hit = $result->next_hit ) { 86 | my $i = 0; 87 | while( my $hsp = $hit->next_hsp ) { 88 | is ($hsp->hit->strand, -1); 89 | is ($hsp->query->strand, 1); 90 | is ($hsp->hit->start,$expectrev[$i]->[0]); 91 | is ($hsp->hit->end,$expectrev[$i]->[1]); 92 | is ($hsp->query->start,$expectrev[$i]->[2]); 93 | is ($hsp->query->end,$expectrev[$i]->[3]); 94 | $i++; 95 | if( $verbose > 0 ) { 96 | warn("TARGET:", $hsp->hit->location->to_FTstring, "\n"); 97 | warn("QUERY: ",$hsp->query->location->to_FTstring, "\n"); 98 | } 99 | } 100 | last; # only show a single HIT 101 | } 102 | last; 103 | } 104 | } 105 | -------------------------------------------------------------------------------- /t/FastTree.t: -------------------------------------------------------------------------------- 1 | # This is -*-Perl-*- code 2 | ## Bioperl Test Harness Script for Modules 3 | # Before `./Build install' is performed this script should be runnable with 4 | # `./Build test --test_files test.t'. After `./Build install' it should work as `perl test.t' 5 | 6 | use strict; 7 | 8 | BEGIN { 9 | use Bio::Root::Test; 10 | test_begin( 11 | -tests => 9, 12 | ); 13 | use_ok('Bio::Root::IO'); 14 | use_ok('Bio::Tools::Run::Phylo::FastTree'); 15 | use_ok('Bio::AlignIO'); 16 | } 17 | 18 | ok (my $ft = Bio::Tools::Run::Phylo::FastTree->new( -quiet => 1 ),"Make the object"); 19 | 20 | SKIP: { 21 | test_skip( 22 | -requires_executable => $ft, 23 | -tests => 5 24 | ); 25 | 26 | # The input could be a SimpleAlign object 27 | my $alignio = Bio::AlignIO->new( 28 | -format => 'fasta', 29 | -file => test_input_file('219877.cdna.fasta') 30 | ); 31 | my $alnobj = $alignio->next_aln; 32 | 33 | my $tree = $ft->run($alnobj); 34 | ok( defined($tree), "Tree is defined" ); 35 | my @nodes = $tree->get_nodes; 36 | is($#nodes,3,"Number of nodes is correct"); 37 | 38 | # The input could be an alignment file (fasta or phylip interleaved) 39 | my $alignfile = test_input_file("sample_dataset_1_aligned.fa"); 40 | my $fastft = Bio::Tools::Run::Phylo::FastTree->new( -quiet => 1, -fastest => 1 ); 41 | $tree = $fastft->run($alignfile); 42 | ok( defined($tree), "Tree is defined" ); 43 | 44 | my $slowft = Bio::Tools::Run::Phylo::FastTree->new( 45 | -quiet => 1, 46 | -mlacc => 2, 47 | -slownni => 1, 48 | -spr => 4 49 | ); 50 | $tree = $slowft->run($alignfile); 51 | ok( defined($tree), "Tree is defined" ); 52 | 53 | # Input is protein sequence alignment 54 | $alignio = Bio::AlignIO->new( 55 | -format => 'msf', 56 | -file => test_input_file('cysprot.msf') 57 | ); 58 | $alnobj = $alignio->next_aln; 59 | 60 | my $ptree = $ft->run($alnobj); 61 | ok( defined($tree), "Tree is defined" ); 62 | } 63 | -------------------------------------------------------------------------------- /t/FootPrinter.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 24); 9 | use_ok('Bio::Tools::Run::FootPrinter'); 10 | use_ok('Bio::SeqIO'); 11 | } 12 | 13 | SKIP: { 14 | my $treefile = test_input_file("tree_of_life"); 15 | 16 | my @params = ( 17 | 'size'=>10, 18 | 'sequence_type'=>'upstream', 19 | 'subregion_size'=>30, 20 | 'position_change_cost'=>5, 21 | 'triplet_filtering'=>1, 22 | 'pair_filtering'=>1, 23 | 'post_filtering'=>1, 24 | 'inversion_cost'=>1, 25 | 'tree' =>$treefile, 26 | 'details'=>0, 27 | 'verbose'=>0); 28 | 29 | my $fact = Bio::Tools::Run::FootPrinter->new(@params); 30 | test_skip(-requires_executable => $fact, -tests => 22); 31 | 32 | is $fact->size, 10; 33 | is $fact->sequence_type, 'upstream'; 34 | is $fact->subregion_size, 30; 35 | is $fact->position_change_cost, 5; 36 | is $fact->triplet_filtering,1; 37 | is $fact->pair_filtering,1; 38 | is $fact->post_filtering,1; 39 | is $fact->inversion_cost,1; 40 | is $fact->tree, $treefile; 41 | 42 | my $input= test_input_file("FootPrinter.seq.fa"); 43 | 44 | my $in = Bio::SeqIO->new(-file => "$input" , '-format' => 'fasta'); 45 | my @seq; 46 | while (my $seq = $in->next_seq){ 47 | push @seq, $seq; # 6 sequences 48 | } 49 | my @fp= $fact->run(@seq); 50 | is @fp, 6; 51 | 52 | my $first = shift @fp; 53 | 54 | my @motifs = $first->sub_SeqFeature; 55 | if (@motifs == 2) { 56 | # older version of FootPrinter? or version 2.1 is buggy with its silly first 57 | # motif of 1 bp below 58 | is $motifs[0]->seq_id,'TETRAODON-motif1'; 59 | is $motifs[0]->seq->seq, 'tacaggatgca'; 60 | is $motifs[0]->start, 352; 61 | is $motifs[0]->end, 362; 62 | is $motifs[1]->seq_id,'TETRAODON-motif2'; 63 | is $motifs[1]->seq->seq, 'ccatatttgga'; 64 | is $motifs[1]->start, 363; 65 | is $motifs[1]->end, 373; 66 | ok 1 for 1..4; 67 | } 68 | elsif (@motifs == 3) { 69 | is $motifs[0]->seq_id,'TETRAODON-motif1'; 70 | is $motifs[0]->seq->seq, 't'; 71 | is $motifs[0]->start, 352; 72 | is $motifs[0]->end, 352; 73 | is $motifs[1]->seq_id,'TETRAODON-motif2'; 74 | is $motifs[1]->seq->seq, 'acaggatgca'; 75 | is $motifs[1]->start, 353; 76 | is $motifs[1]->end, 362; 77 | is $motifs[2]->seq_id,'TETRAODON-motif3'; 78 | is $motifs[2]->seq->seq, 'ccatatttgga'; 79 | is $motifs[2]->start, 363; 80 | is $motifs[2]->end, 373; 81 | } 82 | } 83 | -------------------------------------------------------------------------------- /t/Genemark.hmm.prokaryotic.t: -------------------------------------------------------------------------------- 1 | #-*-Perl-*- 2 | # ## Bioperl Test Harness Script for Modules 3 | # # 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 99, 9 | -requires_modules => [qw(IPC::Run)]); 10 | 11 | use_ok('Bio::Tools::Run::Genemark'); 12 | use_ok('Bio::Root::IO'); 13 | use_ok('Bio::Seq'); 14 | } 15 | 16 | my $verbose = test_debug(); 17 | my $model_dir = $ENV{'GENEMARK_MODELS'} if $ENV{'GENEMARK_MODELS'}; 18 | 19 | SKIP: { 20 | my $fasta_file = test_input_file('H_pylori_J99.fasta'); 21 | test_skip(-tests => 96, 22 | -requires_env => 'GENEMARK_MODELS'); 23 | my $model_file = ''; 24 | 25 | for my $mod (qw(Helicobacter_pylori_26695.mod Helicobacter_pylori.mod)) { 26 | my $modpath = Bio::Root::IO->catfile($model_dir, 'Helicobacter_pylori_26695.mod'); 27 | if (-e $modpath) { 28 | $model_file = $modpath; 29 | last; 30 | } 31 | } 32 | 33 | ok($model_file, "Found model file: $model_file"); 34 | 35 | skip('Test model file not found', 95) if !$model_file; 36 | 37 | my $factory = Bio::Tools::Run::Genemark->new( -m => $model_file, 38 | -program => 'gmhmmp'); 39 | test_skip(-tests => 95, 40 | -requires_executable => $factory); 41 | 42 | isa_ok $factory, 'Bio::Tools::Run::Genemark'; 43 | 44 | my $seqstream = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta'); 45 | my $seq = $seqstream->next_seq(); 46 | 47 | my $gmhmmp = $factory->run($seq); 48 | isa_ok $gmhmmp,'Bio::Tools::Genemark'; 49 | 50 | my $first_gene = $gmhmmp->next_prediction(); 51 | isa_ok $first_gene, 'Bio::Tools::Prediction::Gene'; 52 | is $first_gene->seq_id(), 'gi|15611071|ref|NC_000921.1|'; 53 | 54 | my $ct = 0; 55 | # may fluctuate based on the model, stop after 91 checks 56 | while (my $gene = $gmhmmp->next_prediction()) { 57 | isa_ok $gene, 'Bio::Tools::Prediction::Gene'; 58 | last if $ct++ == 90; 59 | } 60 | } 61 | 62 | 1; 63 | -------------------------------------------------------------------------------- /t/Genewise.t: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | # -*-Perl-*- 3 | ## Bioperl Test Harness Script for Modules 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 20); 9 | use_ok('Bio::Tools::Run::Genewise'); 10 | use_ok('Bio::Root::IO'); 11 | use_ok('Bio::Seq'); 12 | } 13 | 14 | my $verbose = test_debug() || -1; 15 | my @params = ('-verbose' => $verbose, 16 | 'silent' => 1, 17 | 'quiet' => 1); 18 | 19 | my $factory = Bio::Tools::Run::Genewise->new(@params); 20 | 21 | SKIP:{ 22 | test_skip(-requires_executable => $factory, -tests => 17); 23 | 24 | my $version = $factory->version; 25 | warn("version is $version\n") if $verbose > 0; 26 | isa_ok $factory,'Bio::Tools::Run::Genewise'; 27 | 28 | my $bequiet = 1; 29 | $factory->quiet($bequiet); # Suppress pseudowise messages to terminal 30 | 31 | #test with one file with 2 sequences 32 | my $inputfilename = test_input_file('road.pep'); 33 | my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename, 34 | -format => 'fasta'); 35 | my $seq1 = Bio::Seq->new(); 36 | $seq1 = $seqstream1->next_seq(); 37 | 38 | $inputfilename = test_input_file('human.genomic'); 39 | my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename, 40 | -format => 'fasta'); 41 | my $seq2 = Bio::Seq->new(); 42 | $seq2 = $seqstream2->next_seq(); 43 | 44 | my ($genes) = $factory->predict_genes($seq1, $seq2); 45 | 46 | my @transcripts = $genes->transcripts; 47 | my @feat = $transcripts[0]->exons; 48 | my $seqid = $feat[0]->seq_id; 49 | is($seqid, 'HSHNRNPA'); 50 | my ($featpair)= $feat[0]->each_tag_value('supporting_feature'); 51 | is($featpair->feature2->seq_id,'roa1_drome'); 52 | is($featpair->feature1->seq_id,'HSHNRNPA'); 53 | if( defined $version && $version eq 'wise2-2-0' ) { 54 | is($transcripts[0]->start, 1386); 55 | is($transcripts[0]->end, 3963); 56 | is($feat[0]->start, 1386); 57 | is($feat[0]->end, 1493); 58 | is($feat[0]->strand,1); 59 | is($featpair->feature2->start,26); 60 | is($featpair->feature2->end,61); 61 | is($featpair->feature2->strand,1); 62 | is($featpair->feature2->score,'253.10'); 63 | is($featpair->feature1->start,1386); 64 | is($featpair->feature1->end,1493); 65 | is($featpair->feature1->strand,1); 66 | is($featpair->feature1->score,'253.10'); 67 | } else { 68 | warn("These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values\n"); 69 | is($transcripts[0]->start, 1386); 70 | is($transcripts[0]->end, 4304); 71 | 72 | is($feat[0]->start, 1386); 73 | is($feat[0]->end, 1493); 74 | is($feat[0]->strand,1); 75 | is($featpair->feature2->start,26); 76 | is($featpair->feature2->end,61); 77 | is($featpair->feature2->strand,1); 78 | is($featpair->feature2->score,'319.10'); 79 | is($featpair->feature1->start,1386); 80 | is($featpair->feature1->end,1493); 81 | is($featpair->feature1->strand,1); 82 | is($featpair->feature1->score,'319.10'); 83 | 84 | } 85 | 86 | } -------------------------------------------------------------------------------- /t/Genscan.t: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | #-*-Perl-*- 3 | # ## Bioperl Test Harness Script for Modules 4 | # 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 6); 9 | use_ok('Bio::Tools::Run::Genscan'); 10 | use_ok('Bio::Root::IO'); 11 | } 12 | 13 | SKIP: { 14 | test_skip(-requires_env => 'GENSCANDIR', -tests => 4); 15 | 16 | my $paramfile = Bio::Root::IO->catfile($ENV{'GENSCANDIR'},"HumanIso.smat"); 17 | my @params = ('MATRIX',$paramfile); 18 | my $factory = Bio::Tools::Run::Genscan->new(@params); 19 | isa_ok $factory, 'Bio::Tools::Run::Genscan'; 20 | ok $factory->matrix; 21 | 22 | my $inputfilename = test_input_file("Genscan.FastA"); 23 | my $seq1 = Bio::Seq->new(); 24 | my $seqstream = Bio::SeqIO->new(-file => $inputfilename, -format => 'Fasta'); 25 | $seq1 = $seqstream->next_seq(); 26 | 27 | test_skip(-requires_executable => $factory, 28 | -tests => 2); 29 | 30 | $factory->quiet(1); 31 | my @feat = $factory->predict_genes($seq1); 32 | 33 | my $protein = $feat[0]->predicted_protein(); 34 | 35 | isa_ok $feat[0], "Bio::SeqFeatureI"; 36 | isa_ok $protein, "Bio::PrimarySeqI"; 37 | } -------------------------------------------------------------------------------- /t/Gerp.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | 9 | test_begin(-tests => 33); 10 | 11 | use_ok('Bio::Tools::Run::Phylo::Gerp'); 12 | use_ok('Bio::AlignIO'); 13 | use_ok('Bio::TreeIO'); 14 | use_ok('Bio::Root::Utilities'); 15 | } 16 | 17 | END { 18 | unlink(test_input_file('gerp', 'ENr111.mfa')); 19 | } 20 | 21 | # setup input files etc 22 | my $alignfilename = test_input_file('gerp', 'ENr111.mfa.gz'); 23 | my $treefilename = test_input_file('gerp', 'ENr111.gerp.tree'); 24 | ok (-e $alignfilename, 'Found input alignment file'); 25 | ok (-e $treefilename, 'Found input tree file'); 26 | 27 | my $factory = Bio::Tools::Run::Phylo::Gerp->new(-verbose => -1, 28 | -quiet => 1); 29 | isa_ok($factory, 'Bio::Tools::Run::Phylo::Gerp'); 30 | ok $factory->can('e'), 'has a created method not in args supplied to new'; 31 | is $factory->quiet, 1, 'quiet was set'; 32 | 33 | # test default factory values 34 | is ($factory->program_dir, $ENV{'GERPDIR'}, 'program_dir returned correct default'); 35 | is ($factory->program_name(), 'gerpcol', 'Correct exe default name'); 36 | 37 | # test the program itself 38 | SKIP: { 39 | test_skip(-requires_executable => $factory, -tests => 22); 40 | 41 | my $util = Bio::Root::Utilities->new(); 42 | $alignfilename = $util->uncompress(-file => $alignfilename, 43 | -tmp => 1); 44 | 45 | skip("Couldn't uncompress the alingment input file", 22) unless $alignfilename; 46 | 47 | # using filename input 48 | ok my $parser = $factory->run($alignfilename, $treefilename), 'got results using filename input'; 49 | my @result1; 50 | while (my $result = $parser->next_result) { 51 | push(@result1, $result); 52 | } 53 | ok close_enough(scalar(@result1), 121, 20), 'reasonable number of results using filename input'; 54 | 55 | # using SimpleAlign and Bio::Tree::Tree input 56 | my $alignio = Bio::AlignIO->new(-file => $alignfilename); 57 | my $aln = $alignio->next_aln; 58 | my $treeio = Bio::TreeIO->new(-verbose => -1, -file => $treefilename); 59 | my $tree = $treeio->next_tree; 60 | ok $parser = $factory->run($aln, $tree), 'got results using object input'; 61 | my @result2; 62 | while (my $result = $parser->next_result) { 63 | push(@result2, $result); 64 | } 65 | ok close_enough(scalar(@result2), 121, 20), 'reasonable number of results using object input'; 66 | 67 | # spot-test the results 68 | my @spot_results = ($result1[0], $result1[1], $result1[2]); 69 | 70 | foreach my $expected ([294576, 294688, 56.5, 1.76552e-57], 71 | [337735, 337898, 50.9, 3.19063e-57], 72 | [285430, 285608, 44.3, 1.41149e-54]) { 73 | my $feat = shift(@spot_results); 74 | isa_ok $feat, 'Bio::SeqFeature::Annotated'; 75 | is $feat->source->value, 'GERP', 'correct source'; 76 | ok close_enough($feat->start, shift(@{$expected}), 10), 'feature start close enough'; 77 | ok close_enough($feat->end, shift(@{$expected}), 10), 'feature end close enough'; 78 | ok close_enough($feat->score, shift(@{$expected}), 5), 'feature score close enough'; 79 | my ($p_value) = $feat->get_Annotations('pvalue'); 80 | ok close_enough(ref $p_value ? $p_value->value : $p_value, shift(@{$expected}), 100e-57), 'feature pvalue close enough'; 81 | } 82 | } 83 | 84 | sub close_enough { 85 | my ($actual, $expected, $variance) = @_; 86 | return 1 if $actual == $expected; 87 | 88 | if ($actual >= ($expected - $variance) && 89 | $actual <= ($expected + $variance)) { 90 | return 1; 91 | } 92 | return 0; 93 | } 94 | -------------------------------------------------------------------------------- /t/Glimmer2.t: -------------------------------------------------------------------------------- 1 | #-*-Perl-*- 2 | # ## Bioperl Test Harness Script for Modules 3 | # # 4 | use strict; 5 | use vars qw($NTESTS); 6 | 7 | BEGIN { 8 | use Bio::Root::Test; 9 | $NTESTS = 217; 10 | test_begin(-tests => $NTESTS, 11 | -requires_modules => [qw(IPC::Run)]); 12 | use_ok('Bio::Tools::Run::Glimmer'); 13 | use_ok('Bio::Root::IO'); 14 | use_ok('Bio::Seq'); 15 | } 16 | 17 | my $fasta_file = test_input_file('H_pylori_J99.fasta'); 18 | my $icm_file = test_input_file('H_pylori_J99.glimmer2.icm'); 19 | 20 | my $factory = Bio::Tools::Run::Glimmer->new(-program => 'glimmer2', 21 | -model => $icm_file); 22 | isa_ok $factory, 'Bio::Tools::Run::Glimmer'; 23 | 24 | my $seqstream = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta'); 25 | my $seq = $seqstream->next_seq(); 26 | 27 | SKIP: { 28 | test_skip(-requires_executable => $factory, -tests => 213); 29 | 30 | my $glimmer2 = $factory->run($seq); 31 | isa_ok $glimmer2, 'Bio::Tools::Glimmer'; 32 | 33 | my $first_gene = $glimmer2->next_prediction(); 34 | isa_ok $first_gene, 'Bio::SeqFeature::Generic'; 35 | is $first_gene->seq_id(), 'gi|15611071|ref|NC_000921.1|'; 36 | 37 | while (my $gene = $glimmer2->next_prediction()) { 38 | isa_ok $gene, 'Bio::SeqFeature::Generic'; 39 | } 40 | } 41 | 42 | 1; 43 | -------------------------------------------------------------------------------- /t/Glimmer3.t: -------------------------------------------------------------------------------- 1 | #-*-Perl-*- 2 | # ## Bioperl Test Harness Script for Modules 3 | # # 4 | use strict; 5 | use vars qw($NTESTS); 6 | 7 | BEGIN { 8 | use Bio::Root::Test; 9 | $NTESTS = 111; 10 | test_begin(-tests => $NTESTS, 11 | -requires_modules => [qw(IPC::Run)]); 12 | use_ok('Bio::Tools::Run::Glimmer'); 13 | use_ok('Bio::Root::IO'); 14 | use_ok('Bio::Seq'); 15 | } 16 | 17 | my $fasta_file = test_input_file('H_pylori_J99.fasta'); 18 | my $icm_file = test_input_file('H_pylori_J99.glimmer3.icm'); 19 | 20 | my $factory = Bio::Tools::Run::Glimmer->new(-program => 'glimmer3', 21 | -model => $icm_file); 22 | isa_ok $factory, 'Bio::Tools::Run::Glimmer'; 23 | 24 | my $seqstream = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta'); 25 | my $seq = $seqstream->next_seq(); 26 | 27 | SKIP: { 28 | test_skip(-requires_executable => $factory, -tests => 107); 29 | 30 | my $glimmer3 = $factory->run($seq); 31 | isa_ok $glimmer3, 'Bio::Tools::Glimmer'; 32 | 33 | while (my $gene = $glimmer3->next_prediction()) { 34 | isa_ok $gene, 'Bio::SeqFeature::Generic'; 35 | } 36 | } 37 | 38 | 1; 39 | -------------------------------------------------------------------------------- /t/Hyphy.t: -------------------------------------------------------------------------------- 1 | # This is -*-Perl-*- code 2 | ## Bioperl Test Harness Script for Modules 3 | ## 4 | 5 | 6 | use strict; 7 | 8 | BEGIN { 9 | use Bio::Root::Test; 10 | test_begin(-tests => 10, 11 | -requires_module =>'IO::String'); 12 | 13 | use_ok('Bio::Tools::Run::Phylo::Hyphy::SLAC'); 14 | use_ok('Bio::Tools::Run::Phylo::Hyphy::FEL'); 15 | use_ok('Bio::Tools::Run::Phylo::Hyphy::REL'); 16 | use_ok('Bio::Tools::Run::Phylo::Hyphy::Modeltest'); 17 | use_ok('Bio::Tools::Run::Phylo::Hyphy::BatchFile'); 18 | } 19 | 20 | 21 | SKIP: { 22 | my $rel = Bio::Tools::Run::Phylo::Hyphy::REL->new(); 23 | 24 | test_skip(-requires_executable => $rel, 25 | -tests => 5); 26 | 27 | my $alignio = Bio::AlignIO->new(-format => 'fasta', 28 | -file => 't/data/hyphy1.fasta'); 29 | 30 | my $treeio = Bio::TreeIO->new(-format => 'newick', 31 | -file => 't/data/hyphy1.tree'); 32 | 33 | my $aln = $alignio->next_aln; 34 | my $tree = $treeio->next_tree; 35 | my $debug = test_debug(); 36 | my ($rc,$results); 37 | 38 | $rel->alignment($aln); 39 | $rel->tree($tree); 40 | ($rc,$results) = $rel->run(); 41 | if (($rc == 0) && ($debug == 1)){ 42 | warn("ERROR in REL module $rc:" . $rel->error_string() . "\n"); 43 | } 44 | ok ($rc != 0, "REL module"); 45 | 46 | my $fel = Bio::Tools::Run::Phylo::Hyphy::FEL->new(); 47 | $fel->alignment($aln); 48 | $fel->tree($tree); 49 | ($rc,$results) = $fel->run(); 50 | if (($rc == 0) && ($debug == 1)){ 51 | warn("ERROR in FEL module $rc:" . $fel->error_string() . "\n"); 52 | } 53 | ok (defined($results->{'LRT'}), "FEL module"); 54 | 55 | my $modeltest = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new(); 56 | $modeltest->alignment($aln); 57 | $modeltest->tree($tree); 58 | ($rc,$results) = $modeltest->run(); 59 | if (($rc == 0) && ($debug == 1)){ 60 | warn("ERROR in Modeltest module $rc:" . $modeltest->error_string() . "\n"); 61 | } 62 | ok (defined($results->{'AIC'}), "Modeltest module"); 63 | 64 | my $bf_exec = Bio::Tools::Run::Phylo::Hyphy::BatchFile->new( 65 | -params => {'bf' => "ModelTest.bf", 66 | 'order' => [$aln, $tree, '4', 'AIC Test', ""]} 67 | ); 68 | $bf_exec->alignment($aln); 69 | $bf_exec->tree($tree); 70 | my ($tfh, $t) = $bf_exec->io->tempfile; 71 | $bf_exec->set_parameter(5, $t); 72 | $bf_exec->version(); 73 | ($rc,$results) = $bf_exec->run(); 74 | if (($rc == 0) && ($debug == 1)){ 75 | warn("ERROR in Batchfile module $rc:" . $bf_exec->error_string() . "\n"); 76 | } 77 | ok ($rc != 0, "Batchfile module"); 78 | 79 | my $slac = Bio::Tools::Run::Phylo::Hyphy::SLAC->new(); 80 | $slac->alignment($aln); 81 | $slac->tree($tree); 82 | ($rc,$results) = $slac->run(); 83 | if (($rc == 0) && ($debug == 1)){ 84 | warn("ERROR in SLAC module $rc:" . $slac->error_string() . "\n"); 85 | } 86 | ok (defined($results->{'Observed NS Changes'}), "SLAC module"); 87 | } 88 | -------------------------------------------------------------------------------- /t/Kalign.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | BEGIN { 6 | use Bio::Root::Test; 7 | test_begin(-tests => 8); 8 | use_ok('Bio::Tools::Run::Alignment::Kalign'); 9 | use_ok('Bio::AlignIO'); 10 | use_ok('Bio::SeqIO'); 11 | } 12 | 13 | END { unlink qw(cysprot.dnd cysprot1a.dnd) } 14 | 15 | my @params = (); 16 | my $factory = Bio::Tools::Run::Alignment::Kalign->new(@params); 17 | my $inputfilename = test_input_file("cysprot.fa"); 18 | my $aln; 19 | 20 | SKIP: { 21 | test_skip(-requires_executable => $factory, -tests => 5); 22 | my $version = $factory->version; 23 | is($version >= 2, 1, "Code tested only on kalign versions >= 2" ); 24 | $aln = $factory->align($inputfilename); 25 | ok($aln); 26 | is( $aln->num_sequences, 7); 27 | 28 | my $str = Bio::SeqIO->new('-file' => test_input_file("cysprot.fa"), 29 | '-format' => 'Fasta'); 30 | my @seq_array =(); 31 | 32 | while ( my $seq = $str->next_seq() ) { 33 | push (@seq_array, $seq) ; 34 | } 35 | 36 | my $seq_array_ref = \@seq_array; 37 | 38 | $aln = $factory->align($seq_array_ref); 39 | is $aln->num_sequences, 7; 40 | my $s1_perid = $aln->average_percentage_identity; 41 | is(int($s1_perid), 42); 42 | } 43 | 44 | -------------------------------------------------------------------------------- /t/Lagan.t: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | #-*-Perl-*- 3 | # ## Bioperl Test Harness Script for Modules 4 | # # 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 12); 9 | use_ok('Bio::AlignIO'); 10 | use_ok('Bio::Tools::Run::Alignment::Lagan'); 11 | use_ok('Bio::Root::IO'); 12 | use_ok('Bio::SeqIO'); 13 | use_ok('Bio::Seq'); 14 | use_ok('Bio::Matrix::Mlagan'); 15 | } 16 | 17 | my $seq1 = test_input_file("lagan_dna.fa"); 18 | my $sio = Bio::SeqIO->new(-file=>$seq1,-format=>'fasta'); 19 | 20 | my $seq = $sio->next_seq; 21 | $seq->id("first_seq"); 22 | my $seq2= Bio::Seq->new(-id=>"second_seq",-seq=>$seq->seq); 23 | my $seq3= Bio::Seq->new(-id=>"third_seq",-seq=>$seq->seq); 24 | 25 | my @params = 26 | ( 27 | 'order' => "\"-gs -7 -gc -2 -mt 2 -ms -1\"", 28 | 'tree' => "\"(first_seq (second_seq third_seq))\"", 29 | 'match' => 12, 30 | 'mismatch' => -8, 31 | 'gapstart' => -50, 32 | 'gapend' => -50, 33 | 'gapcont' => -2, 34 | ); 35 | 36 | SKIP: { 37 | my $factory = Bio::Tools::Run::Alignment::Lagan->new(@params, 38 | -verbose => -1); 39 | $factory->quiet(1); 40 | isa_ok $factory,'Bio::Tools::Run::Alignment::Lagan'; 41 | test_skip(-requires_executable => $factory, 42 | -tests => 5, 43 | -requires_env => 'LAGAN_DIR'); 44 | 45 | my $simple_align= $factory->lagan($seq,$seq2); 46 | 47 | isa_ok $simple_align, 'Bio::SimpleAlign'; 48 | 49 | is $simple_align->percentage_identity, 100; 50 | 51 | my $multi = $factory->mlagan([$seq,$seq2,$seq3]); 52 | is $multi->percentage_identity, 100; 53 | 54 | my $matrix = Bio::Matrix::Mlagan->new(-values => [[qw(115 -161 -81 -161 0 -72)], 55 | [qw(-161 115 -161 -81 0 -72)], 56 | [qw(-81 -161 115 -161 0 -72)], 57 | [qw(-161 -81 -161 115 0 -72)], 58 | [qw(0 0 0 0 0 0)], 59 | [qw(-72 -72 -72 -72 0 -72)]], 60 | -gap_open => -470, 61 | -gap_continue => -25); 62 | 63 | is $factory->nuc_matrix($matrix), $matrix; 64 | #*** weak test; doesn't show the supplied matrix had any effect on results... 65 | $multi = $factory->mlagan([$seq,$seq2,$seq3]); 66 | is $multi->percentage_identity, 100; 67 | } 68 | -------------------------------------------------------------------------------- /t/MAFFT.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | # 4 | 5 | use strict; 6 | use vars qw($DEBUG); 7 | $DEBUG = test_debug(); 8 | BEGIN { 9 | use Bio::Root::Test; 10 | test_begin(-tests => 23); 11 | use_ok(' Bio::Tools::Run::Alignment::MAFFT'); 12 | use_ok(' Bio::AlignIO'); 13 | use_ok(' Bio::SeqIO'); 14 | } 15 | 16 | END { unlink qw(cysprot.dnd cysprot1a.dnd) } 17 | 18 | my @params = (-verbose => $DEBUG, 19 | 'quiet' => 1); 20 | my $factory = Bio::Tools::Run::Alignment::MAFFT->new(@params); 21 | 22 | isa_ok $factory,'Bio::Tools::Run::Alignment::MAFFT'; 23 | 24 | my $inputfilename = test_input_file("cysprot.fa"); 25 | my $aln; 26 | 27 | SKIP: { 28 | test_skip(-requires_executable => $factory, 29 | -tests => 19); 30 | 31 | $factory->executable($factory->method); 32 | 33 | my $version = $factory->version; 34 | ok($version); 35 | $aln = $factory->align($inputfilename); 36 | ok($aln); 37 | is( $aln->num_sequences, 7); 38 | 39 | my $str = Bio::SeqIO->new('-file' => test_input_file("cysprot.fa"), 40 | '-format' => 'Fasta'); 41 | my @seq_array =(); 42 | 43 | while ( my $seq = $str->next_seq() ) { 44 | push (@seq_array, $seq) ; 45 | } 46 | 47 | my $seq_array_ref = \@seq_array; 48 | 49 | $aln = $factory->align($seq_array_ref); 50 | is $aln->num_sequences, 7; 51 | my $s1_perid = $aln->average_percentage_identity; 52 | cmp_ok(int($s1_perid), '>=', 42, '42 or 43 expected'); 53 | 54 | for my $method ( grep { !/rough/ } $factory->methods ) { 55 | $factory->method($method); 56 | $aln = $factory->align($inputfilename); 57 | is $aln->num_sequences, 7; 58 | my $s1_perid = $aln->average_percentage_identity; 59 | ok($s1_perid); 60 | } 61 | 62 | SKIP: { 63 | skip("Tests require version 6 of MAFFT", 6) unless $factory->_version6; 64 | $factory->localpair(1); 65 | $aln = $factory->align( $inputfilename ); 66 | is $aln->num_sequences, 7; 67 | $s1_perid = $aln->average_percentage_identity; 68 | ok($s1_perid); 69 | 70 | $factory->globalpair(1); 71 | throws_ok { $aln = $factory->align( $inputfilename ) } 72 | qr/You can't specify more than one of/, 73 | 'More than one alignment method throws'; 74 | 75 | my @extra_params = qw/ localpair 1 maxiterate 10000 /; 76 | $factory = Bio::Tools::Run::Alignment::MAFFT->new(@params, @extra_params); 77 | isa_ok $factory,'Bio::Tools::Run::Alignment::MAFFT'; 78 | $aln = $factory->align( $inputfilename ); 79 | is $aln->num_sequences, 7; 80 | $s1_perid = $aln->average_percentage_identity; 81 | ok($s1_perid); 82 | } 83 | } 84 | -------------------------------------------------------------------------------- /t/MCS.t: -------------------------------------------------------------------------------- 1 | use strict; 2 | 3 | BEGIN { 4 | use Bio::Root::Test; 5 | 6 | test_begin(-tests => 24, 7 | -requires_modules => [qw(Config::Any)]); 8 | 9 | use_ok('Bio::Location::Atomic'); 10 | } 11 | 12 | # setup input files etc 13 | my $alignfilename = test_input_file('gumby', 'hmrd.mfa'); 14 | ok (-e $alignfilename, 'Found input alignment file'); 15 | 16 | SKIP: { 17 | test_skip(-requires_module => 'Bio::FeatureIO', 18 | -tests => 22); 19 | use_ok('Bio::Tools::Run::MCS'); 20 | use_ok('Bio::SeqFeature::Annotated'); 21 | my $factory = Bio::Tools::Run::MCS->new(-verbose => -1, 22 | -quiet => 1); 23 | isa_ok($factory, 'Bio::Tools::Run::MCS'); 24 | ok $factory->can('neutral'), 'has a created method not in args supplied to new'; 25 | is $factory->quiet, 1, 'quiet was set'; 26 | 27 | # test default factory values 28 | is ($factory->program_dir, $ENV{'MCSDIR'}, 'program_dir returned correct default'); 29 | is ($factory->program_name(), 'align2binomial.pl', 'Correct exe default name'); 30 | 31 | # test the program itself 32 | SKIP: { 33 | test_skip(-requires_executable => $factory, 34 | -tests => 15); 35 | 36 | my $alignio = Bio::AlignIO->new(-file => $alignfilename); 37 | my $align = $alignio->next_aln; 38 | 39 | my @cds_feats; 40 | foreach my $data ([47367820, 47367830], [47367850, 47367860], [47367870, 47367880]) { 41 | my $cds_feat = Bio::SeqFeature::Annotated->new( 42 | -seq_id => 'Homo_sapiens', 43 | -start => $data->[0], 44 | -end => $data->[1], 45 | -frame => 0, 46 | -strand => 1, 47 | -primary => 'CDS', 48 | -type => 'CDS', 49 | -source => 'UCSC'); 50 | push(@cds_feats, $cds_feat); 51 | } 52 | my $location = Bio::Location::Atomic->new(-start => 47367748, -end => 47427851, -strand => 1, -seq_id => 'chr1'); 53 | 54 | # run the program 55 | my @feats = $factory->run($align, $location, \@cds_feats); 56 | 57 | # spot-test the results 58 | my @spot_results = ($feats[0], $feats[1], $feats[2]); 59 | foreach my $expected ([47373765, 47373846, 1000], 60 | [47373848, 47373883, 1000], 61 | [47377883, 47377908, 1000]) { 62 | my $feat = shift(@spot_results); 63 | isa_ok $feat, 'Bio::SeqFeature::Annotated'; 64 | is $feat->source->value, 'MCS', 'correct source'; 65 | is $feat->start, shift(@{$expected}), 'feature start correct'; 66 | is $feat->end, shift(@{$expected}), 'feature end correct'; 67 | is $feat->score, shift(@{$expected}), 'feature score correct'; 68 | } 69 | } 70 | 71 | } -------------------------------------------------------------------------------- /t/MSAProbs.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | # 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 19); 9 | use_ok('Bio::Tools::Run::Alignment::MSAProbs'); 10 | use_ok('Bio::Tools::GuessSeqFormat'); 11 | use_ok('Bio::AlignIO'); 12 | use_ok('Bio::SeqIO'); 13 | use_ok('Bio::Root::IO'); 14 | use_ok('POSIX'); 15 | } 16 | 17 | END { 18 | unlink('muscle.log', 'muscle.out'); 19 | unlink qw(cysprot.dnd cysprot1a.dnd); 20 | } 21 | 22 | my @params = ('quiet' => 1); 23 | my $factory = Bio::Tools::Run::Alignment::MSAProbs->new(@params); 24 | is($factory->quiet, 1); 25 | my $inputfilename = test_input_file("cysprot.fa"); 26 | my $aln; 27 | 28 | SKIP: { 29 | test_skip(-requires_executable => $factory, 30 | -tests => 12); 31 | my $version = $factory->version; 32 | unless ($version >= 0.94) { 33 | skip("Only muscle version 0.9.4 or higher is supported by these tests. Skipping tests", 7); 34 | exit(0); 35 | } 36 | cmp_ok ($version, '>=', 0.94, "Code tested only on msaprobs versions > 0.9.4" ); 37 | $aln = $factory->align($inputfilename); 38 | ok($aln); 39 | is( $aln->num_sequences, 7); 40 | 41 | my $str = Bio::SeqIO->new('-file' => 42 | test_input_file("cysprot.fa"), 43 | '-format' => 'Fasta'); 44 | my @seq_array =(); 45 | 46 | while ( my $seq = $str->next_seq() ) { 47 | push (@seq_array, $seq) ; 48 | } 49 | 50 | my $seq_array_ref = \@seq_array; 51 | 52 | $aln = $factory->align($seq_array_ref); 53 | is $aln->num_sequences, 7; 54 | my $s1_perid = POSIX::ceil($aln->average_percentage_identity); 55 | is($s1_perid == 43, 1); 56 | 57 | my $annotfile = test_output_file(); 58 | my $outfile = test_output_file(); 59 | # add some more params 60 | @params = ('-quiet' => 1, 61 | '-verbose' => 0, 62 | '-outfile' => $outfile, 63 | '-iterations' => 5, 64 | '-clustalw' => 1, 65 | '-consistency' => 2, 66 | '-alignment_order' => 1, 67 | '-annot_file' => $annotfile, 68 | 69 | ); 70 | $factory = Bio::Tools::Run::Alignment::MSAProbs->new(@params); 71 | my @methods = qw(quiet verbose outfile iterations clustalw consistency 72 | alignment_order annot_file version num_threads); 73 | can_ok($factory, @methods); 74 | is($factory->annot_file, $annotfile,'annotation file'); 75 | $aln = $factory->align($seq_array_ref); 76 | is $aln->num_sequences, 7; 77 | $s1_perid = POSIX::ceil($aln->average_percentage_identity); 78 | is($s1_perid == 43, 1 ); 79 | 80 | my $guesser = Bio::Tools::GuessSeqFormat->new(-file => $outfile); 81 | my $type = $guesser->guess; 82 | is($type, 'clustalw', "Expected output is clustalw formatted"); 83 | $inputfilename = test_input_file("cysprot1a.fa"); 84 | $aln = $factory->align($inputfilename); 85 | is $aln->num_sequences, 3; 86 | $s1_perid = POSIX::ceil($aln->average_percentage_identity); 87 | 88 | is($s1_perid == 42, 1 ); 89 | } 90 | -------------------------------------------------------------------------------- /t/Match.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 7, 9 | -requires_modules => ['Config::Any']); 10 | } 11 | 12 | # setup input files etc 13 | my $seq_file = test_input_file('fasta.fa'); 14 | my $mxlib = test_input_file('transfac.dat'); 15 | 16 | SKIP: { 17 | test_skip(-tests => 7, 18 | -requires_module => 'Bio::FeatureIO'); 19 | 20 | use_ok('Bio::Tools::Run::Match'); 21 | my $factory = Bio::Tools::Run::Match->new(-quiet => 1, 22 | -mxlib => $mxlib); 23 | 24 | isa_ok($factory, 'Bio::Tools::Run::Match'); 25 | is $factory->mxlib, $mxlib, 'mxlib parameter was set'; 26 | 27 | # test default factory values 28 | is ($factory->program_dir, $ENV{'MATCHDIR'}, 'program_dir returned correct default'); 29 | is ($factory->program_name(), 'match', 'Correct exe default name'); 30 | 31 | # test the program itself 32 | SKIP: { 33 | test_skip(-tests => 2, 34 | -requires_module => 'Bio::FeatureIO', 35 | -requires_executable => $factory); 36 | 37 | 38 | use_ok('Bio::SeqIO'); 39 | my $si = Bio::SeqIO->new(-file => $seq_file, -format => 'fasta'); 40 | my $seq = $si->next_seq; 41 | 42 | my @results = $factory->run($seq); 43 | is @results, 246; 44 | } 45 | 46 | } -------------------------------------------------------------------------------- /t/Mdust.t: -------------------------------------------------------------------------------- 1 | use strict; 2 | use vars qw($NUMTESTS); 3 | BEGIN { 4 | use Bio::Root::Test; 5 | test_begin(-tests => 5); 6 | use_ok('Bio::Tools::Run::Mdust'); 7 | use_ok('Bio::SeqIO'); 8 | } 9 | 10 | my $input = Bio::SeqIO->new( -file => test_input_file('NM_002254.gb'), 11 | -format => 'Genbank' ); 12 | 13 | my $seq = $input->next_seq; 14 | 15 | my $mdust = Bio::Tools::Run::Mdust->new( 16 | -target => $seq, 17 | ); 18 | isa_ok $mdust, "Bio::Tools::Run::Mdust"; 19 | 20 | SKIP: { 21 | test_skip(-requires_executable => $mdust, 22 | -tests => 2); 23 | 24 | $mdust->run; 25 | 26 | my @excluded = grep { $_->primary_tag eq 'Excluded' } $seq->top_SeqFeatures; 27 | 28 | is (scalar(@excluded),3); 29 | 30 | my $input2 = Bio::SeqIO->new( -file => test_input_file('NM_002254.tfa'), 31 | -format => 'Fasta'); 32 | 33 | my $seq2 = $input2->next_seq; 34 | 35 | $mdust->coords(0); 36 | my $masked = $mdust->run($seq2); 37 | 38 | like $masked->seq, qr/N+/; 39 | } 40 | -------------------------------------------------------------------------------- /t/Molphy.t: -------------------------------------------------------------------------------- 1 | # This is -*-Perl-*- code 2 | ## Bioperl Test Harness Script for Modules 3 | ## 4 | 5 | 6 | # Before `make install' is performed this script should be runnable with 7 | # `make test'. After `make install' it should work as `perl test.t' 8 | 9 | use strict; 10 | use vars qw($NUMTESTS); 11 | 12 | my $error; 13 | my $serror; 14 | 15 | BEGIN { 16 | use Bio::Root::Test; 17 | test_begin(-tests => 10, 18 | -requires_module => 'IO::String'); 19 | use_ok('Bio::Tools::Phylo::Molphy'); # PAML parser 20 | use_ok('Bio::Tools::Run::Phylo::Molphy::ProtML'); 21 | use_ok('Bio::AlignIO'); 22 | } 23 | 24 | my $verbose = test_debug(); 25 | 26 | END { unlink('protml.eps'); } 27 | ## End of black magic. 28 | ## 29 | ## Insert additional test code below but remember to change 30 | ## the print "1..x\n" in the BEGIN block to reflect the 31 | ## total number of tests that will be run. 32 | 33 | my %args = ( 'models' => 'jtt', 34 | 'search' => 'quick', 35 | "other" => [ '-information', '-w']); 36 | my $protml = Bio::Tools::Run::Phylo::Molphy::ProtML->new(-verbose => $verbose, 37 | -flags => \%args); 38 | 39 | SKIP: { 40 | test_skip(-requires_executable => $protml, 41 | -tests => 7); 42 | 43 | my $in = Bio::AlignIO->new(-format => 'clustalw', 44 | -file => test_input_file('cel-cbr-fam.aln')); 45 | my $aln = $in->next_aln; 46 | $protml->alignment($aln); 47 | 48 | my ($rc,$results) = $protml->run(); 49 | is($rc,1); 50 | my $r = $results->next_result; 51 | ok($r); 52 | my @trees; 53 | while( my $t = $r->next_tree ) { 54 | push @trees, $t; 55 | } 56 | is(@trees,1); 57 | is($r->model, 'JTT'); 58 | is($r->search_space,50); 59 | is($trees[0]->score, -453.1); 60 | ok($protml->error_string !~ /Error/); # we don't expect any errors; 61 | 62 | } -------------------------------------------------------------------------------- /t/Muscle.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin( -tests => 16 ); 9 | use_ok('Bio::Tools::Run::Alignment::Muscle'); 10 | use_ok('Bio::AlignIO'); 11 | use_ok('Bio::SeqIO'); 12 | use_ok('Bio::Root::IO'); 13 | use_ok('POSIX'); 14 | } 15 | 16 | END { 17 | unlink qw(cysprot.dnd cysprot1a.dnd muscle.log muscle.out mlc); 18 | } 19 | 20 | my @params = ( 'quiet' => 1 ); 21 | my $factory = Bio::Tools::Run::Alignment::Muscle->new(@params); 22 | is( $factory->quiet, 1 ); 23 | my $inputfilename = test_input_file("cysprot.fa"); 24 | my $aln; 25 | 26 | SKIP: { 27 | test_skip( 28 | -requires_executable => $factory, 29 | -tests => 10 30 | ); 31 | 32 | my $version = $factory->version; 33 | unless ( $version >= 3.6 ) { 34 | skip( 35 | "Only muscle version 3.6 or higher is supported by these tests. Skipping tests", 36 | 7 37 | ); 38 | exit(0); 39 | } 40 | cmp_ok( $version, '>=', 3.6, "Code tested only on muscle versions > 3.6" ); 41 | 42 | $aln = $factory->align($inputfilename); 43 | ok($aln); 44 | is( $aln->num_sequences, 7 ); 45 | 46 | my $str = Bio::SeqIO->new( 47 | -file => test_input_file("cysprot.fa"), 48 | -format => 'Fasta' 49 | ); 50 | my @seq_array = (); 51 | while ( my $seq = $str->next_seq() ) { 52 | push( @seq_array, $seq ); 53 | } 54 | my $seq_array_ref = \@seq_array; 55 | 56 | $aln = $factory->align($seq_array_ref); 57 | is $aln->num_sequences, 7; 58 | my $s1_perid = POSIX::ceil( $aln->average_percentage_identity ); 59 | is( $s1_perid == 43 || $s1_perid == 44, 60 | 1, 'diff versions of MUSCLE have different vals' ); 61 | 62 | my $logfile = test_output_file(); 63 | my $outfile = test_output_file(); 64 | 65 | # add some more params 66 | my @params = ( 67 | 'quiet' => 1, 68 | '-outfile_name' => $outfile, 69 | 'diags' => 1, 70 | 'maxmb' => 50, 71 | 'maxhours' => 1, 72 | 'maxiters' => 20, 73 | 'log' => $logfile, 74 | -seqtype => 'protein', 75 | ); 76 | $factory = Bio::Tools::Run::Alignment::Muscle->new(@params); 77 | is( $factory->log, $logfile, 'log file' ); 78 | $aln = $factory->align($seq_array_ref); 79 | is $aln->num_sequences, 7; 80 | $s1_perid = POSIX::ceil( $aln->average_percentage_identity ); 81 | is( $s1_perid == 43 || $s1_perid == 44, 82 | 1, 'diff versions of MUSCLE have different vals' ); 83 | 84 | $inputfilename = test_input_file("cysprot1a.fa"); 85 | $aln = $factory->align($inputfilename); 86 | is $aln->num_sequences, 3; 87 | $s1_perid = POSIX::ceil( $aln->average_percentage_identity ); 88 | 89 | is( $s1_perid == 41 || $s1_perid == 42, 90 | 1, 'diff versions of MUSCLE have different vals' ); 91 | } -------------------------------------------------------------------------------- /t/Njtree.t: -------------------------------------------------------------------------------- 1 | # This is -*-Perl-*- code 2 | ## Bioperl Test Harness Script for Modules 3 | ## 4 | 5 | # Before `make install' is performed this script should be runnable with 6 | # `make test'. After `make install' it should work as `perl test.t' 7 | 8 | use strict; 9 | 10 | BEGIN { 11 | use Bio::Root::Test; 12 | test_begin(-tests => 6, 13 | -requires_module => 'IO::String'); 14 | use_ok('Bio::Root::IO'); 15 | use_ok('Bio::Tools::Run::Phylo::Njtree::Best'); 16 | use_ok('Bio::AlignIO'); 17 | use_ok('Bio::TreeIO'); 18 | } 19 | 20 | ok my $njtree_best = Bio::Tools::Run::Phylo::Njtree::Best->new(); 21 | 22 | SKIP: { 23 | test_skip(-requires_executable => $njtree_best, 24 | -tests => 1); 25 | 26 | my $alignio = Bio::AlignIO->new(-format => 'fasta', 27 | -file => test_input_file('njtree_aln2.nucl.mfa')); 28 | my $aln = $alignio->next_aln; 29 | 30 | my $treeio = Bio::TreeIO->new( 31 | -format => 'nhx', 32 | -file => test_input_file('species_tree_njtree.nh')); 33 | my $tree = $treeio->next_tree; 34 | 35 | $njtree_best->alignment($aln); 36 | $njtree_best->tree($tree); 37 | $njtree_best->check_names(); 38 | 39 | my ($rc,$nhx_tree) = $njtree_best->run(); 40 | print $njtree_best->error_string, "\n"; 41 | ok $nhx_tree; 42 | 43 | #*** where are the tests?! 44 | } 45 | -------------------------------------------------------------------------------- /t/Pal2Nal.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 9); 9 | use_ok('Bio::Tools::Run::Alignment::Pal2Nal'); 10 | } 11 | 12 | # setup input files etc 13 | my $nucleotide_filename = test_input_file('pal2nal.nuc'); 14 | my $protein_alignfilename = test_input_file('pal2nal.aln'); 15 | my $mxlib = test_input_file('transfac.dat'); 16 | 17 | my $factory = Bio::Tools::Run::Alignment::Pal2Nal->new(); 18 | 19 | isa_ok($factory, 'Bio::Tools::Run::Alignment::Pal2Nal'); 20 | 21 | # test default factory values 22 | is ($factory->program_dir, $ENV{'PAL2NALDIR'}, 'program_dir returned correct default'); 23 | is ($factory->program_name(), 'pal2nal.pl', 'Correct exe default name'); 24 | 25 | # test the program itself 26 | SKIP: { 27 | test_skip(-requires_executable => $factory, 28 | -tests => 5); 29 | 30 | # Run Pal2Nal with a protein alignment file and a multi-fasta nucleotide 31 | # file 32 | ok my $aln1 = $factory->run($protein_alignfilename, $nucleotide_filename); 33 | 34 | # or with Bioperl objects 35 | use_ok('Bio::AlignIO'); 36 | use_ok('Bio::SeqIO'); 37 | my $ai = Bio::AlignIO->new(-file => $protein_alignfilename); 38 | my $protein_bio_simplalign = $ai->next_aln; 39 | my $si = Bio::SeqIO->new(-file => $nucleotide_filename, -format => 'fasta'); 40 | my $nucleotide_bio_seq1 = $si->next_seq; 41 | my $nucleotide_bio_seq2 = $si->next_seq; 42 | ok my $aln2 = $factory->run($protein_bio_simplalign, 43 | [$nucleotide_bio_seq1, $nucleotide_bio_seq2]); 44 | 45 | is_deeply($aln1, $aln2); 46 | } 47 | -------------------------------------------------------------------------------- /t/Primate.t: -------------------------------------------------------------------------------- 1 | ## Bioperl Test Harness Script for Modules 2 | 3 | # Before `make install' is performed this script should be runnable with 4 | # `make test'. After `make install' it should work as `perl test.t' 5 | 6 | use strict; 7 | 8 | BEGIN { 9 | use Bio::Root::Test; 10 | test_begin(-tests => 8); 11 | use_ok('Bio::Tools::Run::Primate'); 12 | use_ok('Bio::SeqIO'); 13 | } 14 | 15 | my $verbose = 0; 16 | 17 | my $query = test_input_file('primate_query.fa'); 18 | my $target= test_input_file('primate_target.fa'); 19 | 20 | my @params = ("query" => $query,"target" => $target,"m"=>0,"b"=>"TRUE"); 21 | my $fact = Bio::Tools::Run::Primate->new(@params); 22 | 23 | SKIP: { 24 | test_skip(-requires_executable => $fact, 25 | -tests => 6); 26 | 27 | isa_ok($fact,"Bio::Tools::Run::Primate"); 28 | my @feat = $fact->search; 29 | 30 | isa_ok ($feat[0],"Bio::SeqFeature::Generic"); 31 | 32 | is ($feat[2]->start,11); 33 | is ($feat[5]->end,33); 34 | is ($feat[6]->seq->seq,"TATTTCTAC"); 35 | is ($feat[12]->strand,-1); 36 | 37 | } -------------------------------------------------------------------------------- /t/Primer3.t: -------------------------------------------------------------------------------- 1 | #-*-Perl-*- 2 | # 3 | 4 | # test for Bio::Tools::Run::Primer3 5 | # written by Rob Edwards 6 | 7 | use strict; 8 | 9 | BEGIN { 10 | use Bio::Root::Test; 11 | test_begin(-tests => 9, 12 | -requires_module => 'Clone'); 13 | use_ok('Bio::Tools::Run::Primer3'); 14 | use_ok('Bio::SeqIO'); 15 | } 16 | 17 | my ($seqio, $seq, $primer3, $args, $results, $num_results); 18 | $seqio=Bio::SeqIO->new(-file => test_input_file('Primer3.fa')); 19 | $seq=$seqio->next_seq; 20 | 21 | ok $primer3 = Bio::Tools::Run::Primer3->new(-seq=>$seq); 22 | 23 | SKIP: { 24 | test_skip(-requires_executable => $primer3, 25 | -tests => 6); 26 | my $v = $primer3->version; 27 | skip("Primer3 wrapper only supports Primer3 v1", 6) if 28 | !defined $v || $v ge '1.2'; 29 | $args = $primer3->arguments; 30 | is($$args{'PRIMER_SEQUENCE_ID'}, "(string, optional) an id. Optional. Note must be present if PRIMER_FILE_FLAG is set"); 31 | ok $primer3->add_targets('PRIMER_SEQUENCE_ID'=>'test seq'); 32 | ok $results = $primer3->run; 33 | is( $num_results = $results->number_of_results,5); 34 | is( $results->{input_options}->{PRIMER_SEQUENCE_ID},'test seq'); 35 | like( $primer3->program_name, qr/primer3/, 'program_name'); 36 | } 37 | -------------------------------------------------------------------------------- /t/Prints.t: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | #-*-Perl-*- 3 | # ## Bioperl Test Harness Script for Modules 4 | # # 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 7); 9 | use_ok('Bio::Tools::Run::Prints'); 10 | use_ok('Bio::SeqIO'); 11 | use_ok('Bio::Seq'); 12 | } 13 | 14 | my $db = test_input_file("prints.dat"); 15 | my @params = ('DB' => $db); 16 | 17 | my $factory = Bio::Tools::Run::Prints->new(@params); 18 | isa_ok $factory,'Bio::Tools::Run::Prints'; 19 | my $prot_file= test_input_file('Prints_prot.FastA'); 20 | 21 | my $seq1 = Bio::Seq->new(); 22 | my $seqstream = Bio::SeqIO->new(-file => $prot_file, -fmt => 'Fasta'); 23 | $seq1 = $seqstream->next_seq(); 24 | 25 | SKIP: { 26 | test_skip(-requires_executable => $factory, 27 | -tests => 3); 28 | my @feat = $factory->predict_protein_features($seq1); 29 | 30 | isa_ok $feat[0],'Bio::SeqFeatureI'; 31 | is ($feat[0]->start,29); 32 | is ($feat[0]->end,53); 33 | } 34 | 35 | -------------------------------------------------------------------------------- /t/Probalign.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | # 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 13); 9 | 10 | use_ok('Bio::Tools::Run::Alignment::Probalign'); 11 | use_ok('Bio::AlignIO'); 12 | use_ok('Bio::SeqIO'); 13 | use_ok('Cwd', qw(cwd)); 14 | use_ok('POSIX'); 15 | } 16 | 17 | END { unlink qw(cysprot.dnd cysprot1a.dnd) } 18 | 19 | END { 20 | unlink('probalign.log', 'probalign.out'); 21 | } 22 | 23 | my @params = (); 24 | my $factory = Bio::Tools::Run::Alignment::Probalign->new(@params); 25 | my $inputfilename = test_input_file('cysprot.fa'); 26 | my $aln; 27 | 28 | SKIP: { 29 | test_skip(-requires_executable => $factory, 30 | -tests => 8); 31 | my $version = $factory->version; 32 | cmp_ok ($version, '>=', 3.3,"Code tested only on probalign versions > 3.3" ); 33 | $aln = $factory->align($inputfilename); 34 | ok($aln); 35 | is( $aln->num_sequences, 7); 36 | 37 | my $str = Bio::SeqIO->new('-file' => $inputfilename, 38 | '-format' => 'Fasta'); 39 | my @seq_array =(); 40 | 41 | while ( my $seq = $str->next_seq() ) { 42 | push (@seq_array, $seq) ; 43 | } 44 | 45 | my $seq_array_ref = \@seq_array; 46 | 47 | $aln = $factory->align($seq_array_ref); 48 | is $aln->num_sequences, 7; 49 | my $s1_perid = POSIX::ceil($aln->average_percentage_identity); 50 | is($s1_perid == 43 || $s1_perid == 44, 1, 51 | 'diff versions of PROBALIGN have different vals'); 52 | 53 | my $outfile = test_output_file(); 54 | # add some more params 55 | @params = ('-outfile_name' => $outfile); 56 | $factory = Bio::Tools::Run::Alignment::Probalign->new(@params); 57 | $aln = $factory->align($seq_array_ref); 58 | is $aln->num_sequences, 7; 59 | $s1_perid = POSIX::ceil($aln->average_percentage_identity); 60 | is($s1_perid == 43 || $s1_perid == 44, 1, 61 | 'diff versions of PROBALIGN have different vals'); 62 | 63 | 64 | $inputfilename = test_input_file("cysprot1a.fa"); 65 | $aln = $factory->align($inputfilename); 66 | is $aln->num_sequences, 3; 67 | $s1_perid = POSIX::ceil($aln->average_percentage_identity); 68 | 69 | is($s1_perid == 41 || $s1_perid == 42, 1, 70 | 'diff versions of PROBALIGN have different vals'); 71 | } 72 | -------------------------------------------------------------------------------- /t/Probcons.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | BEGIN { 6 | use Bio::Root::Test; 7 | test_begin(-tests => 11); 8 | use_ok(' Bio::Tools::Run::Alignment::Probcons'); 9 | use_ok(' Bio::AlignIO'); 10 | use_ok(' Bio::SeqIO'); 11 | } 12 | 13 | END { unlink qw(cysprot.dnd cysprot1a.dnd) } 14 | 15 | my @params = (); 16 | my $factory = Bio::Tools::Run::Alignment::Probcons->new(@params); 17 | my $inputfilename = test_input_file('cysprot.fa'); 18 | my $aln; 19 | 20 | SKIP: { 21 | test_skip(-requires_executable => $factory, 22 | -tests => 8); 23 | my $version = $factory->version; 24 | cmp_ok ($version, '>=', 1.09, "Code tested only on probcons versions > 1.09" ); 25 | $aln = $factory->align($inputfilename); 26 | ok($aln); 27 | is( $aln->num_sequences, 7); 28 | 29 | my $str = Bio::SeqIO->new('-file' => $inputfilename, 30 | '-format' => 'Fasta'); 31 | my @seq_array =(); 32 | 33 | while ( my $seq = $str->next_seq() ) { 34 | push (@seq_array, $seq) ; 35 | } 36 | 37 | my $seq_array_ref = \@seq_array; 38 | 39 | $aln = $factory->align($seq_array_ref); 40 | is $aln->num_sequences, 7; 41 | my $s1_avg_perid = $aln->average_percentage_identity; 42 | is(int($s1_avg_perid), 43); 43 | my $s1_ovl_perid = $aln->overall_percentage_identity; 44 | is(int($s1_ovl_perid), 15); 45 | 46 | my ($paramsfilename) = test_output_file(); 47 | my ($annotfilename) = test_output_file(); 48 | my ($dummyfilename) = test_output_file(); 49 | my $factory2 = Bio::Tools::Run::Alignment::Probcons->new 50 | ( 51 | 'iterative-refinement' => '1000', 52 | 'consistency' => '5', 53 | 'emissions' => '', 54 | 'verbose' => '', 55 | 'train' => $paramsfilename, 56 | ); 57 | $factory2->outfile_name($dummyfilename); 58 | 59 | my $aln2 = $factory2->align($seq_array_ref); 60 | $aln2 = ''; 61 | $factory2 = ''; 62 | 63 | $factory2 = Bio::Tools::Run::Alignment::Probcons->new 64 | ( 65 | 'iterative-refinement' => '1000', 66 | 'consistency' => '5', 67 | 'annot' => $annotfilename, 68 | 'paramfile' => $paramsfilename, 69 | ); 70 | $factory->outfile_name($dummyfilename); 71 | $aln2 = $factory2->align($seq_array_ref); 72 | my $s2_avg_perid = $aln2->average_percentage_identity; 73 | my $s2_ovl_perid = $aln2->overall_percentage_identity; 74 | cmp_ok(int($s2_avg_perid), '>=', 42); 75 | cmp_ok(int($s2_ovl_perid), '>=', 15); 76 | } 77 | 78 | END { 79 | if (-e 'iterative-refinement') { 80 | unlink('iterative-refinement'); 81 | } 82 | } -------------------------------------------------------------------------------- /t/Profile.t: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | #-*-Perl-*- 3 | # ## Bioperl Test Harness Script for Modules 4 | # # 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 7); 9 | use_ok('Bio::Tools::Run::Profile'); 10 | use_ok('Bio::SeqIO'); 11 | use_ok('Bio::Seq'); 12 | } 13 | 14 | my @params; 15 | my $db = test_input_file('prosite.dat'); 16 | push @params, ('DB',$db); 17 | my $factory = Bio::Tools::Run::Profile->new(@params); 18 | isa_ok $factory,'Bio::Tools::Run::Profile'; 19 | my $prot_file= test_input_file('profile_prot.FastA'); 20 | 21 | my $seq1 = Bio::Seq->new(); 22 | my $seqstream = Bio::SeqIO->new(-file =>$prot_file, -fmt =>'Fasta'); 23 | $seq1 = $seqstream->next_seq(); 24 | 25 | SKIP: { 26 | test_skip(-requires_executable => $factory, 27 | -tests => 3); 28 | 29 | my @feat = $factory->predict_protein_features($seq1); 30 | 31 | isa_ok $feat[0],'Bio::SeqFeatureI'; 32 | ok ($feat[0]->start, 15); 33 | ok ($feat[0]->end, 340); 34 | 35 | } 36 | -------------------------------------------------------------------------------- /t/Promoterwise.t: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | # -*-Perl-*- 3 | ## Bioperl Test Harness Script for Modules 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 9); 9 | use_ok('Bio::Tools::Run::Promoterwise'); 10 | use_ok('Bio::Seq'); 11 | } 12 | 13 | my $verbose = -1; 14 | my @params = ('-verbose' => test_debug(), 'silent' => 1, 'quiet' => 1); 15 | my $factory = Bio::Tools::Run::Promoterwise->new(@params); 16 | isa_ok $factory,'Bio::Tools::Run::Promoterwise'; 17 | 18 | SKIP: { 19 | test_skip(-requires_executable => $factory, 20 | -tests => 6); 21 | 22 | my $bequiet = 1; 23 | $factory->quiet($bequiet); # Suppress pseudowise messages to terminal 24 | 25 | #test with one file with 2 sequences 26 | my $inputfilename = test_input_file('sim4_cdna.fa'); 27 | my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename, 28 | -format => 'fasta'); 29 | my $seq1 = Bio::Seq->new(); 30 | $seq1 = $seqstream1->next_seq(); 31 | 32 | $inputfilename = test_input_file('sim4_genomic.fa'); 33 | my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename, 34 | -format => 'fasta'); 35 | my $seq2 = Bio::Seq->new(); 36 | $seq2 = $seqstream2->next_seq(); 37 | 38 | my @fp = $factory->run($seq1, $seq2); 39 | my $first = $fp[0]->feature1; 40 | my $second = $fp[0]->feature2; 41 | 42 | my @sub = $first->sub_SeqFeature; 43 | my @sub2 = $second->sub_SeqFeature; 44 | 45 | is $sub[0]->start,4; 46 | is $sub2[0]->start,29; 47 | is $sub[0]->end,18; 48 | is $sub2[0]->end,43; 49 | is $sub[0]->seq->seq,'GTTGTGCTGGGGGGG'; 50 | is $sub[0]->score,1596.49; 51 | } -------------------------------------------------------------------------------- /t/ProtDist.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | # 4 | 5 | use strict; 6 | use vars qw($DEBUG); 7 | $DEBUG = test_debug() || -1; 8 | 9 | BEGIN { 10 | use Bio::Root::Test; 11 | test_begin(-tests => 14); 12 | use_ok('Bio::Tools::Run::Phylo::Phylip::ProtDist'); 13 | } 14 | 15 | my $verbose = $DEBUG; 16 | my @params = ( 17 | 'idlength' =>30, 18 | 'model' =>'pam', 19 | 'gencode' =>'U', 20 | 'category' =>'H', 21 | 'probchange'=>'0.4', 22 | 'trans' =>'5', 23 | 'freq' =>'0.25,0.5,0.125,0.125'); 24 | 25 | my $dist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params); 26 | 27 | SKIP: { 28 | test_skip(-requires_executable => $dist_factory, 29 | -requires_module => 'Bio::Tools::Run::Alignment::Clustalw', 30 | -tests => 13); 31 | 32 | use_ok('Bio::Tools::Run::Alignment::Clustalw'); 33 | isa_ok $dist_factory,'Bio::Tools::Run::Phylo::Phylip::ProtDist'; 34 | 35 | my $model = 'KIMURA'; 36 | $dist_factory->model($model); 37 | 38 | my $new_model= $dist_factory->model(); 39 | is $new_model , 'KIMURA', "set factory parameter"; 40 | 41 | my $gencode = 'M'; 42 | $dist_factory->gencode($gencode); 43 | 44 | my $new_gencode= $dist_factory->gencode(); 45 | is $new_gencode, 'M', "set factory parameter"; 46 | 47 | my $category= "H"; 48 | $dist_factory->category($category); 49 | 50 | my $new_category= $dist_factory->category(); 51 | is $new_category, "H", "set factory parameter"; 52 | 53 | my $probchange= 0.4; 54 | $dist_factory->probchange($probchange); 55 | 56 | my $new_probchange= $dist_factory->probchange(); 57 | is $new_probchange, 0.4, "set factory parameter"; 58 | 59 | my $trans= 5; 60 | $dist_factory->trans($trans); 61 | 62 | my $new_trans= $dist_factory->trans(); 63 | is $new_trans, 5, "set factory parameter"; 64 | 65 | my $freq= "0.25,0.5,0.125,0.125"; 66 | $dist_factory->freq($freq); 67 | 68 | my $new_freq= $dist_factory->freq(); 69 | is $new_freq, "0.25,0.5,0.125,0.125", "set factory parameter"; 70 | 71 | my $bequiet = 1; 72 | $dist_factory->quiet($bequiet); # Suppress protpars messages to terminal 73 | 74 | my $inputfilename = test_input_file("protpars.phy"); 75 | my $matrix; 76 | 77 | $dist_factory->verbose($verbose); 78 | ($matrix) = $dist_factory->create_distance_matrix($inputfilename); 79 | 80 | is(sprintf("%.3f", $matrix->get_entry('ENSP000003','SINFRUP001')),0.277); 81 | 82 | $inputfilename = test_input_file("cysprot.fa"); 83 | @params = ('ktuple' => 2, 'matrix' => 'BLOSUM', 84 | -verbose => $verbose); 85 | my $align_factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); 86 | 87 | SKIP: { 88 | test_skip(-requires_executable => $align_factory, 89 | -tests => 4); 90 | 91 | my $aln = $align_factory->align($inputfilename); 92 | ($matrix) = $dist_factory->create_distance_matrix($aln); 93 | 94 | is (int($matrix->get_entry('ALEU_HORVU','ALEU_HORVU')),0, 95 | "creating distance matrix"); 96 | ok(sprintf("%.2f",$matrix->get_entry('CATL_HUMAN','CYS1_DICDI'),'1.30', "creating distance matrix")); 97 | 98 | # Test name preservation and restoration: 99 | $inputfilename = test_input_file("longnames.aln"); 100 | $aln = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln; 101 | my ($aln_safe, $ref_name) =$aln->set_displayname_safe(3); 102 | ($matrix) = $dist_factory->create_distance_matrix($aln_safe); 103 | is (int($matrix->get_entry('S03','S03')),0, "failed creating matrix on safe names"); 104 | ok(sprintf("%.4f",$matrix->get_entry('S01','S02'),'0.0205', "failed creating distance matrix")); 105 | } 106 | } 107 | 108 | -------------------------------------------------------------------------------- /t/ProtPars.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use vars qw($DEBUG ); 5 | $DEBUG = test_debug(); 6 | 7 | use strict; 8 | BEGIN { 9 | use Bio::Root::Test; 10 | test_begin(-tests => 11); 11 | use_ok('Bio::Tools::Run::Phylo::Phylip::ProtPars'); 12 | } 13 | 14 | my @params = ('threshold'=>10,'jumble'=>'17,10',outgroup=>2,'idlength'=>10); 15 | my $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params); 16 | isa_ok $tree_factory,'Bio::Tools::Run::Phylo::Phylip::ProtPars'; 17 | 18 | SKIP: { 19 | test_skip(-requires_executable => $tree_factory, 20 | -requires_module => 'Bio::Tools::Run::Alignment::Clustalw', 21 | -tests => 9); 22 | use_ok('Bio::Tools::Run::Alignment::Clustalw'); 23 | 24 | my $threshold = 5; 25 | $tree_factory->threshold($threshold); 26 | 27 | my $new_threshold= $tree_factory->threshold(); 28 | is $new_threshold, 5, "set factory parameter"; 29 | 30 | my $outgroup = 3; 31 | $tree_factory->outgroup($outgroup); 32 | 33 | my $new_outgroup= $tree_factory->outgroup(); 34 | is $new_outgroup, 3, "set factory parameter"; 35 | 36 | my $jumble = "7,5"; 37 | $tree_factory->jumble($jumble); 38 | 39 | my $new_jumble= $tree_factory->jumble(); 40 | is $new_jumble, "7,5", "set factory parameter"; 41 | 42 | my $bequiet = 1; 43 | $tree_factory->quiet($bequiet); # Suppress protpars messages to terminal 44 | 45 | my $inputfilename = test_input_file("protpars.phy"); 46 | my $tree; 47 | 48 | $tree = $tree_factory->create_tree($inputfilename); 49 | 50 | # have to sort the since there is polytomy here. 51 | my @nodes = sort { $a->id cmp $b->id } grep { $_->id } $tree->get_nodes(); 52 | is ($nodes[2]->id, 'SINFRUP002', 53 | "creating tree by protpars"); 54 | 55 | $inputfilename = test_input_file("cysprot1a.fa"); 56 | @params = ('ktuple' => 2, 'matrix' => 'BLOSUM', 57 | -verbose => -1); 58 | my $align_factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); 59 | 60 | SKIP: { 61 | test_skip(-requires_executable => $align_factory, 62 | -tests => 4); 63 | 64 | my $aln = $align_factory->align($inputfilename); 65 | 66 | $tree = $tree_factory->create_tree($aln); 67 | 68 | @nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id } $tree->get_nodes(); 69 | is (scalar(@nodes),5, "creating tree by protpars"); 70 | 71 | # test name preservation and restoration: 72 | @params = ('threshold'=>10,'jumble'=>'7,5',outgroup=>2,'idlength'=>10); 73 | $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params); 74 | $tree_factory->quiet($bequiet); # Suppress protpars messages to terminal 75 | $inputfilename = test_input_file("longnames.aln"); 76 | my $aln2 = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln; 77 | my ($aln_safe, $ref_name) = $aln2->set_displayname_safe(3); 78 | my $tree2 = $tree_factory->create_tree($aln_safe); 79 | @nodes = sort { $a->id cmp $b->id } $tree2->get_nodes(); 80 | is (scalar(@nodes),27, 81 | "creating tree by protpars"); 82 | is ($nodes[12]->id, 'S01',"assign serial names"); 83 | foreach my $nd (@nodes){ 84 | $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf; 85 | } 86 | is ($nodes[12]->id, 'Spar_21273',"restore original names"); 87 | } 88 | } 89 | -------------------------------------------------------------------------------- /t/Pseudowise.t: -------------------------------------------------------------------------------- 1 | 2 | # -*-Perl-*- 3 | ## Bioperl Test Harness Script for Modules 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 18); 9 | use_ok('Bio::Tools::Run::Pseudowise'); 10 | use_ok('Bio::Root::IO'); 11 | use_ok('Bio::Seq'); 12 | } 13 | my $DEBUG = test_debug(); 14 | 15 | #my @params = ('dymem', 'linear', 'kbyte', '5000','erroroffstd'=>1); 16 | my @params = ('erroroffstd'=>1,'-verbose' => $DEBUG, 17 | quiet => $DEBUG); 18 | my $factory = Bio::Tools::Run::Pseudowise->new(@params); 19 | ok($factory); 20 | 21 | SKIP:{ 22 | test_skip(-requires_executable => $factory, 23 | -tests => 14); 24 | 25 | warn($factory->executable."\n") if $DEBUG; 26 | isa_ok $factory, 'Bio::Tools::Run::Pseudowise'; 27 | 28 | #test with one file with 3 sequences 29 | my $inputfilename = test_input_file("ps1.fa"); 30 | my $seqstream = Bio::SeqIO->new(-file => $inputfilename, 31 | -format => 'fasta'); 32 | my $seq1 = $seqstream->next_seq(); 33 | my $seq2 = $seqstream->next_seq(); 34 | my $seq3 = $seqstream->next_seq(); 35 | 36 | my @feat = $factory->predict_genes($seq1, $seq2, $seq3); 37 | my $geneno = scalar(@feat); 38 | ok($geneno,1); 39 | my @subfeat = $feat[0]->sub_SeqFeature; 40 | my $exonno = scalar(@subfeat); 41 | 42 | is($geneno, 1); 43 | is($exonno, 2); 44 | isa_ok($feat[0],"Bio::SeqFeatureI"); 45 | isa_ok($subfeat[0],"Bio::SeqFeatureI"); 46 | is($feat[0]->primary_tag, 'pseudogene'); 47 | is($subfeat[0]->primary_tag, 'exon'); 48 | is($feat[0]->start, 163); 49 | is($subfeat[0]->start, 163); 50 | is($feat[0]->end, 626); 51 | is($subfeat[0]->end, 213); 52 | is($subfeat[1]->start,585); 53 | is($subfeat[1]->end, 626); 54 | } 55 | -------------------------------------------------------------------------------- /t/QuickTree.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 13); 9 | use_ok('Bio::Tools::Run::Phylo::QuickTree'); 10 | use_ok('Bio::AlignIO'); 11 | } 12 | 13 | 14 | # setup input files etc 15 | my $inputfilename = test_input_file('cysprot.stockholm'); 16 | ok (-e $inputfilename, 'Found input file'); 17 | 18 | my $factory = Bio::Tools::Run::Phylo::QuickTree->new(); 19 | isa_ok($factory, 'Bio::Tools::Run::Phylo::QuickTree'); 20 | 21 | # test default factory values 22 | is ($factory->program_dir, $ENV{'QUICKTREEDIR'}, 'program_dir returned correct default'); 23 | is ($factory->program_name(), 'quicktree', 'Correct exe default name'); 24 | 25 | # test the program itself 26 | SKIP: { 27 | test_skip(-requires_executable => $factory, 28 | -tests => 7); 29 | 30 | # using filename input 31 | my $tree = $factory->run($inputfilename); 32 | isa_ok($tree, 'Bio::Tree::Tree'); 33 | my @leaves = $tree->get_leaf_nodes; 34 | is (@leaves, 7, 'Result tree from filename input had correct number of leaves'); 35 | 36 | # using align input 37 | my $alignio = Bio::AlignIO->new(-file => $inputfilename); 38 | my $aln = $alignio->next_aln; 39 | $tree = $factory->run($aln); 40 | @leaves = $tree->get_leaf_nodes; 41 | is (@leaves, 7, 'Result tree from SimpleAlign input had correct number of leaves'); 42 | 43 | # do simple checks on possible options 44 | is ($factory->upgma(1), 1, 'UPGMA could be set'); 45 | is ($factory->kimura(1), 1, 'kimura could be set'); 46 | is ($factory->boot(100), 100, 'boot could be set'); 47 | $tree = $factory->run($inputfilename); 48 | 49 | my @nodes = $tree->get_nodes; 50 | my %non_internal = map { $_ => 1 } ($tree->get_leaf_nodes, $tree->get_root_node); 51 | my @bootstraps; 52 | foreach my $node (@nodes) { 53 | next if exists $non_internal{$node}; 54 | push(@bootstraps, $node->bootstrap); 55 | } 56 | is_deeply([sort { $a <=> $b } @bootstraps], [qw(74 84 100 100 100)], 'bootstraps were correct'); 57 | } 58 | -------------------------------------------------------------------------------- /t/Raxml.t: -------------------------------------------------------------------------------- 1 | # This is -*-Perl-*- code 2 | ## Bioperl Test Harness Script for Modules 3 | # Before `./Build install' is performed this script should be runnable with 4 | # `./Build test --test_files test.t'. After `./Build install' it should work as `perl test.t' 5 | 6 | use strict; 7 | 8 | BEGIN { 9 | use Bio::Root::Test; 10 | test_begin( 11 | -tests => 12, 12 | ); 13 | use_ok('Bio::Root::IO'); 14 | use_ok('Bio::Tools::Run::Phylo::Raxml'); 15 | use_ok('Bio::AlignIO'); 16 | } 17 | 18 | END { unlink glob "RAxML_*.*"; } 19 | 20 | ok(my $raxml = Bio::Tools::Run::Phylo::Raxml->new(-p => 100, -quiet => 1, -d => 1), "Make the object"); 21 | isa_ok( $raxml, 'Bio::Tools::Run::Phylo::Raxml'); 22 | 23 | SKIP: { 24 | test_skip( 25 | -requires_executable => $raxml, 26 | -tests => 7 27 | ); 28 | 29 | # The input could be an alignment file in phylip format 30 | my $alignfile = test_input_file("testaln.phylip"); 31 | my $tree = $raxml->run($alignfile); 32 | ok( defined($tree), "Tree is defined" ); 33 | 34 | # The working directory could be different, i.e. -w set 35 | $raxml->w($raxml->tempdir); 36 | $tree = $raxml->run($alignfile); 37 | ok( defined($tree), "Tree is defined" ); 38 | my $out = $raxml->w . '/RAxML_bestTree.' . $raxml->outfile_name; 39 | ok( -e $out, "File containing best tree exists in tempdir" ); 40 | 41 | # Test RAxML's rapid bootstrap option ( -f a ) 42 | $raxml = Bio::Tools::Run::Phylo::Raxml->new(-N => 100, -p => 12345, -quiet => 1, -f => 'a', -x => 1); 43 | $tree = $raxml->run($alignfile); 44 | ok( defined($tree), "Tree is defined" ); 45 | 46 | # The input could be a SimpleAlign object 47 | my $alignio = Bio::AlignIO->new( 48 | -format => 'phylip', 49 | -file => test_input_file('testaln.phylip') 50 | ); 51 | my $alnobj = $alignio->next_aln; 52 | 53 | $raxml = Bio::Tools::Run::Phylo::Raxml->new(-p => 100, -quiet => 1, -d => 1); 54 | $tree = $raxml->run($alnobj); 55 | ok( defined($tree), "Tree is defined" ); 56 | my @nodes = $tree->get_nodes; 57 | is($#nodes,5, "Number of nodes is correct"); 58 | 59 | # Input is protein sequence alignment 60 | $alignio = Bio::AlignIO->new( 61 | -format => 'msf', 62 | -file => test_input_file('cysprot.msf') 63 | ); 64 | $alnobj = $alignio->next_aln; 65 | 66 | $raxml = Bio::Tools::Run::Phylo::Raxml->new(-quiet => 1, -p => 100); 67 | my $ptree = $raxml->run($alnobj); 68 | ok( defined($ptree), "Tree is defined" ); 69 | } 70 | -------------------------------------------------------------------------------- /t/RepeatMasker.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 12); 9 | use_ok('Bio::Tools::Run::RepeatMasker'); 10 | use_ok('Bio::SeqIO'); 11 | } 12 | 13 | my $inputfilename= test_input_file('repeatmasker.fa'); 14 | my $createdfile = test_output_file(); 15 | 16 | my $verbose = test_debug(); 17 | my @params=("species" => "mammal", 'noint' => 1, 'qq' => 1, '-verbose' => $verbose); 18 | my $fact = Bio::Tools::Run::RepeatMasker->new(@params); 19 | $fact->quiet(1); 20 | 21 | SKIP: { 22 | test_skip(-requires_executable => $fact, 23 | -tests => 10); 24 | 25 | is ($fact->species, 'mammal'); 26 | is ($fact->noint,1); 27 | 28 | my $in = Bio::SeqIO->new(-file => $inputfilename , '-format' => 'fasta'); 29 | my $seq = $in->next_seq(); 30 | my @feats = $fact->mask($seq); 31 | 32 | my $version = $fact->version; 33 | 34 | is ($feats[0]->feature1->primary_tag, "Simple_repeat"); 35 | is ($feats[0]->feature1->source_tag, "RepeatMasker"); 36 | is ($feats[0]->feature2->seq_id, "(TTAGGG)n"); 37 | 38 | if( $version =~ /open-(\S+)/) { 39 | my $num = $1; 40 | if( $num ge '3.1.0' ) { 41 | is ($feats[0]->feature1->start, 1337); 42 | is ($feats[0]->feature1->end, 1411); 43 | is ($feats[0]->feature1->strand, 1); 44 | is ($feats[1]->feature1->start, 1710); 45 | is ($feats[1]->feature1->end, 2052); 46 | } elsif( $num ge '3.0.8' ) { 47 | is ($feats[0]->feature1->start, 1337); 48 | is ($feats[0]->feature1->end, 1407); 49 | is ($feats[0]->feature1->strand, 1); 50 | is ($feats[1]->feature1->start, 1712); 51 | is ($feats[1]->feature1->end, 2225); 52 | } else { 53 | skip("unknown RepeatMasker Version, cannot test",1) for ( 1..3); 54 | } 55 | } else { 56 | is ($feats[0]->feature1->start, 1337); 57 | is ($feats[0]->feature1->end, 1407); 58 | is ($feats[0]->feature1->strand, 1); 59 | } 60 | 61 | } -------------------------------------------------------------------------------- /t/SLR.t: -------------------------------------------------------------------------------- 1 | # This is -*-Perl-*- code 2 | ## Bioperl Test Harness Script for Modules 3 | ## 4 | 5 | 6 | # Before `make install' is performed this script should be runnable with 7 | # `make test'. After `make install' it should work as `perl test.t' 8 | 9 | use strict; 10 | 11 | BEGIN { 12 | use Bio::Root::Test; 13 | test_begin(-tests => 7, 14 | -requires_module => 'IO::String'); 15 | use_ok('Bio::Root::IO'); 16 | use_ok('Bio::Tools::Run::Phylo::SLR'); 17 | use_ok('Bio::AlignIO'); 18 | use_ok('Bio::TreeIO'); 19 | } 20 | 21 | ok my $slr = Bio::Tools::Run::Phylo::SLR->new(); 22 | 23 | SKIP: { 24 | test_skip(-requires_executable => $slr, 25 | -tests => 2); 26 | 27 | # first set 28 | my $alignio1 = Bio::AlignIO->new 29 | (-format => 'fasta', 30 | -file => test_input_file('219877.cdna.fasta')); 31 | 32 | my $treeio1 = Bio::TreeIO->new 33 | (-format => 'newick', 34 | -file => test_input_file('219877.tree')); 35 | 36 | my $aln1 = $alignio1->next_aln; 37 | my $tree1 = $treeio1->next_tree; 38 | 39 | $slr->alignment($aln1); 40 | $slr->tree($tree1); 41 | my ($rc,$results1) = $slr->run(); 42 | ok defined($results1); 43 | 44 | # second set 45 | $slr = Bio::Tools::Run::Phylo::SLR->new(); 46 | my $alignio2 = Bio::AlignIO->new 47 | (-format => 'fasta', 48 | -file => test_input_file('277523.cdna.fasta')); 49 | 50 | my $treeio2 = Bio::TreeIO->new 51 | (-format => 'newick', 52 | -file => test_input_file('277523.tree')); 53 | 54 | my $aln2 = $alignio2->next_aln; 55 | my $tree2 = $treeio2->next_tree; 56 | 57 | $slr->alignment($aln2); 58 | $slr->tree($tree2); 59 | my($rc2,$results2) = $slr->run(); 60 | ok defined($results2); 61 | # my $positive_sites = $results2->{'constant'}; 62 | # print "Site,Omega\n"; 63 | # foreach my $site (@{$positive_sites}) { 64 | # # print "# Site Neutral Optimal Omega lower upper LRT_Stat Pval Adj.Pval Result Note\n"; 65 | # print $site->[0], ",", $site->[3], "\n"; 66 | # } 67 | 68 | # # third set 69 | # $slr = Bio::Tools::Run::Phylo::SLR->new(); 70 | # my $alignio3 = Bio::AlignIO->new 71 | # (-format => 'fasta', 72 | # -file => 't/data/799906.cdna.fasta'); 73 | 74 | # my $treeio3 = Bio::TreeIO->new 75 | # (-format => 'newick', 76 | # -file => 't/data/799906.tree'); 77 | 78 | # my $aln3 = $alignio3->next_aln; 79 | # my $tree3 = $treeio3->next_tree; 80 | 81 | # $slr->alignment($aln3); 82 | # $slr->tree($tree3); 83 | # my ($rc,$results3) = $slr->run(); 84 | # my $sites = $results3->{'constant'}; 85 | # ok defined($results3); 86 | # print "Site,Omega\n"; 87 | # foreach my $site (@{$sites}) { 88 | # # print "# Site Neutral Optimal Omega lower upper LRT_Stat Pval Adj.Pval Result Note\n"; 89 | # print $site->[0], ",", $site->[3], "\n"; 90 | # } 91 | 92 | } 93 | -------------------------------------------------------------------------------- /t/Seg.t: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/perl 2 | #-*-Perl-*- 3 | # ## Bioperl Test Harness Script for Modules 4 | # # 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 8); 9 | use_ok('Bio::Tools::Run::Seg'); 10 | use_ok('Bio::SeqIO'); 11 | use_ok('Bio::Seq'); 12 | } 13 | 14 | my $factory = Bio::Tools::Run::Seg->new(); 15 | isa_ok $factory, 'Bio::Tools::Run::Seg'; 16 | my $prot_file= test_input_file('test_prot.FastA'); 17 | 18 | my $seq1 = Bio::Seq->new(); 19 | my $seqstream = Bio::SeqIO->new(-file =>$prot_file, -fmt =>'Fasta'); 20 | $seq1 = $seqstream->next_seq(); 21 | 22 | SKIP: { 23 | test_skip(-requires_executable => $factory, 24 | -tests => 4); 25 | 26 | my @feat = $factory->predict_protein_features($seq1); 27 | 28 | isa_ok $feat[0],'Bio::SeqFeatureI'; 29 | is ($feat[0]->start, 214); 30 | is ($feat[0]->end, 226); 31 | is ($feat[0]->score, 2.26); 32 | 33 | } 34 | -------------------------------------------------------------------------------- /t/Semphy.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 19); 9 | use_ok('Bio::Tools::Run::Phylo::Semphy'); 10 | } 11 | 12 | # setup input files 13 | my $alignfilename = test_input_file('semphy.seq'); 14 | my $treefilename = test_input_file('semphy.tree'); 15 | 16 | # object setup and testing 17 | my $factory = Bio::Tools::Run::Phylo::Semphy->new(-quiet => 1, -z => '2.0', -H => 1, -jtt => 1, -S => 1); 18 | 19 | isa_ok($factory, 'Bio::Tools::Run::Phylo::Semphy'); 20 | ok $factory->can('alphabet'), 'has a created method not in args'; 21 | is $factory->ratio, '2.0', 'ratio param was set via -z'; 22 | ok $factory->jtt, 'jtt switch was set'; 23 | 24 | is ($factory->program_dir, $ENV{'SEMPHYDIR'}, 'program_dir returned correct default'); 25 | is ($factory->program_name(), 'semphy', 'Correct exe default name'); 26 | 27 | # test the program itself 28 | SKIP: { 29 | test_skip(-requires_executable => $factory, 30 | -tests => 12); 31 | use_ok('Bio::TreeIO'); 32 | my $tree_out_file = test_output_file(); 33 | my $to = Bio::TreeIO->new(-format => 'newick', 34 | -file => ">$tree_out_file"); 35 | 36 | # run Semphy with an alignment 37 | ok my $tree1 = $factory->run($alignfilename); 38 | $to->write_tree($tree1); 39 | 40 | # or with alignment object 41 | use_ok('Bio::AlignIO'); 42 | my $ai = Bio::AlignIO->new(-file => $alignfilename); 43 | my $bio_simplalign = $ai->next_aln; 44 | ok my $tree2 = $factory->run($bio_simplalign); 45 | $to->write_tree($tree2); 46 | 47 | # you can supply an initial tree as well, which can be a newick tree file, 48 | # Bio::Tree::Tree object... 49 | my $ti = Bio::TreeIO->new(-file => $treefilename); 50 | my $tree_obj = $ti->next_tree; 51 | ok my $tree3 = $factory->run($bio_simplalign, $tree_obj); 52 | $to->write_tree($tree3); 53 | 54 | # ... or Bio::DB::Taxonomy object 55 | my $expected_count = 3; 56 | SKIP: { 57 | test_skip(-tests => 2, -requires_networking => 1); 58 | 59 | use_ok('Bio::DB::Taxonomy'); 60 | my $bio_db_taxonomy = Bio::DB::Taxonomy->new(-source => 'entrez'); 61 | ok my $tree4 = $factory->run($bio_simplalign, $bio_db_taxonomy); 62 | $to->write_tree($tree4); 63 | $expected_count++; 64 | } 65 | 66 | $to->close; 67 | 68 | my $expected_result = '(Cow:0.280119,((Baboon:0.035422,Human:0.080635):0.000213,(Rat:0.198658,Horse:0.642019):0.120910):0.074791,Semnopithecus_entellus:0.016396);'; 69 | 70 | open(my $res_fh, $tree_out_file); 71 | my $count = 0; 72 | while (<$res_fh>) { 73 | chomp; 74 | /\S/ || last; 75 | $count++; 76 | is $_, $expected_result; 77 | } 78 | close($res_fh); 79 | 80 | is $count, $expected_count; 81 | if ($expected_count == 3) { 82 | ok 1; 83 | } 84 | } 85 | -------------------------------------------------------------------------------- /t/SeqBoot.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | # 4 | 5 | use strict; 6 | use vars qw($DEBUG); 7 | $DEBUG = test_debug(); 8 | 9 | BEGIN { 10 | use Bio::Root::Test; 11 | test_begin(-tests => 9); 12 | use_ok('Bio::Tools::Run::Phylo::Phylip::SeqBoot'); 13 | use_ok('Bio::AlignIO'); 14 | } 15 | my $verbose = $DEBUG; 16 | my @params = ('-verbose' => $verbose, 17 | 'idlength' =>30, 18 | 'datatype' =>'GENEFREQ', 19 | 'REPLICATES'=>50); 20 | 21 | my $sb_factory = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params); 22 | 23 | SKIP: { 24 | test_skip(-requires_executable => $sb_factory, 25 | -tests => 7); 26 | isa_ok $sb_factory,'Bio::Tools::Run::Phylo::Phylip::SeqBoot'; 27 | 28 | my $dt= 'SEQUENCE'; 29 | $sb_factory->datatype($dt); 30 | 31 | is $sb_factory->datatype, "SEQUENCE", "couldn't set datatype parameter"; 32 | 33 | $sb_factory->replicates(2); 34 | 35 | is $sb_factory->replicates, 2, "coludn't set number of replicates"; 36 | 37 | 38 | my $bequiet = $verbose > 0 ? 0 : 1; 39 | 40 | $sb_factory->quiet($bequiet); # Suppress protpars messages to terminal 41 | 42 | my $inputfilename = test_input_file("protpars.phy"); 43 | 44 | my $aln_ref = $sb_factory->run($inputfilename); 45 | 46 | is scalar(@{$aln_ref}), 2; 47 | 48 | my $aln = Bio::AlignIO->new(-file=>$inputfilename, -format=>"phylip")->next_aln; 49 | 50 | $aln_ref = $sb_factory->run($aln); 51 | 52 | is scalar(@{$aln_ref}), 2; 53 | 54 | # Test name preservation and restoration: 55 | $inputfilename = test_input_file("longnames.aln"); 56 | $aln = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln; 57 | my ($aln_safe, $ref_name) =$aln->set_displayname_safe(); 58 | $aln_ref = $sb_factory->run($aln_safe); 59 | my $first=shift @{$aln_ref}; 60 | is $first->get_seq_by_pos(3)->id(), "S000000003", "ailed to assign serial names"; 61 | my $aln_restored=$first->restore_displayname($ref_name); 62 | is $aln_restored->get_seq_by_pos(3)->id(), "Smik_Contig1103.1", "fail to restore original names"; 63 | 64 | } 65 | -------------------------------------------------------------------------------- /t/Signalp.t: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | #-*-Perl-*- 3 | # ## Bioperl Test Harness Script for Modules 4 | # # 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 7); 9 | use_ok('Bio::Tools::Run::Signalp'); 10 | use_ok('Bio::SeqIO'); 11 | use_ok('Bio::Seq'); 12 | } 13 | 14 | my $factory = Bio::Tools::Run::Signalp->new(); 15 | isa_ok $factory,'Bio::Tools::Run::Signalp'; 16 | 17 | my $prot_file = test_input_file("signalp_input_protein"); 18 | 19 | my $seq1 = Bio::Seq->new(); 20 | my $seqstream = Bio::SeqIO->new(-file =>$prot_file, -fmt =>'Fasta'); 21 | $seq1 = $seqstream->next_seq(); 22 | 23 | SKIP: { 24 | test_skip(-requires_executable => $factory, 25 | -tests => 3); 26 | my @feat = $factory->predict_protein_features($seq1); 27 | 28 | isa_ok $feat[0],'Bio::SeqFeatureI'; 29 | is ($feat[0]->start,1); 30 | is ($feat[0]->end,29); 31 | } 32 | -------------------------------------------------------------------------------- /t/Sim4.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 23); 9 | use_ok('Bio::Tools::Run::Alignment::Sim4'); 10 | use_ok('Bio::SimpleAlign'); 11 | use_ok('Bio::AlignIO'); 12 | use_ok('Bio::SeqIO'); 13 | } 14 | 15 | my $verbose = -1; 16 | 17 | my $cdna = test_input_file("sim4_cdna.fa"); 18 | my $genomic = test_input_file("sim4_genomic.fa"); 19 | my @params = (W=>15,K=>17,D=>10,N=>10,cdna_seq=>$cdna,genomic_seq=>$genomic); 20 | my $factory = Bio::Tools::Run::Alignment::Sim4->new(@params); 21 | 22 | SKIP: { 23 | test_skip(-requires_executable => $factory, 24 | -tests => 19); 25 | isa_ok $factory,'Bio::Tools::Run::Alignment::Sim4'; 26 | my $bequiet = 1; 27 | $factory->quiet($bequiet); # Suppress clustal messages to terminal 28 | 29 | #test by having inputs in constructor 30 | my @exon_set = $factory->align; 31 | 32 | my @exons = $exon_set[0]->sub_SeqFeature; 33 | is $exons[0]->start, 26; 34 | is $exons[0]->end, 268; 35 | is $exons[0]->strand, 1; 36 | 37 | 38 | my $sio = Bio::SeqIO->new(-file=>$cdna,-format=>"fasta"); 39 | my $sio2 = Bio::SeqIO->new(-file=>$genomic,-format=>"fasta"); 40 | 41 | #test with 2 seq objs 42 | my @cdna_seq; 43 | while(my $seq = $sio->next_seq){ 44 | push @cdna_seq,$seq; 45 | } 46 | my @genomic_seq; 47 | while(my $seq = $sio2->next_seq){ 48 | push @genomic_seq,$seq; 49 | } 50 | 51 | @exon_set = $factory->align($cdna_seq[0],$genomic_seq[0]); 52 | 53 | @exons = $exon_set[0]->sub_SeqFeature; 54 | is $exons[0]->start, 26; 55 | is $exons[0]->end, 268; 56 | is $exons[0]->strand, 1; 57 | 58 | #test with cdna database as file 59 | 60 | my $db = test_input_file("sim4_database.fa"); 61 | @params = (W=>15,K=>17,D=>10,N=>10,cdna_seq=>$db,genomic_seq=>$genomic); 62 | $factory = Bio::Tools::Run::Alignment::Sim4->new(@params); 63 | 64 | @exon_set = $factory->align(); 65 | @exons = $exon_set[0]->sub_SeqFeature; 66 | is $exons[0]->start, 26; 67 | is $exons[0]->end, 268; 68 | is $exons[0]->strand, 1; 69 | 70 | @exons = $exon_set[1]->sub_SeqFeature; 71 | is $exons[0]->start, 26; 72 | is $exons[0]->end, 268; 73 | is $exons[0]->strand, 1; 74 | 75 | 76 | #test with cdna database as object 77 | 78 | $sio = Bio::SeqIO->new(-file=>$db,-format=>"fasta"); 79 | @cdna_seq=(); 80 | while(my $seq = $sio->next_seq){ 81 | push @cdna_seq,$seq; 82 | } 83 | 84 | $factory->align(\@cdna_seq,$genomic); 85 | 86 | @exon_set = $factory->align(); 87 | @exons = $exon_set[0]->sub_SeqFeature; 88 | is $exons[0]->start, 26; 89 | is $exons[0]->end, 268; 90 | is $exons[0]->strand, 1; 91 | 92 | @exons = $exon_set[1]->sub_SeqFeature; 93 | is $exons[0]->start, 26; 94 | is $exons[0]->end, 268; 95 | is $exons[0]->strand, 1; 96 | } -------------------------------------------------------------------------------- /t/Simprot.t: -------------------------------------------------------------------------------- 1 | # This is -*-Perl-*- code 2 | ## Bioperl Test Harness Script for Modules 3 | ## 4 | 5 | 6 | # Before `make install' is performed this script should be runnable with 7 | # `make test'. After `make install' it should work as `perl test.t' 8 | 9 | use strict; 10 | BEGIN { 11 | use Bio::Root::Test; 12 | test_begin(-tests => 6, 13 | -requires_module => 'IO::String'); 14 | 15 | use_ok('Bio::Root::IO'); 16 | use_ok('Bio::Tools::Run::Simprot'); 17 | use_ok('Bio::AlignIO'); 18 | use_ok('Bio::TreeIO'); 19 | } 20 | 21 | ok my $simprot = Bio::Tools::Run::Simprot->new(); 22 | 23 | SKIP: { 24 | test_skip(-requires_executable => $simprot, 25 | -tests => 1); 26 | 27 | my $treeio = Bio::TreeIO->new( 28 | -format => 'nhx', -file => 't/data/simprot_tree.nh'); 29 | 30 | my $tree = $treeio->next_tree; 31 | 32 | $simprot->tree($tree); 33 | $simprot->set_parameter("variablegamma",1); 34 | $simprot->set_parameter("alpha",0.01); 35 | $simprot->set_parameter("rootLength",1000); 36 | $simprot->set_parameter("eFactor",15); 37 | $simprot->set_parameter("indelFrequncy",0.99); 38 | $simprot->set_parameter("maxIndel",999999); 39 | $simprot->set_parameter("Benner",0); 40 | $simprot->set_parameter("bennerk",-2); 41 | $simprot->set_parameter("subModel",2); 42 | $simprot->set_parameter("interleaved",1); 43 | my @nodes = map { $_->id } $tree->get_leaf_nodes; 44 | 45 | my ($rc,$alnio,$seq) = $simprot->run(); 46 | my $aln = $alnio->next_aln; 47 | my @seqs = map { $_->display_name} $aln->each_seq; 48 | is (scalar(@seqs),scalar(@nodes)); 49 | 50 | #*** where are the tests?! 51 | } 52 | -------------------------------------------------------------------------------- /t/StandAloneFasta.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | # 4 | # 5 | 6 | use strict; 7 | BEGIN { 8 | use Bio::Root::Test; 9 | test_begin(-tests => 15); 10 | use_ok('Bio::Tools::Run::Alignment::StandAloneFasta'); 11 | use_ok('Bio::SeqIO'); 12 | } 13 | 14 | my $verbose = -1; 15 | 16 | my $version = '35'; 17 | my @params = ( 'b' =>'15', 18 | 'd' => 0, 19 | 'O' => test_output_file(), 20 | 'm'=>'9', 21 | "program"=>"fasta$version"); 22 | my $factory = Bio::Tools::Run::Alignment::StandAloneFasta->new 23 | ('-verbose' => $verbose, 24 | @params); 25 | ok $factory; 26 | my $inputfilename = test_input_file("fasta.fa"); 27 | 28 | SKIP: { 29 | test_skip(-requires_executable => $factory, 30 | -tests => 12); 31 | my $lib = test_input_file("fastalib.fa"); 32 | $factory->library($lib); 33 | my ($fastareport) = $factory->run($inputfilename); 34 | my $result = $fastareport->next_result; 35 | my $hit = $result->next_hit(); 36 | my $hsp = $hit->next_hsp(); 37 | is $hsp->algorithm, 'FASTN'; 38 | is $hsp->num_identical, 2982; 39 | is $hsp->length, 2982; 40 | 41 | $factory->program_name('ssearch'.$version); 42 | ($fastareport) = $factory->run($inputfilename); 43 | $result = $fastareport->next_result; 44 | $hit = $result->next_hit(); 45 | $hsp = $hit->next_hsp(); 46 | like $hsp->algorithm, qr/SMITH-WATERMAN|SSEARCH/; 47 | is $hsp->num_identical, 2982; 48 | is $hsp->length, 2982; 49 | 50 | $factory->program_name('fastx'.$version); 51 | $factory->library(test_input_file("fastaprot.fa")); 52 | ($fastareport) = $factory->run($inputfilename); 53 | $result = $fastareport->next_result; 54 | $hit = $result->next_hit(); 55 | $hsp = $hit->next_hsp(); 56 | is $hsp->algorithm, 'FASTX'; 57 | is $hsp->num_identical, 994; 58 | is $hsp->length, 994; 59 | 60 | my $sio = Bio::SeqIO->new(-file=>$inputfilename, 61 | -format=>"fasta"); 62 | my $seq = $sio->next_seq; 63 | 64 | #test with objects 65 | ($fastareport) = $factory->run($seq); 66 | $result = $fastareport->next_result; 67 | $hit = $result->next_hit(); 68 | $hsp = $hit->next_hsp(); 69 | is $hsp->algorithm, 'FASTX'; 70 | is $hsp->num_identical, 994; 71 | is $hsp->length, 994; 72 | } 73 | 74 | -------------------------------------------------------------------------------- /t/Tmhmm.t: -------------------------------------------------------------------------------- 1 | #-*-Perl-*- 2 | # $id$ 3 | # ## Bioperl Test Harness Script for Modules 4 | # # 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 9); 9 | use_ok('Bio::Tools::Run::Tmhmm'); 10 | use_ok('Bio::SeqIO'); 11 | } 12 | 13 | # AHEM - Fugu guys, can you make sure this is genericized? 14 | 15 | my $factory = Bio::Tools::Run::Tmhmm->new(); 16 | isa_ok $factory,'Bio::Tools::Run::Tmhmm'; 17 | SKIP:{ 18 | test_skip(-requires_executable => $factory, 19 | -tests => 6); 20 | my $prot_file= test_input_file("test_prot.FastA"); 21 | ok(-e $prot_file); 22 | 23 | my $seqstream = Bio::SeqIO->new(-file => $prot_file, -fmt => 'Fasta'); 24 | my $seq1 = $seqstream->next_seq(); 25 | isa_ok( $seq1,'Bio::Seq'); 26 | my @feat = $factory->run($seq1); 27 | is @feat, 5; 28 | 29 | isa_ok $feat[0],'Bio::SeqFeatureI'; 30 | is ($feat[0]->start,121); 31 | is ($feat[0]->end,143); 32 | } 33 | -------------------------------------------------------------------------------- /t/Tools/Run/Dummy.pm: -------------------------------------------------------------------------------- 1 | package Dummy; 2 | use strict; 3 | use warnings; 4 | 5 | use lib '.'; 6 | use lib '..'; 7 | use Dummy::Config; 8 | 9 | use Bio::Tools::Run::WrapperBase; 10 | use Bio::Tools::Run::WrapperBase::CommandExts; 11 | 12 | use base qw(Bio::Tools::Run::WrapperBase Bio::Root::Root); 13 | 14 | sub new { 15 | my ($class,@args) = @_; 16 | my $self = $class->SUPER::new(@args); 17 | return $self; 18 | } 19 | 20 | 1; 21 | 22 | -------------------------------------------------------------------------------- /t/Tools/Run/Dummy/Config.pm: -------------------------------------------------------------------------------- 1 | package Dummy::Config; 2 | use strict; 3 | use warnings; 4 | no warnings qw(qw); 5 | use Exporter; 6 | our (@ISA, @EXPORT, @EXPORT_OK); 7 | push @ISA, 'Exporter'; 8 | @EXPORT = qw( 9 | $program_name 10 | $program_dir 11 | $use_dash 12 | $join 13 | @program_commands 14 | %command_prefixes 15 | @program_params 16 | @program_switches 17 | %param_translation 18 | %command_files 19 | %composite_commands 20 | ); 21 | 22 | @EXPORT_OK = qw(); 23 | 24 | our $program_name = '*flurb'; 25 | #our $program_dir = 'C:\cygwin\usr\local\bin'; 26 | our $use_dash = 'mixed'; 27 | our $join = ' '; 28 | 29 | 30 | our @program_commands = qw( 31 | rpsblast 32 | find 33 | goob 34 | blorb 35 | multiglob 36 | ); 37 | 38 | our %command_prefixes = ( 39 | blastp => 'blp', 40 | tblastn => 'tbn', 41 | goob => 'g', 42 | blorb => 'b', 43 | multiglob => 'm' 44 | ); 45 | 46 | our @program_params = qw( 47 | command 48 | g|narf 49 | g|schlurb 50 | b|scroob 51 | b|frelb 52 | m|trud 53 | ); 54 | 55 | our @program_switches = qw( 56 | g|freen 57 | b|klep 58 | ); 59 | 60 | our %param_translation = ( 61 | 'g|narf' => 'n', 62 | 'g|schlurb' => 'schlurb', 63 | 'g|freen' => 'f', 64 | 'b|scroob' => 's', 65 | 'b|frelb' => 'frelb' 66 | ); 67 | 68 | our %command_files = ( 69 | 'goob' => [qw( fas faq )], 70 | ); 71 | 72 | our %composite_commands = ( 73 | 'multiglob' => [qw( blorb goob )] 74 | ); 75 | 1; 76 | -------------------------------------------------------------------------------- /t/Tools/Run/WBCommandExts.t: -------------------------------------------------------------------------------- 1 | #-*-perl-*- 2 | 3 | # testing CommandExts 4 | use strict; 5 | use warnings; 6 | our $home; 7 | BEGIN { 8 | use Bio::Root::Test; 9 | use lib '.'; 10 | use lib 't/Tools/Run'; 11 | $home = '../../..'; # set to '.' for Build use, 12 | # '../../..' for debugging from .t file 13 | unshift @INC, $home; 14 | test_begin(-tests => 25, 15 | -requires_modules => [qw(Bio::Tools::Run::WrapperBase 16 | Bio::Tools::Run::WrapperBase::CommandExts)]); 17 | } 18 | 19 | use_ok( 'Dummy::Config' ); 20 | use_ok( 'Dummy' ); 21 | use_ok('Bio::Tools::Run::WrapperBase'); 22 | use_ok('Bio::Tools::Run::WrapperBase::CommandExts'); 23 | 24 | ok my $fac = Dummy->new( -command => 'goob', 25 | -narf => 42.0, 26 | -schlurb => 'breb', 27 | -freen => 1 ), "make factory"; 28 | ok $fac->parameters_changed, "parm changed flag set"; 29 | is $fac->program_name, 'flurb', "correct prog name"; 30 | ok $fac->is_pseudo, "is pseudo"; 31 | is $fac->narf, 42, "correct parm set"; 32 | ok !$fac->parameters_changed, "parm flag cleared"; 33 | my $param_str = join(' ',@{$fac->_translate_params}); 34 | 35 | like ($param_str, qr/--schlurb breb/, 'translate opts to command line'); 36 | like ($param_str, qr/-n 42/, 'translate opts to command line'); 37 | like ($param_str, qr/-f/, 'translate opts to command line'); 38 | 39 | my @a = @{$fac->_translate_params}; 40 | my ($k, %h); 41 | for (@a) { 42 | (/^-/) ? ( $h{$k = $_} = undef ) : ( $h{$k} = $_ ); 43 | } 44 | is_deeply( \%h, { '--schlurb' => 'breb', '-n' => 42, '-f' => undef }, 'translate_params: options correct'); 45 | 46 | ok $fac->reset_parameters, "parm reset"; 47 | ok !$fac->narf, "parm cleared after reset"; 48 | 49 | is_deeply( [$fac->available_parameters('parameters')], [qw( command narf schlurb )], "avail parms"); 50 | is_deeply( [$fac->available_parameters('switches')], ['freen'], "avail switches"); 51 | is_deeply( [$fac->available_parameters('commands')], [qw(rpsblast find goob blorb multiglob)], "avail commands"); 52 | 53 | ok $fac = Dummy->new( -command => 'multiglob', 54 | -g_freen => 1, 55 | -b_scroob => 10.5, 56 | -trud => 'sklim' ), "make composite cmd factory"; 57 | 58 | is $fac->trud, 'sklim', "comp cmd parm set"; 59 | 60 | ok my %facs = $fac->_create_factory_set, "make subfactories"; 61 | is $facs{goob}->freen, 1, "subfactory 1 parm correct"; 62 | is $facs{blorb}->scroob, 10.5, "subfactory 2 parm correct"; 63 | 64 | $fac->program_dir('.'); 65 | # ok $fac->executables('rpsblast'), "find in program_dir"; 66 | ok $fac->executables('find'), "find in syspath"; 67 | 68 | 1; 69 | -------------------------------------------------------------------------------- /t/TribeMCL.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | 5 | use strict; 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 24, 9 | -requires_modules => ['Algorithm::Diff', 'Bio::Cluster::SequenceFamily']); 10 | use_ok('Bio::Tools::Run::TribeMCL'); 11 | use_ok('Bio::SearchIO'); 12 | } 13 | 14 | my $blast_out = test_input_file("TribeMCL.bls"); 15 | 16 | #do from raw blast output 17 | my @params=('inputtype'=>'blastfile',I=>'3.0'); 18 | my $fact = Bio::Tools::Run::TribeMCL->new(@params); 19 | 20 | SKIP : { 21 | unless ($fact){ 22 | skip("Couldn't create a TribeMCL wrapper",22); 23 | } 24 | my $desc = test_input_file("TribeMCL.desc"); 25 | $fact->description_file($desc); 26 | 27 | isa_ok $fact,'Bio::Tools::Run::TribeMCL'; 28 | unless ($fact->matrix_executable){ 29 | skip("Tribe Matrix program not found. Skipping tests...", 21); 30 | } 31 | unless ($fact->mcl_executable){ 32 | skip("Markov Clustering program not found. Skipping tests...",21); 33 | } 34 | 35 | my $bequiet = 1 ; 36 | $fact->quiet($bequiet); 37 | 38 | my ($fam) = $fact->run($blast_out); 39 | my @members = $fam->get_members; 40 | isa_ok $fam,"Bio::Cluster::SequenceFamily"; 41 | isa_ok $members[0],"Bio::Seq"; 42 | is ($members[0]->id, 'ENSANGP00000008485'); 43 | is ($members[1]->id, 'ENSDRMP3263'); 44 | is ($members[2]->id, 'ENSMUSP00000026170'); 45 | is ($fam->description,'ubiquitin'); 46 | is ($fam->annotation_score,45.0549450549451); 47 | is ($fam->size,91); 48 | 49 | #do from searchio 50 | 51 | my $sio = Bio::SearchIO->new(-format=>'blast', 52 | -file=>$blast_out); 53 | 54 | @params=('inputtype'=>'searchio',I=>'3.0'); 55 | $fact = Bio::Tools::Run::TribeMCL->new(@params); 56 | $fact->description_file($desc); 57 | 58 | isa_ok $fact,'Bio::Tools::Run::TribeMCL'; 59 | $bequiet =1 ; 60 | $fact->quiet($bequiet); 61 | 62 | ($fam) = $fact->run($sio); 63 | isa_ok $fam,"Bio::Cluster::SequenceFamily"; 64 | isa_ok $members[0],"Bio::Seq"; 65 | is ($members[0]->id, 'ENSANGP00000008485'); 66 | is ($members[1]->id, 'ENSDRMP3263'); 67 | is ($members[2]->id, 'ENSMUSP00000026170'); 68 | is ($fam->description,'ubiquitin'); 69 | is ($fam->annotation_score,45.0549450549451); 70 | is ($fam->size,91); 71 | 72 | @params=('inputtype'=>'pairs',I=>'3.0'); 73 | $fact = Bio::Tools::Run::TribeMCL->new(@params); 74 | isa_ok $fact,'Bio::Tools::Run::TribeMCL'; 75 | $bequiet =1 ; 76 | $fact->quiet($bequiet); 77 | 78 | ($fam) = $fact->run( [[qw(ENSP00000257547 ENSP00000261659 1 50)], 79 | [qw(O42187 ENSP00000257547 1 119)]]); 80 | @members = $fam->get_members; 81 | is ($members[0]->id, 'ENSP00000257547'); 82 | is ($members[1]->id, 'ENSP00000261659'); 83 | is ($members[2]->id, 'O42187'); 84 | } 85 | -------------------------------------------------------------------------------- /t/Vista.t: -------------------------------------------------------------------------------- 1 | # -*-Perl-*- 2 | ## Bioperl Test Harness Script for Modules 3 | 4 | use strict; 5 | BEGIN { 6 | use Bio::Root::Test; 7 | test_begin(-tests => 7); 8 | 9 | use_ok('Bio::Tools::Run::Vista'); 10 | use_ok('Bio::AlignIO'); 11 | } 12 | 13 | SKIP: { 14 | #Java and java version check 15 | my $v; 16 | if (-d "java") { 17 | skip("Skipping because no java present to run vista", 5); 18 | } 19 | 20 | open(PIPE,"java -version 2>&1 |"); 21 | while () { 22 | if (/Java\sVersion\:\s(\d+\.\d+)/) { 23 | $v = $1; 24 | last; 25 | } 26 | elsif (/java version\s.(\d+\.\d+)/) { 27 | $v = $1; 28 | last; 29 | } 30 | elsif (/java version\s\"(\d\.\d)"/) { 31 | $v = $1; 32 | last; 33 | } 34 | } 35 | if ($v < 1.2) { 36 | skip("Skipping due to old java version", 5); 37 | } 38 | 39 | open (PIPE ,'java Vista 2>&1 |'); 40 | while(){ 41 | if ( /NoClassDefFoundError/ 42 | # For JRE 1.7.0_25 - Win7 - Spanish, the message is: 43 | # "Error: no se ha encontrado o cargado la clase principal Vista" 44 | or /^Error\:/ 45 | ){ 46 | diag('Vista.jar is not in your class path: '.$_); 47 | skip("Vista.jar is not in your class path",5); 48 | } 49 | } 50 | my $inputfilename= test_input_file("vista.cls"); 51 | my $gff_file = test_input_file("vista.gff"); 52 | my $aio = Bio::AlignIO->new(-file => $inputfilename, 53 | -format => 'clustalw'); 54 | my $aln = $aio->next_aln; 55 | 56 | my $out= test_output_file(); 57 | my $vis = Bio::Tools::Run::Vista->new('outfile' => $out, 58 | 'title' => "My Vista Plot", 59 | 'annotation' => $gff_file, 60 | 'annotation_format' => 'GFF', 61 | 'min_perc_id' => 75, 62 | 'min_length' => 100, 63 | 'plotmin' => 50, 64 | 'tickdist' => 2000, 65 | 'window' => 40, 66 | 'numwindows' => 4, 67 | 'start' => 50, 68 | 'end' => 1500, 69 | 'tickdist' => 100, 70 | 'bases' => 1000, 71 | 'color' => {'EXON'=>'45 25 54','CNS'=>'0 0 100'}, 72 | 'quiet' =>1); 73 | isa_ok $vis,'Bio::Tools::Run::Vista'; 74 | is $vis->plotmin, 50; 75 | is $vis->annotation, $gff_file; 76 | 77 | $vis->run($aln,1); 78 | ok -e $out; 79 | $vis->run($aln,'mouse'); 80 | ok -e $out; 81 | } 82 | -------------------------------------------------------------------------------- /t/data/1.bg: -------------------------------------------------------------------------------- 1 | chr1 1000 1500 10 2 | chr1 2000 2100 20 3 | -------------------------------------------------------------------------------- /t/data/2.bg: -------------------------------------------------------------------------------- 1 | chr1 900 1600 60 2 | chr1 1700 2050 50 3 | -------------------------------------------------------------------------------- /t/data/219877.cdna.fasta: -------------------------------------------------------------------------------- 1 | >ENSP00000346536 2 | ATGTCCTACAACTGCTGCTGTGGAAACTTCTCCTCCCATTCCTGTGAGGGCTACCTGTGC 3 | TACTCAGGCTACTCCCGTGGTGGCTCCTCGTACCCCAGCAACCTGGTCTACAGCACTGAA 4 | CCTTTGATCTCCCAGCACCTGCCAGCTGGGTTCCTCTCTCTGCAAGGGCTTTCAGGAGAC 5 | TTGCTGGGAAACCCC--- 6 | >ENSDNOP00000011417 7 | ATGACTTCCAAAAGCTACTCTGGAAACTTCTCCTCCTGCTCCCTTGGTGGCAACCTGTGC 8 | TACTCAGGCTCCTCTTAT---CGCTCTTCCTGTCCCAGCAACCTGGTTTACACCACT--- 9 | CCTCTGCTCTCCCAGCACCTGCCACCTGGGTTCCTCTCTCTACAGTGGCTGCCAGGAGCC 10 | CTGCTACAAGCCCAGCAA 11 | >ENSPTRP00000023821 12 | CTATCCTACAACTGCTGCTGTGGAAACTTCTCCTCCCATTCCTGTGGGGGCTACCTGTGC 13 | TACTCAGGCTACTCCCGTGGTGGCTCCTCGTACCCCAGCAACCTGGTCTACAGCACTGAA 14 | CCTTTGATCTCCCAGCGCCTGCCAGCTGGGTTCCTCTCTCTGCAAGGGTTTTCAGGAGAC 15 | TTGCTGGGAAACCCC--- 16 | -------------------------------------------------------------------------------- /t/data/219877.tree: -------------------------------------------------------------------------------- 1 | ((ENSP00000346536:0.0049,ENSPTRP00000023821:0.0208):0.1113,ENSDNOP00000011417:0.1113); 2 | -------------------------------------------------------------------------------- /t/data/277523.cdna.fasta: -------------------------------------------------------------------------------- 1 | >ENSP00000334085 2 | ATGGCATCTTGGCCTGTCCAAAAATGTTGTGCTTTCAGACATTCTTGCAATATTCTAGAG 3 | GAAGATTTGGAAGTAGACAGTTGCCAAATACCATTAGTTTCCGTGGGAAGCCAGCTAAGA 4 | AAGGTAATTCTCAGGGAGAGTAATGCGAGGAAACAATTAGCCATTTTGACAACC 5 | >ENSPTRP00000011204 6 | ATGGCATCTTGGCCTGTCCAAAAATGTTGTGCTTTCAGACATTCTTGCAATATTCTAGAG 7 | GAAGATTTGGAAGTAGACAGTTGCCAAATACCATCAGTTTCCGTGGGAAGCCAGCTAAGA 8 | AAGGTAATTCTCAGGGAGAGTAATGCGAAGAAACAATTAGCCATTTTGACAACC 9 | >ENSMMUP00000015622 10 | ATGGCATCTTGGCCTGTCCAAAAATGTTGTGCTTTCAGACATTCTTGCAATATTCTAGAG 11 | GAAGATTTGGAAGTCGACAGTTGCCAGATGCCATCAGTTCCCATGGGGAGCCAGCTAAAG 12 | AAAGGAATTCTCAGGGAGAGTAATGCAAGG------------------------ 13 | -------------------------------------------------------------------------------- /t/data/277523.tree: -------------------------------------------------------------------------------- 1 | ((ENSPTRP00000011204:0.0057,ENSP00000334085:0.0057):0.0371,ENSMMUP00000015622:0.0371); 2 | -------------------------------------------------------------------------------- /t/data/3.bg: -------------------------------------------------------------------------------- 1 | chr1 1980 2070 80 2 | chr1 2090 2100 20 3 | -------------------------------------------------------------------------------- /t/data/Ft.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioperl/bioperl-run/f9a864a1214361f281d31e9b8baaf70f760f6687/t/data/Ft.bam -------------------------------------------------------------------------------- /t/data/Ft.frag.fas.fai: -------------------------------------------------------------------------------- 1 | NC_009749_frag 32800 16 60 61 2 | -------------------------------------------------------------------------------- /t/data/Genscan.FastA: -------------------------------------------------------------------------------- 1 | >description 2 | GTATTGCGTCACTTCCTGTCTTCTCAATCGTTCGTTGGTTGCACTGTGCATGGGGTGTTGTATTCACTTAATATTGAACACTTGGTGTGTTGTATTCACTTAATATTGAACACTTGGTGTGTTGTATTCACTTTACTTAAAATTTTGAACACTTGGGACATTCTAGTCACCTGATAACAACAGTGAGAAACAACCCATATTAAACAAATACAGGGCTCCACCGATTATCAGCGTTAGCATGGCCTCACCGTCTGTTTCACCCGGTGTCTTTGTCTGTTCAGCGTGTGAAATGTTTAGTTACTCCTCTGCCTCCTTTAGTGAAGGGAATAGGTGCAGAAAGTGTAGTTTATTTATGGCTATGGAGGCGAGACTTAGCGAGCTTGAGACGCGGTTCCGCAGCTTGGAGTTAGCTGGAGTTGCGTCAGGTAGCCAGGAGAAGCTAGCTGCTGCGGAGCCGCCTAGCGTAGCTACAGCTAGCGGTCCCCCGGCAGCAGCCGAGCAGCCGGCTAGCCAGGGCGGCTGGGTGACGGTTCGTAGGAAGCGTAGCCCAAAACAAAGGCCCACGGTGCACCACCAACCGCTTCCCGTGGCTAACCGCTTTTCCCCACTCGGCGACACACCCGCTGAGAAACCGACCCTGGTAATTGGCGACTCTGTTTTGCGCTACGTGAAGCCGACTCCAGCGACCATAGTTAAGTGCATTCCGGGGGCCAGAGCGGGCGACATAGAAGCAAATTTACGGCTGCTGGCGAGACGTAATCGTAAATTTGGTAAAGTTATTATTCACGTCGGAGCCAACGACACCCGGCTTCGTCAGTCGGAGGTCACCAAAATTAACTTGGAGTCGGTGTGTAACTACGCAAAAACGATGTCGGACTCCGTAGCATTCTCTGGTCCCCTCCCCAATCTGGCCAGCGAGGAGATGTTTAGCCGCATGTCGTCGCTTCGTCGCTGGCTGTCACGGTGGTGCCCCGAAAACCAGGTGGCCTTTATAGACAATTGGAGCACTTTTTGGGGAAAACCTGGTCTGATTAGGAGAGACGGTGTCCATCCCACACGGGATGGTGCTTCTCTCATTTCTAGTAATTTGGCTAATTTTATT 3 | -------------------------------------------------------------------------------- /t/data/H_pylori_J99.glimmer2.icm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioperl/bioperl-run/f9a864a1214361f281d31e9b8baaf70f760f6687/t/data/H_pylori_J99.glimmer2.icm -------------------------------------------------------------------------------- /t/data/H_pylori_J99.glimmer3.icm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioperl/bioperl-run/f9a864a1214361f281d31e9b8baaf70f760f6687/t/data/H_pylori_J99.glimmer3.icm -------------------------------------------------------------------------------- /t/data/Primer3.fa: -------------------------------------------------------------------------------- 1 | >Test1 2 | AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 3 | TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA 4 | TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC 5 | -------------------------------------------------------------------------------- /t/data/Prints_prot.FastA: -------------------------------------------------------------------------------- 1 | >Prints_prot 2 | WWIMGKDNASYLQAFILVGSSDRPGLEKILFAVILIFCILTLVGNTAIILLLVMDVRLHTPMYFFLGNLSFLDLCFTASIAPQLLWNLGGPEKTITYHGCVAQLYIYMMLGSTECVLLVVMSHDRYVAVCRSLHYMAVMRPHLCLQLVTVAWCCGFLNSFIMCPQTMQLSRCGRRRVDHFLCEMPALIAMSCEETMLVEAIHLCPGGGSPPGAALPHPHLLWRDCSRGAEDEVSSRAKESLPHLLFSPHSGLSLLRNHHLRVPEAGQQLLPRSGEVPDSLLHHRHSQHQPPHLHFEEQGCEGDHEETSGVGERGWGASTRGTL 3 | -------------------------------------------------------------------------------- /t/data/amino.fa: -------------------------------------------------------------------------------- 1 | >CYS1_DICDI fragment 2 | SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE 3 | 4 | >ALEU_HORVU 5 | MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK 6 | SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD 7 | AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG 8 | GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF 9 | QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA 10 | IATCASYPVVAA 11 | -------------------------------------------------------------------------------- /t/data/apes.multi_fasta: -------------------------------------------------------------------------------- 1 | >human 2 | AACCTGGCCAATTGGCCAATTGGGCGTACGTACGT 3 | >chimpanzee 4 | ACCCTGGCCAATTGGCCAATTGTAAGTACGTACGT 5 | >Cross_river_gorilla 6 | AAGCTGGCCAATTGGCCAATTAGACTTACGTACGT 7 | >orangutan 8 | AACATGGCCAATTGGCCAATCGGACGTACGTCCGT 9 | >common_gibbon 10 | AACCGGGCCAATTGGCCAAGTGGACGTACGTATGT 11 | >crested_gibbon 12 | AACCTAGCCAATTGGCCACTTGGACGTACGTACAT 13 | >siamang 14 | AACCTGCCCAATTGGCCGATTGGACGTACGTACGC 15 | >mountain_gorilla 16 | AACCTGGGCAATTGGCAAATTGGACGTACGTACGT 17 | >Hoolock_gibbon 18 | AACCTGGCTAATTGGTCAATTGGACGTACGTACGT 19 | >silvery_gibbon 20 | AACCTGGCCGATTGGCCAATTGGACGTACGTACGT -------------------------------------------------------------------------------- /t/data/apes.newick: -------------------------------------------------------------------------------- 1 | ((((human,chimpanzee,(Cross_river_gorilla,mountain_gorilla)"Gorilla gorilla")"Homo/Pan/Gorilla group",orangutan)Hominidae,((common_gibbon,silvery_gibbon)Hylobates,crested_gibbon,siamang,Hoolock_gibbon)Hylobatidae)Hominoidea)"cellular organisms"; -------------------------------------------------------------------------------- /t/data/blat_dna.fa: -------------------------------------------------------------------------------- 1 | >sequence_10 2 | CAATGCACATGAACACATACATTTATTAAATTATCGAACGCATCTGTATGATGAATAATGTGGCATTTCACTGAATAATT 3 | AAAGCGCCGGCGTTTAAAGTTCCGTTTTAACGACGTGAATTAATTGAGTTGATCTTGTTTGCAAATATATATAACAAGCT 4 | GTTTGTGGACCGCTACTTTATCCGTATCACTTTCTTGGCCCTACAGCACGCGCTACAAACAACTATCACAGGTGCAAATA 5 | TAGACGACCGCGCACAAGTAAACACATAGCAGACATCAAACAAAGGGAAGGCGAAGGTCGGATTGAGATTCCACAACGAA 6 | TCGAAATATTCGCCATTGTCGGTCTCGGATTACACAATGACGGGCAATAAAACAGTCATTTTTTGTAAATATTTTATAAC 7 | GATTAAAACTTCATGTTCCGCTTTCAAAGGGCGTTTTTTTAATAATAATAACACATAGGAGAAAATCGTAGTGGGATAGA 8 | AGTTAGACTAGACATTAAAACGTGGGAAAAGTAGTTAATTTCCTTTACAATGCTAAGCGACACGACTTCTTTTTCGTTGC 9 | CAAAGCTAATTGCCGTGCCGAAGCGGAACTGATGTCGCGCAGTTGTTAGGAACCGGTTATTACAAAGCGGACGCGCGTGT 10 | CGCAACACTAGGCATTATTCTTCAGCGCTTCATCGCTGTACATTGAAATGTGCGGCATGAATTATTATAACTTGAAGTTA 11 | GCCGCAGCAAAGGGATATCCTGGCTGCGGTGGCGCGTTTATCTGATAAACGGGACAATTATCCAAATTACCATAGAAGCT 12 | CACACCTGCGCGACTGGAAATTATTTTGAAATTACTTTTTTTCAGAAACACGGAGTGGGTTGCAGGTTACAAATTATTTT 13 | GTTTGCTTTTTGATTAAAATACCACTACTACATGTTGCAACATGGTGCTGTATTATTACAGTTTGGGTGTGATGTTTTTC 14 | AAATGTGAATTCGACTTATTGGCGGTTTGATTTTGACAGAACACTTAGACCTGTCAGTTCCAGTTTAAAGTTATTAGTTA 15 | ATATTGACAGATTTATTAGGCATTAGTGACAAGCGAAGACGAAGTTTTCACGTCCTTTTAACCATCAAATCTCCGATAAA 16 | CCGGATCTTCTCGGTTTATCGGAGATTTGATGTACTGCCGTGACGCACGACGTTGTTGAAATAAAACCAATACGCTGCTA 17 | ACAATGCTGCAAAAACTCAGTGTCTAGTTTTCCGTGTTTCTGAAGAACGCATTTGTAACGAAGTAAAGACTGCAGATTAA 18 | TTTGGTGATGCACAAATATGCCCAAGTATCTGACACATCAGCACTTTTACATAGCATAGTGCACAACCAATTGACAATGT 19 | TAAAATAACACATTTATAAGTTTACTAGTGCATTAAAGGTGAAACGCCCCTACAAATCATAACCCCCCAACAAAATCTTA 20 | ATTGATTCATCGAGTAACACTATGCTCGCGGGTTTGAGCTTTCACGAACCTTACATATAGATATGTAAGCAAAACTACTA 21 | CGGTCACGCCCGCGATCAGCCAAGCGATTCAATCTATAAATACAAACACCGCGAGTTAGCTCACACAGGTATGTCTTGGC 22 | AAAGGGGAGTTCCCTTGGTCTAACCGTCGAGTAACCCGAAGACTTATCATGATTGGGATGTTGCCGTGGTCGGTAGATAA 23 | AACTCCGGGACAATGTAAGACAGATGTAAATCGTCAAGGTGGTTCAGTTACTCCCTGTTTACAATGTCAAAACTGGGGTA 24 | AGTGTGAACTGAATG 25 | -------------------------------------------------------------------------------- /t/data/cel-cbr-fam.aln: -------------------------------------------------------------------------------- 1 | CLUSTAL W (1.82) multiple sequence alignment 2 | 3 | 4 | 0023.fg162 MISAKLFFLVILLIACLVAVTEAQWGYGY--RPYGGYGGYGG-FRRP-YRPWGYRPYGYG 5 | 0023.fg163 MISAKLFFIVLLLIACLFAVSEAQWGYGY--RPYGGYGGYGG-FRRP-YRPWGYRPYGYG 6 | 0023.fg159 MISAKLFFLVVLLIACLLAVAEAQWGYGYGYRPYG-YGGYGGGWRRPYYRPWGYRPYGYG 7 | 0023.fg220 MISAQLFFLVLLLVACMLAVHAHSRADGN------VEGGLG-QFILSSHGSDNHGPHGK- 8 | 0023.fg221 MFTAQLLFLVLLVISCTLMVQGLNALDEQ------AEGGAGGQQHVVGYGSFNNGPHGK- 9 | *::*:*:*:*:*:::* . * . . . . ** *. : . . *:* . 10 | 11 | 0023.fg162 WGK 12 | 0023.fg163 WGK 13 | 0023.fg159 WGK 14 | 0023.fg220 --- 15 | 0023.fg221 --- 16 | .. 17 | -------------------------------------------------------------------------------- /t/data/coil_protein_input: -------------------------------------------------------------------------------- 1 | >coil_protein_input 2 | KRSGIPAPREIPSALTKGRTSLRDQLRTSSTKKIVSSASTSSLSALAKQTRGPTKSQDTEGLERGLLECQIKELLAEAKAKDLEISNLRAELQHFMVKPSTPSSSAPSKCVTDEEQRQVDEALLLVGELREKNGTFQNELAVLREDNQILNGKLLSLEAYIASTPSKPFVNGLPYSSLRTSVSSSSDMTKDSPSPDSSEFEKIPSCSESLHSGASGETGSIGAVMSSMGQNLSVQSLAEQIHKMEENQHSTAEELQATLQELADQQKMVQELTAENERLAEEKRLLQTSVQQQQECVEVLAQKNESLARRLQEQVQVQAQREEEICSQGPRLAELEQRYANLMESSHFEREKLVDIQQQLTGSLRSLEEEHQIAQGQVCCLREEMDRLQAQLDQELESVGQATLVAEEQRATAESLRLENSRLKVQVDIERQKIGEMKTIQNASDTAEVLSMLKAAHAERDRMEAELTTLREKLLHAQAETEHTRAALSMVEAKCQQVQEQAEEREQVLHNQISSVEEERILAENQVKDLKENIFELEDQVEQQRAVNCHTNQAALDMENLAKKLEDQKAEAERQLKVLTRKLK 3 | -------------------------------------------------------------------------------- /t/data/consense.treefile: -------------------------------------------------------------------------------- 1 | ((CATH_HUMAN:0.08786,CATH_RAT:0.09500):0.21987,ALEU_HORVU:0.44318,((CATL_HUMAN:0.15617,CATL_RAT:0.18062):0.43288,(CYS1_DICDI:0.62753,PAPA_CARPA:0.81289):0.11919):0.09964); 2 | (ALEU_HORVU:0.44716,(CATH_RAT:0.09342,CATH_HUMAN:0.10659):0.36011,((CATL_HUMAN:0.15535,CATL_RAT:0.16947):0.36918,(CYS1_DICDI:0.60820,PAPA_CARPA:0.72070):0.13684):0.10612); 3 | (((CATH_RAT:0.09483,CATH_HUMAN:0.12603):0.34462,ALEU_HORVU:0.54357):0.14458,PAPA_CARPA:0.70028,((CATL_RAT:0.15534,CATL_HUMAN:0.19769):0.39935,CYS1_DICDI:0.74672):0.06901); 4 | (PAPA_CARPA:0.61578,((ALEU_HORVU:0.40173,(CATH_RAT:0.09901,CATH_HUMAN:0.10973):0.36375):0.13133,(CATL_HUMAN:0.16294,CATL_RAT:0.19286):0.48430):0.03829,CYS1_DICDI:0.73659); 5 | (CYS1_DICDI:0.67199,PAPA_CARPA:0.67396,((CATL_RAT:0.13150,CATL_HUMAN:0.18018):0.42155,((CATH_RAT:0.08030,CATH_HUMAN:0.11992):0.24622,ALEU_HORVU:0.44758):0.19315):0.07207); 6 | (PAPA_CARPA:0.73776,(CATL_RAT:0.12334,CATL_HUMAN:0.20192):0.54622,((ALEU_HORVU:0.36664,(CATH_RAT:0.06005,CATH_HUMAN:0.08971):0.42937):0.19542,CYS1_DICDI:0.73584):0.06629); 7 | (PAPA_CARPA:0.69358,CYS1_DICDI:0.69675,((CATL_HUMAN:0.17589,CATL_RAT:0.19458):0.44444,((CATH_HUMAN:0.08889,CATH_RAT:0.14186):0.27740,ALEU_HORVU:0.45087):0.29681):0.01821); 8 | (CYS1_DICDI:0.61816,PAPA_CARPA:0.66948,(((CATH_RAT:0.07860,CATH_HUMAN:0.09222):0.22277,ALEU_HORVU:0.46677):0.15738,(CATL_RAT:0.15970,CATL_HUMAN:0.18766):0.45668):0.10442); 9 | (PAPA_CARPA:0.67765,CYS1_DICDI:0.69179,((CATL_HUMAN:0.15320,CATL_RAT:0.17013):0.44308,((CATH_HUMAN:0.09871,CATH_RAT:0.11258):0.20787,ALEU_HORVU:0.51859):0.22188):0.07599); 10 | (CYS1_DICDI:0.63279,PAPA_CARPA:0.65342,((CATL_HUMAN:0.16325,CATL_RAT:0.16601):0.37681,((CATH_RAT:0.09060,CATH_HUMAN:0.12039):0.21197,ALEU_HORVU:0.45197):0.21260):0.07103); 11 | -------------------------------------------------------------------------------- /t/data/consensus.cns: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioperl/bioperl-run/f9a864a1214361f281d31e9b8baaf70f760f6687/t/data/consensus.cns -------------------------------------------------------------------------------- /t/data/cysprot.fa: -------------------------------------------------------------------------------- 1 | >CYS1_DICDI 2 | MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHK 3 | ADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG 4 | SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT 5 | ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCN 6 | PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 7 | 8 | 9 | >ALEU_HORVU 10 | MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK 11 | SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD 12 | AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG 13 | GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF 14 | QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA 15 | IATCASYPVVAA 16 | 17 | 18 | >CATH_HUMAN 19 | MWATLPLLCAGAWLLGVPVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHNN 20 | GNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGNFVSPVKNQGACGS 21 | CWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGK 22 | DGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVN 23 | HAVLAVGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV 24 | 25 | 26 | >CATH_RAT 27 | MWTALPLLCAGAWLLSAGATAELTVNAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRN 28 | HTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCW 29 | TFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNG 30 | QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHA 31 | VLAVGYGEQNGLLYWIVKNSWGSNWGNNGYFLIERGKNMCGLAACASYPIPQV 32 | 33 | 34 | >CATL_HUMAN 35 | MNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGK 36 | HSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWA 37 | FSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES 38 | CKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLV 39 | VGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV 40 | 41 | 42 | >CATL_RAT 43 | MTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGK 44 | HGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQEPLMLQIPKTVDWREKGCVTPVKNQGQCGSCWA 45 | FSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS 46 | CKYRAEYAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLV 47 | VGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIVN 48 | 49 | 50 | >PAPA_CARPA 51 | MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFE 52 | IFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDW 53 | RQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQ 54 | YGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGG 55 | IFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 56 | 57 | 58 | 59 | -------------------------------------------------------------------------------- /t/data/cysprot.stockholm: -------------------------------------------------------------------------------- 1 | # STOCKHOLM 1.0 2 | 3 | #=GF ID NoName 4 | 5 | CATH_HUMAN/1-335 ....MWATLPLLCAGAWLLGVPVCGAAELSVN..........................SLEKFHFKSWMSKHRKTYS.TEEYHHRLQTFASNWRKINAHN....NGNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKS..NYLRGTG..PYPPSVDWRKKGNFVSPVKNQGACGSCWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDF........NNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGKDGY.CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVT.QDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNG.....IPYWIVKNSWGPQWGMNGYFLIERGK....NMCGLAACASYPIPLV 6 | CATH_RAT/1-333 ....MWTALPLLCAGAWLLSAGAT..AELTVN..........................AIEKFHFTSWMKQHQKTYS.SREYSHRLQVFANNWRKIQAHN....QRNHTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKS..NYLRGTG..PYPSSMDWRKKGNVVSPVKNQGACGSCWTFSTTGALESAVAIASGKMMTLAEQQLVDCAQNF........NNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNGQ.CKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVT.EDFMMYKSGVYSSNSCHKTPDKVNHAVLAVGYGEQNG.....LLYWIVKNSWGSNWGNNGYFLIERGK....NMCGLAACASYPIPQV 7 | ALEU_HORVU/1-362 ....MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN....RKGLPYRLGINRFSDMSWEEFQATRLG.AAQTCSATLAGNHLMRDAA..ALPETKDWREDG.IVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGF........NNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGV.CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI.DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENG.....VPYWLIKNSWGADWGDNGYFKMEMGK....NMCAIATCASYPVVAA 8 | PAPA_CARPA/1-345 MAMIPSISKLLFVAICLFVYMGLSFGDFSIVG.................YSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETN....KKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKG.AVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDR..........RSYGCNGGYPWSALQLVAQYG.IHYRNTYPYEGVQRY.CRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVG....PCGNKVDHAVAAVGYGPN.........YILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN. 9 | CATL_HUMAN/1-333 ......MNPTLILAAFCLGIASATLTFDHSLE..............................AQWTKWKAMHNRLYG.MNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQ....NRKPRKGKVFQEPLFYEAPRSVDWREKG.YVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGP....QG....NEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES.CKYNPKYSVANDTGFVDIPK.QEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPD..CSSEDMDHGVLVVGYGFESTESDNNK.YWLVKNSWGEEWGMGGYVKMAKDRR...NHCGIASAASYPTV.. 10 | CATL_RAT/1-334 ......MTPLLLLAVLCLGTALATPKFDQTFN..............................AQWHQWKSTHRRLYG.TNEEEWRRAVWEKNMRMIQLHNGEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYR....HQKHKKGRLFQEPLMLQIPKTVDWREKG.CVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGKLISLSEQNLVDCSHD....QG....NQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS.CKYRAEYAVANDTGFVDIPQ.QEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPN..CSSKDLDHGVLVVGYGYEGTDSNKDK.YWLVKNSWGKEWGMDGYIKIAKDRN...NHCGLATAASYPIVN. 11 | CYS1_DICDI/1-343 ......MKVILLFVLAVFTVFVSSRGIPPEEQ..............................SQFLEFQDKFNKKYS.HEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG.AVTPVKNQGQCGSCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPK.NETVMAGYIVSTGPLAIAADA..VEWQFYIGGVFDIP...CNPNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGK....NTCGVSNFVSTSII.. 12 | // 13 | -------------------------------------------------------------------------------- /t/data/cysprot1a.fa: -------------------------------------------------------------------------------- 1 | >CYS1_DICDI 2 | MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHK 3 | ADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG 4 | SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT 5 | ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCN 6 | PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII 7 | 8 | 9 | >ALEU_HORVU 10 | MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK 11 | SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD 12 | AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG 13 | GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF 14 | QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA 15 | IATCASYPVVAA 16 | 17 | 18 | >CATH_HUMAN 19 | MWATLPLLCAGAWLLGVPVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHNN 20 | GNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGNFVSPVKNQGACGS 21 | CWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGK 22 | DGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVN 23 | HAVLAVGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV 24 | 25 | -------------------------------------------------------------------------------- /t/data/cysprot1a.msf: -------------------------------------------------------------------------------- 1 | PileUp 2 | 3 | 4 | 5 | MSF: 383 Type: P Check: 3696 .. 6 | 7 | Name: ALEU_HORVU oo Len: 383 Check: 9840 Weight: 34.4 8 | Name: CATH_HUMAN oo Len: 383 Check: 7134 Weight: 30.1 9 | Name: CYS1_DICDI oo Len: 383 Check: 6722 Weight: 35.4 10 | 11 | // 12 | 13 | 14 | 15 | ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 16 | CATH_HUMAN ......MWAT LPLLCAGAWL LG........ VPVCGAAELS VNSLEK.... 17 | CYS1_DICDI .....MKVIL LFVLAVFTVF VS........ .......SRG IPPEEQ.... 18 | 19 | 20 | ALEU_HORVU ALGRTRHALR FARFAVRYGK SYESAAEVRR RFRIFSESLE EVRSTN.... 21 | CATH_HUMAN ........FH FKSWMSKHRK TYS.TEEYHH RLQTFASNWR KINAHN.... 22 | CYS1_DICDI ........SQ FLEFQDKFNK KYS.HEEYLE RFEIFKSNLG KIEELNLIAI 23 | 24 | 25 | ALEU_HORVU RKGLPYRLGI NRFSDMSWEE FQATRLG.AA QTCSATLAGN HLMRDAAA.. 26 | CATH_HUMAN NGNHTFKMAL NQFSDMSFAE IKHKYLWSEP QNCSATKS.. NYLRGTGP.. 27 | CYS1_DICDI NHKADTKFGV NKFADLSSDE FKNYYLNNKE AIFTDDLPVA DYLDDEFINS 28 | 29 | 30 | ALEU_HORVU LPETKDWRED G.IVSPVKNQ AHCGSCWTFS TTGALEAAYT QATGKNISLS 31 | CATH_HUMAN YPPSVDWRKK GNFVSPVKNQ GACGSCWTFS TTGALESAIA IATGKMLSLA 32 | CYS1_DICDI IPTAFDWRTR G.AVTPVKNQ GQCGSCWSFS TTGNVEGQHF ISQNKLVSLS 33 | 34 | 35 | ALEU_HORVU EQQLVDCAGG FNNF...... ..GCNGGLPS QAFEYIKYNG GIDTEESYPY 36 | CATH_HUMAN EQQLVDCAQD FNNY...... ..GCQGGLPS QAFEYILYNK GIMGEDTYPY 37 | CYS1_DICDI EQNLVDCDHE CMEYEGEEAC DEGCNGGLQP NAYNYIIKNG GIQTESSYPY 38 | 39 | 40 | ALEU_HORVU KGVNGVCHYK AENAAVQVLD SVNITLNAED ELKNAVGLVR PVSVAFQVID 41 | CATH_HUMAN QGKDGYCKFQ PGKAIGFVKD VANITIYDEE AMVEAVALYN PVSFAFEVTQ 42 | CYS1_DICDI TAETGTQCNF NSANIGAKIS NFTMIPKNET VMAGYIVSTG PLAIAADAVE 43 | 44 | 45 | ALEU_HORVU GFRQYKSGVY TSDHCGTTPD DVNHAVLAVG YGVEN..... GVPYWLIKNS 46 | CATH_HUMAN DFMMYRTGIY SSTSCHKTPD KVNHAVLAVG YGEKN..... GIPYWIVKNS 47 | CYS1_DICDI .WQFYIGGVF DIPCN...PN SLDHGILIVG YSAKNTIFRK NMPYWIVKNS 48 | 49 | 50 | ALEU_HORVU WGADWGDNGY FKMEMGKNMC AIATCASYPV VAA 51 | CATH_HUMAN WGPQWGMNGY FLIERGKNMC GLAACASYPI PLV 52 | CYS1_DICDI WGADWGEQGY IYLRRGKNTC GVSNFVSTSI I.. 53 | 54 | -------------------------------------------------------------------------------- /t/data/cysprot1b.fa: -------------------------------------------------------------------------------- 1 | >CATH_RAT 2 | MWTALPLLCAGAWLLSAGATAELTVNAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRN 3 | HTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCW 4 | TFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNG 5 | QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHA 6 | VLAVGYGEQNGLLYWIVKNSWGSNWGNNGYFLIERGKNMCGLAACASYPIPQV 7 | 8 | 9 | >CATL_HUMAN 10 | MNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGK 11 | HSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWA 12 | FSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES 13 | CKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLV 14 | VGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV 15 | 16 | 17 | >CATL_RAT 18 | MTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGK 19 | HGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQEPLMLQIPKTVDWREKGCVTPVKNQGQCGSCWA 20 | FSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS 21 | CKYRAEYAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLV 22 | VGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIVN 23 | 24 | 25 | >PAPA_CARPA 26 | MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFE 27 | IFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDW 28 | RQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQ 29 | YGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGG 30 | IFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /t/data/cysprot1b.msf: -------------------------------------------------------------------------------- 1 | PileUp 2 | 3 | 4 | 5 | MSF: 366 Type: P Check: 8252 .. 6 | 7 | Name: CATL_HUMAN oo Len: 366 Check: 9087 Weight: 21.6 8 | Name: CATL_RAT oo Len: 366 Check: 271 Weight: 20.7 9 | Name: CATH_RAT oo Len: 366 Check: 8974 Weight: 27.9 10 | Name: PAPA_CARPA oo Len: 366 Check: 9920 Weight: 29.7 11 | 12 | // 13 | 14 | 15 | 16 | CATL_HUMAN ......MNPT LILAAFCLGI .......... ...ASATLTF DHSLEAQWTK 17 | CATL_RAT ......MTPL LLLAVLCLGT .......... ...ALATPKF DQTFNAQWHQ 18 | CATH_RAT ...MWTALPL LCAGAWLLSA G......... ...ATAELTV NAIEKFHFTS 19 | PAPA_CARPA MAMIPSISKL LFVAICLFVY MGLSFGDFSI VGYSQNDLTS TERLIQLFES 20 | 21 | 22 | CATL_HUMAN WKAMHNRLYG .MNEEGWRRA VWEKNMKMIE LHNQEYREGK HSFTMAMNAF 23 | CATL_RAT WKSTHRRLYG .TNEEEWRRA VWEKNMRMIQ LHNGEYSNGK HGFTMEMNAF 24 | CATH_RAT WMKQHQKTYS .SREYSHRLQ VFANNWRKIQ AHNQRN.... HTFKMGLNQF 25 | PAPA_CARPA WMLKHNKIYK NIDEKIYRFE IFKDNLKYID ETNKKN.... NSYWLGLNVF 26 | 27 | 28 | CATL_HUMAN GDMTSEEFRQ VMNGFQNRKP RKGKVFQEPL FY....EAPR SVDWREKG.Y 29 | CATL_RAT GDMTNEEFRQ IVNGYRHQKH KKGRLFQEPL ML....QIPK TVDWREKG.C 30 | CATH_RAT SDMSFAEIKH KYLWSEPQNC SATKSNYLRG TG....PYPS SMDWRKKGNV 31 | PAPA_CARPA ADMSNDEFKE KYTGSIAGNY TTTELSYEEV LNDGDVNIPE YVDWRQKG.A 32 | 33 | 34 | CATL_HUMAN VTPVKNQGQC GSCWAFSATG ALEGQMFRKT GRLISLSEQN LVDCSGPQGN 35 | CATL_RAT VTPVKNQGQC GSCWAFSASG CLEGQMFLKT GKLISLSEQN LVDCSHDQGN 36 | CATH_RAT VSPVKNQGAC GSCWTFSTTG ALESAVAIAS GKMMTLAEQQ LVDCAQNFNN 37 | PAPA_CARPA VTPVKNQGSC GSCWAFSAVV TIEGIIKIRT GNLNEYSEQE LLDCDRR..S 38 | 39 | 40 | CATL_HUMAN EGCNGGLMDY AFQYVQDNGG LDSEESYPYE ATEESCKYNP KYSVANDTGF 41 | CATL_RAT QGCNGGLMDF AFQYIKENGG LDSEESYPYE AKDGSCKYRA EYAVANDTGF 42 | CATH_RAT HGCQGGLPSQ AFEYILYNKG IMGEDSYPYI GKNGQCKFNP EKAVAFVKNV 43 | PAPA_CARPA YGCNGGYPWS ALQLVAQYG. IHYRNTYPYE GVQRYCRSRE KGPYAAKTDG 44 | 45 | 46 | CATL_HUMAN VDIPK.QEKA LMKAVATVGP ISVAIDAGHE SFLFYKEGIY FEPDCSS..E 47 | CATL_RAT VDIPQ.QEKA LMKAVATVGP ISVAMDASHP SLQFYSSGIY YEPNCSS..K 48 | CATH_RAT VNITLNDEAA MVEAVALYNP VSFAFEVT.E DFMMYKSGVY SSNSCHKTPD 49 | PAPA_CARPA VRQVQPYNEG ALLYSIANQP VSVVLEAAGK DFQLYRGGIF VGP.CGN... 50 | 51 | 52 | CATL_HUMAN DMDHGVLVVG YGFESTESDN NKYWLVKNSW GEEWGMGGYV KMAKDRR... 53 | CATL_RAT DLDHGVLVVG YGYEGTDSNK DKYWLVKNSW GKEWGMDGYI KIAKDRN... 54 | CATH_RAT KVNHAVLAVG YG....EQNG LLYWIVKNSW GSNWGNNGYF LIERGK.... 55 | PAPA_CARPA KVDHAVAAVG YG........ PNYILIKNSW GTGWGENGYI RIKRGTGNSY 56 | 57 | 58 | CATL_HUMAN NHCGIASAAS YPTV.. 59 | CATL_RAT NHCGLATAAS YPIVN. 60 | CATH_RAT NMCGLAACAS YPIPQV 61 | PAPA_CARPA GVCGLYTSSF YPVKN. 62 | 63 | -------------------------------------------------------------------------------- /t/data/dba1a.fa: -------------------------------------------------------------------------------- 1 | >Test1 2 | AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 3 | TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA 4 | TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC 5 | -------------------------------------------------------------------------------- /t/data/dba1b.fa: -------------------------------------------------------------------------------- 1 | >Test2 2 | AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 3 | TTCTGAACTGGTTACCTGAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA 4 | TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC 5 | -------------------------------------------------------------------------------- /t/data/dba2.fa: -------------------------------------------------------------------------------- 1 | >Test1 2 | AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 3 | TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA 4 | TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC 5 | >Test2 6 | AGCTTTTTTTTTTTTTTTTTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 7 | TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTAACTTAGGTCACTAAATACTTTAACCAA 8 | TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC 9 | -------------------------------------------------------------------------------- /t/data/dna1.fa: -------------------------------------------------------------------------------- 1 | >Test1 2 | AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 3 | TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA 4 | TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC 5 | -------------------------------------------------------------------------------- /t/data/dna2.fa: -------------------------------------------------------------------------------- 1 | >Test1 2 | AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 3 | TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA 4 | TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC 5 | ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG 6 | >Test2 7 | CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA 8 | GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC 9 | AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG 10 | AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT -------------------------------------------------------------------------------- /t/data/dna_seqs1.phy: -------------------------------------------------------------------------------- 1 | 5 60 2 | Tax1 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAG 3 | Tax2 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGG 4 | Tax3 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGG 5 | Tax4 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGG 6 | Tax5 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGG 7 | 8 | GAAATGGTCAATATTACAAGGT 9 | GAAATGGTCAACATTAAAAGAT 10 | GAAATCGTCAATATTAAAAGGT 11 | GAAATGGTCAATCTTAAAAGGT 12 | GAAATGGTCAATATTAAAAGGT 13 | -------------------------------------------------------------------------------- /t/data/ecolitst.fa: -------------------------------------------------------------------------------- 1 | >gi|1786183|gb|AAC73113.1| (AE000111) aspartokinase I, homoserine dehydrogenase I [Escherichia coli] 2 | MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAA 3 | AQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHY 4 | LESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 5 | PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSV 6 | SGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIIS 7 | VVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL 8 | LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAV 9 | ADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSL 10 | SYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA 11 | NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGND 12 | VTAAGVFADLLRTLSWKLGV 13 | -------------------------------------------------------------------------------- /t/data/elink_result.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | gene 8 | 9 | 790 10 | 11 | 12 | taxonomy 13 | gene_taxonomy 14 | 15 | 9606 16 | 17 | 18 | 19 | 20 | 21 | gene 22 | 23 | 828392 24 | 25 | 26 | taxonomy 27 | gene_taxonomy 28 | 29 | 3702 30 | 31 | 32 | 33 | 34 | 35 | gene 36 | 37 | 470338 38 | 39 | 40 | taxonomy 41 | gene_taxonomy 42 | 43 | 9598 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | -------------------------------------------------------------------------------- /t/data/eponine.fa: -------------------------------------------------------------------------------- 1 | >ZFEM-P3-16-10-01-E06 2 | GAAGACGAGCGCAGNGAGTAGTGAGCGAGGAAGCGGCCGCATAACTTCGTATAGCATACATTATACGAAGTTATCAGTCGACGGTACCGGACATATGCCCGGGAATTCGGCCATTACGGCCGGGGACACGCGCACGCGTACTGTGAGCGCGCGGACTTCGAGACGTGACGTCAAACTGTGCGCGATCAGTCGTGGCGGGAGATTTTCGAGTGTCTTGTCGGTCTGCTTCGCATTCAGAAGAAAAACATTCACGAGTGAAATGTGGAACCAAGGTAAATACGGAGAGGCCAGTATGGCTGGGTACACACAGTCTCCTGGAGGATTCGGGTCACCAGCCGCTTCTCAAGGAGGAGACAAAAAGGGGAGGACACGAGCGCAGCAGATCGTTCCCTGTACTGTATCTCAGCTGTNTGTCGGCG 3 | 4 | -------------------------------------------------------------------------------- /t/data/esearch_result.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 777200 5 | 4212556 6 | 7103559 7 | 7036330 8 | 7005509 9 | 6515581 10 | 6333573 11 | 6067533 12 | 5849183 13 | 5625162 14 | 5613996 15 | 5451592 16 | 5188376 17 | 5182770 18 | 5174340 19 | 5132346 20 | 5079123 21 | 4625535 22 | 4233539 23 | 4227906 24 | 4171988 25 | shine[All Fields] All Fields 781 Y dalgarno[All Fields] All Fields 777 Y AND GROUP shine[All Fields] AND dalgarno[All Fields] 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /t/data/exonerate_cdna.fa: -------------------------------------------------------------------------------- 1 | >MUSSPSYN Mouse spermidine synthase mRNA, complete cds. 2 | CGGGTTGTGCTGGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCG 3 | GCCCGCCCGCCCGCCATGGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCC 4 | ATCCGTGAGGGCTGGTTCCGAGAGACCTGCAGCCTGTGGCCCGGCCAGGCCCTGTCGCTG 5 | CAAGTGGAGCAGCTGCTTCACCACCGGCGATCGCGGTACCAAGACATCCTCGTCTTCCGC 6 | AGTAAAACCTACGGCAACGTGCTGGTTCTGGATGGCGTCATCCAGTGTACTGAGAGGGAT 7 | GAGTTCTCCTACCAGGAGATGATCGCCAACCTGCCGCTCTGCAGCCACCCCAACCCGCGG 8 | AAGGTGCTGATCATCGGGGGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCC 9 | TCTGTGGAGTCGGTGGTCCAGTGCGAGATTGATGAGGATGTCATTGAAGTCTCTAAGAAG 10 | TTCCTGCCTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGGGCGAT 11 | GGCTTTGAGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCCTCA 12 | GACCCCATGGGCCCTGCTGAGAGCCTCTTCAAGGAGTCCTATTACCAGCTCATGAAGACA 13 | GCACTCAAAGAAGATGGCATCCTGTGCTGCCAGGGTGAGTGCCAGTGGCTGCACCTGGAC 14 | CTCATCAAGGAGATGAGGCACTTCTGCAAATCTCTCTTCCCCGTGGTGGACTACGCCTAC 15 | TGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGCTTCATGCTGTGTAGCAAAAACCCG 16 | AGCACCAACTTCCGGGAGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAG 17 | CTGAAATACTATAACTCGGACATGCACCGTGCCGCCTTCGTACTGCCTGAGTTCACCCGG 18 | AAGGCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACCACCCGAGACCTCAA 19 | TCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCTGGACCAGACTCC 20 | CAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCATGATGCTGCCTGGCCTGGCC 21 | TGGCCTGGCCTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGTCTATCTCT 22 | GTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTGTGACCC 23 | AACAAAATACATGTGTATTCCG 24 | -------------------------------------------------------------------------------- /t/data/exonerate_cdna_rev.fa: -------------------------------------------------------------------------------- 1 | >MUSSPSYN Mouse spermidine synthase mRNA, complete cds. 2 | CGGAATACACATGTATTTTGTTGGGTCACAGGGCATAGGCGGTGCTGTAC 3 | AGAGCTGGTATAGGCGTGGGGCTGAACGCCACAGAGATAGACAGACAGAG 4 | ACTGAGTCCACCCAGCAGGGCAGGCCAGGCCAGGCCAGGCCAGGCCAGGC 5 | CAGGCAGCATCATGGGGCCTGTAACACTTGGTTGGTGGGCAAGAGTCATC 6 | TGGGAGTCTGGTCCAGGACTGGTGGTCCCCAGACAACTTGGAAGATCCTT 7 | GGTCCAATCCGATTGAGGTCTCGGGTGGTGTCACAGTGGCACCTGGATTC 8 | AGCTTATGTCATTGAGGGCCTTCCGGGTGAACTCAGGCAGTACGAAGGCG 9 | GCACGGTGCATGTCCGAGTTATAGTATTTCAGCTGCATCTGCTCCACCTG 10 | GGCCTGTGTCAACTGCTGCACTGGCTCCCGGAAGTTGGTGCTCGGGTTTT 11 | TGCTACACAGCATGAAGCCGATCTGGCCGCTGGGATAGGTAGGAATGCTA 12 | CAGTAGGCGTAGTCCACCACGGGGAAGAGAGATTTGCAGAAGTGCCTCAT 13 | CTCCTTGATGAGGTCCAGGTGCAGCCACTGGCACTCACCCTGGCAGCACA 14 | GGATGCCATCTTCTTTGAGTGCTGTCTTCATGAGCTGGTAATAGGACTCC 15 | TTGAAGAGGCTCTCAGCAGGGCCCATGGGGTCTGAGGAGTCGGTGATGAT 16 | GACGTCAAAGGCATCTTGGTTCTGTTTCATGAACTCAAAGCCATCGCCCA 17 | CGTGGAGAGTCAGCTTTGAGCTGGAGAAGCCAACGGCCATGCCAGGCAGG 18 | AACTTCTTAGAGACTTCAATGACATCCTCATCAATCTCGCACTGGACCAC 19 | CGACTCCACAGAGGGGTGCTTCACCACTTCCCGTAGGACGCCCCCATCTC 20 | CACCCCCGATGATCAGCACCTTCCGCGGGTTGGGGTGGCTGCAGAGCGGC 21 | AGGTTGGCGATCATCTCCTGGTAGGAGAACTCATCCCTCTCAGTACACTG 22 | GATGACGCCATCCAGAACCAGCACGTTGCCGTAGGTTTTACTGCGGAAGA 23 | CGAGGATGTCTTGGTACCGCGATCGCCGGTGGTGAAGCAGCTGCTCCACT 24 | TGCAGCGACAGGGCCTGGCCGGGCCACAGGCTGCAGGTCTCTCGGAACCA 25 | GCCCTCACGGATGGCGGCGGGGCCGGGCGCGGCTGGGCCGTCGGGGCCAG 26 | GCTCCATGGCGGGCGGGCGGGCCGACGGAGCGCGTAGCGGGTTCGGGACT 27 | GCAGGGCGCGCGGACCCCCCCAGCACAACCCG 28 | -------------------------------------------------------------------------------- /t/data/exonerate_genomic.fa: -------------------------------------------------------------------------------- 1 | >4.143962167-143965267 Slice, no description 2 | GGCGCGGGCAGCGGGCAGAGCTGGTCACGTTGTGCTGGGGGGGGTCCGCGCGCCCTGCAG 3 | TCCCGAACCCGCTACGCGCTCCGTCGGCCCGCCCGCCCGCCATGGAGCCTGGCCCCGACG 4 | GCCCAGCCGCGCCCGGCCCCGCCGCCATCCGTGAGGGCTGGTTCCGAGAGACCTGCAGCC 5 | TGTGGCCCGGCCAGGCCCTGTCGCTGCAAGTGGAGCAGCTGCTTCACCACCGGCGATCGC 6 | GGTACCAAGACATCCTCGTCTTCCGCAGGTATGGCCCGCCGCGCGCCGGTGCAGCTGTCA 7 | GAAGTTCTGCGCTGGGCCCGGCCCTGCGTCCACGTGTCACTATCGGGACACGTCAGCCGA 8 | GGGGACCCCGGGACCCACCCAGCCCCCACACGTGGCTCGCCTGCCACGTGTCACCCCGAA 9 | TGCCCACCCCTGGACCCCATGGCGGCCACGTGCACGCCCAGGGAGGACAGGGACCTAACC 10 | TCCCAGTGTCCCAGGACCCACGTCCCCGACTGTCTCTGCCCGCAGTAAAACCTACGGCAA 11 | CGTGCTGGTTCTGGATGGCGTCATCCAGTGTACTGAGAGGGATGAGTTCTCCTACCAGGA 12 | GATGATCGCCAACCTGCCGCTCTGCAGCCACCCCAACCCGCGGAAGGTACCGCATTGCCC 13 | CTGGGTTCAGCCCTGAGCTCGGGGTCCTAGAAAAGCATGTCGGGCTGACACTAGGTGAGG 14 | ATGTTTGGGGGCAGATGCTACCCAGATGACTGTCAGAAAATGCGGGTCGGTCAGGATGAA 15 | TAGAGCTCCTGGGAGAGCTGGTCTCCTTAGAAGCCCCGAGAGGGGAACCCAGGCTGCCAG 16 | GAAGGACCCCGTGGCACAGAAGCGTTCTGGAGAGTAGAGAATGACTCAGAGTCCTGTAGC 17 | TGGGAAGATCAGGTTCTGTGGGAGTGGGCCTGCTCAGTCCTGACTTGTCCTTCCCTGGCC 18 | CAGGTGCTGATCATCGGGGGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCC 19 | TCTGTGGAGTCGGTGGTCCAGTGCGAGATTGATGAGGTGGGTGCAGTCCAGGAGGCCTGG 20 | ATTTGAGTCACCAGAGTCAGCTCTGTCCCATCCTGACTCTGCACCCCGAGGCGCAATGTT 21 | CTTACCATCCCTGCCCTGTTTCCTCAGTCTGAAAAGAGGGTTCAGTAGGAAAACCAGATT 22 | GTTAAGGCCTGGCACACACCACACCATGGATGTTAACTCTTAGTGCTTTCAGAGCCCAGG 23 | CAGAGCCAGAGAGCTCAACAACTTATGGCATCTCCCCTTGAGACCCAGCATGGTTTTAGT 24 | GAGCACTTACTGTATGCTGAGTGTTACCCAAGGTGCTGGGTTGATACGGCCATGGACAGG 25 | TGAGCCCCTGAGTGTAGAGCTGGTGTTTGGGTTGGAGAAGACACCATAACACAGCATGAC 26 | ATGATGAGGCCAGACAGGGATAAAAGATATGGAGAACACAGGCTGATAGGAAGTGTGCAG 27 | CCACGCATGCTTACAGCCCCAGCACTTGGGTAGAAGCAGGACGATCAAGAGTTTGAGGCC 28 | AGCGTGAGTTATCTGAGACCATCTCTCAAAAATGCAGAAGCTCAGATGGGACTTGGTCTG 29 | CAGGGAGTTGAGGCCTGAAAACCATGAAGAGCTGAGGTGGTGTAGATCTGGGGGAAAGGG 30 | TTTTCAAAAGAGAAGACTTGTCCAAAGAAACCCCACCAGGAGTCCCCAGCCTCTAGTCCA 31 | GCCCAGCCCTTCCTCTCCCCCCTCTTCAGGATGTCATTGAAGTCTCTAAGAAGTTCCTGC 32 | CTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGGGCGATGGCTTTG 33 | AGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCCTCAGACCCCA 34 | TGGGTGAGCCAGGGCACGCGCGTCCTGCAGCACACAGCAGCCCCAGACTAGAGCCATGTG 35 | ATGATGGAGGCCTGAGGACGGTGGGGGTCTAGCCTTGGTCCATAGTGACCTCTGCTTCCT 36 | CTTTGGCTTCTTCCCTGTGCTTGTTGGCCAGCATCCGGGTGTGCTATGGTGCAGTGGGGG 37 | AGGGTTTGAATGCAGGGCCTCCCAGGTGCTAAGGCAGTAGGGGGCCACATCCCACAAACA 38 | TGGGTCCAGCACCTGCTTTGCCACTGAGCTGCTGTGGGTGACTGTGGCCTGGAGGTCTCA 39 | GGCAGGATGGCCATGCTCTACCCCTCTAGGCCCTGCTGAGAGCCTCTTCAAGGAGTCCTA 40 | TTACCAGCTCATGAAGACAGCACTCAAAGAAGATGGCATCCTGTGCTGCCAGGGTGAGTG 41 | CCAGTGGCTGCACCTGGACCTCATCAAGGAGATGAGGCACTTCTGCAAATCTCTCTTCCC 42 | CGTGGTGGACTACGCCTACTGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGCTTCAT 43 | GCTGTGTAGCAAAAACCCGGTGAGCTGGGGGTGACTGCCTGCAGGGTGGGGCGAGGGCAG 44 | GCACTAAGAGCCCCATCTTGATGCTCTTTGTCCCTGGTTCCCAGAGCACCAACTTCCGGG 45 | AGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAGCTGAAATACTATAACT 46 | CGGACATGCACCGTGCCGCCTTCGTACTGCCCGAGTTCACCCGGAAGGTGAGTGGCCTGC 47 | CAGGCTCCCTGCTGGGCCTCATCCTGCACAGCTTGCACATCCTCCTGACTGCCTTCATGT 48 | CCCACCAGGCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACCACCCGAGAC 49 | CTCAATCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCTGGACCAG 50 | ACTCCCAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCACGATGCTGCCTGGCC 51 | TGGCCTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGTCTATCTCTGTGGC 52 | GTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTGTGACCCAACAA 53 | AATACATGTGTATTTATAACAAGCTCAGTCATGACCTCTGA 54 | -------------------------------------------------------------------------------- /t/data/exonerate_genomic_rev.fa: -------------------------------------------------------------------------------- 1 | >4.143962167-143965267 Slice, no description 2 | TCAGAGGTCATGACTGAGCTTGTTATAAATACACATGTATTTTGTTGGGT 3 | CACAGGGCATAGGCGGTGCTGTACAGAGCTGGTATAGGCGTGGGGCTGAA 4 | CGCCACAGAGATAGACAGACAGAGACTGAGTCCACCCAGCAGGGCAGGCC 5 | AGGCCAGGCCAGGCCAGGCAGCATCGTGGGGCCTGTAACACTTGGTTGGT 6 | GGGCAAGAGTCATCTGGGAGTCTGGTCCAGGACTGGTGGTCCCCAGACAA 7 | CTTGGAAGATCCTTGGTCCAATCCGATTGAGGTCTCGGGTGGTGTCACAG 8 | TGGCACCTGGATTCAGCTTATGTCATTGAGGGCCTGGTGGGACATGAAGG 9 | CAGTCAGGAGGATGTGCAAGCTGTGCAGGATGAGGCCCAGCAGGGAGCCT 10 | GGCAGGCCACTCACCTTCCGGGTGAACTCGGGCAGTACGAAGGCGGCACG 11 | GTGCATGTCCGAGTTATAGTATTTCAGCTGCATCTGCTCCACCTGGGCCT 12 | GTGTCAACTGCTGCACTGGCTCCCGGAAGTTGGTGCTCTGGGAACCAGGG 13 | ACAAAGAGCATCAAGATGGGGCTCTTAGTGCCTGCCCTCGCCCCACCCTG 14 | CAGGCAGTCACCCCCAGCTCACCGGGTTTTTGCTACACAGCATGAAGCCG 15 | ATCTGGCCGCTGGGATAGGTAGGAATGCTACAGTAGGCGTAGTCCACCAC 16 | GGGGAAGAGAGATTTGCAGAAGTGCCTCATCTCCTTGATGAGGTCCAGGT 17 | GCAGCCACTGGCACTCACCCTGGCAGCACAGGATGCCATCTTCTTTGAGT 18 | GCTGTCTTCATGAGCTGGTAATAGGACTCCTTGAAGAGGCTCTCAGCAGG 19 | GCCTAGAGGGGTAGAGCATGGCCATCCTGCCTGAGACCTCCAGGCCACAG 20 | TCACCCACAGCAGCTCAGTGGCAAAGCAGGTGCTGGACCCATGTTTGTGG 21 | GATGTGGCCCCCTACTGCCTTAGCACCTGGGAGGCCCTGCATTCAAACCC 22 | TCCCCCACTGCACCATAGCACACCCGGATGCTGGCCAACAAGCACAGGGA 23 | AGAAGCCAAAGAGGAAGCAGAGGTCACTATGGACCAAGGCTAGACCCCCA 24 | CCGTCCTCAGGCCTCCATCATCACATGGCTCTAGTCTGGGGCTGCTGTGT 25 | GCTGCAGGACGCGCGTGCCCTGGCTCACCCATGGGGTCTGAGGAGTCGGT 26 | GATGATGACGTCAAAGGCATCTTGGTTCTGTTTCATGAACTCAAAGCCAT 27 | CGCCCACGTGGAGAGTCAGCTTTGAGCTGGAGAAGCCAACGGCCATGCCA 28 | GGCAGGAACTTCTTAGAGACTTCAATGACATCCTGAAGAGGGGGGAGAGG 29 | AAGGGCTGGGCTGGACTAGAGGCTGGGGACTCCTGGTGGGGTTTCTTTGG 30 | ACAAGTCTTCTCTTTTGAAAACCCTTTCCCCCAGATCTACACCACCTCAG 31 | CTCTTCATGGTTTTCAGGCCTCAACTCCCTGCAGACCAAGTCCCATCTGA 32 | GCTTCTGCATTTTTGAGAGATGGTCTCAGATAACTCACGCTGGCCTCAAA 33 | CTCTTGATCGTCCTGCTTCTACCCAAGTGCTGGGGCTGTAAGCATGCGTG 34 | GCTGCACACTTCCTATCAGCCTGTGTTCTCCATATCTTTTATCCCTGTCT 35 | GGCCTCATCATGTCATGCTGTGTTATGGTGTCTTCTCCAACCCAAACACC 36 | AGCTCTACACTCAGGGGCTCACCTGTCCATGGCCGTATCAACCCAGCACC 37 | TTGGGTAACACTCAGCATACAGTAAGTGCTCACTAAAACCATGCTGGGTC 38 | TCAAGGGGAGATGCCATAAGTTGTTGAGCTCTCTGGCTCTGCCTGGGCTC 39 | TGAAAGCACTAAGAGTTAACATCCATGGTGTGGTGTGTGCCAGGCCTTAA 40 | CAATCTGGTTTTCCTACTGAACCCTCTTTTCAGACTGAGGAAACAGGGCA 41 | GGGATGGTAAGAACATTGCGCCTCGGGGTGCAGAGTCAGGATGGGACAGA 42 | GCTGACTCTGGTGACTCAAATCCAGGCCTCCTGGACTGCACCCACCTCAT 43 | CAATCTCGCACTGGACCACCGACTCCACAGAGGGGTGCTTCACCACTTCC 44 | CGTAGGACGCCCCCATCTCCACCCCCGATGATCAGCACCTGGGCCAGGGA 45 | AGGACAAGTCAGGACTGAGCAGGCCCACTCCCACAGAACCTGATCTTCCC 46 | AGCTACAGGACTCTGAGTCATTCTCTACTCTCCAGAACGCTTCTGTGCCA 47 | CGGGGTCCTTCCTGGCAGCCTGGGTTCCCCTCTCGGGGCTTCTAAGGAGA 48 | CCAGCTCTCCCAGGAGCTCTATTCATCCTGACCGACCCGCATTTTCTGAC 49 | AGTCATCTGGGTAGCATCTGCCCCCAAACATCCTCACCTAGTGTCAGCCC 50 | GACATGCTTTTCTAGGACCCCGAGCTCAGGGCTGAACCCAGGGGCAATGC 51 | GGTACCTTCCGCGGGTTGGGGTGGCTGCAGAGCGGCAGGTTGGCGATCAT 52 | CTCCTGGTAGGAGAACTCATCCCTCTCAGTACACTGGATGACGCCATCCA 53 | GAACCAGCACGTTGCCGTAGGTTTTACTGCGGGCAGAGACAGTCGGGGAC 54 | GTGGGTCCTGGGACACTGGGAGGTTAGGTCCCTGTCCTCCCTGGGCGTGC 55 | ACGTGGCCGCCATGGGGTCCAGGGGTGGGCATTCGGGGTGACACGTGGCA 56 | GGCGAGCCACGTGTGGGGGCTGGGTGGGTCCCGGGGTCCCCTCGGCTGAC 57 | GTGTCCCGATAGTGACACGTGGACGCAGGGCCGGGCCCAGCGCAGAACTT 58 | CTGACAGCTGCACCGGCGCGCGGCGGGCCATACCTGCGGAAGACGAGGAT 59 | GTCTTGGTACCGCGATCGCCGGTGGTGAAGCAGCTGCTCCACTTGCAGCG 60 | ACAGGGCCTGGCCGGGCCACAGGCTGCAGGTCTCTCGGAACCAGCCCTCA 61 | CGGATGGCGGCGGGGCCGGGCGCGGCTGGGCCGTCGGGGCCAGGCTCCAT 62 | GGCGGGCGGGCGGGCCGACGGAGCGCGTAGCGGGTTCGGGACTGCAGGGC 63 | GCGCGGACCCCCCCCAGCACAACGTGACCAGCTCTGCCCGCTGCCCGCGC 64 | C 65 | -------------------------------------------------------------------------------- /t/data/fasta.fa: -------------------------------------------------------------------------------- 1 | >SINFRUT00000067802 2 | CTGGACGAGGACCAGTTATCCCATAGCAGCAGTCGTCTCTCCAGGTCTCC 3 | CCTGAAAGGAGTCAAGAAAGCGAAGATAATGCAGTGTAAAGTCACATTGC 4 | TGGACAACTCCGACTACACAATTGATGTAGAGAAAGGAGCCAGGGGCCAA 5 | ATGCTCTTTGATAAAGTATGTGAGCATCTAAATTTACTCGAGAGAGACTA 6 | CTTTGGCATCACATATAGAGACGTTGAGAATCAGAAGAATTGGCTGGATC 7 | CTTCTAAAGAGCTGAAAAAGCAGATCCGGACTGGTCCCTGGAACTTTGCC 8 | TTCAATGTCAAGTTTTACCCTCCAGATCCTGTCCAGCTGGCTGAGGACAT 9 | CACAAGGTACTATTTGTGTCTGCAGCTGAGAGATGATGTGGTTTCGGGCC 10 | GTCTGCCCTGCTCTTTTGCCACCCACACAGTTCTAGGCTCTTACACGGTG 11 | CAGTCTGAACTGGGAGACTATGACCATGAGGAGCTGGGCAGCGACTACCT 12 | CAGTGAGCTGCGCCTTGCACCCAACCAGACCAAAGAGCTTGAGGAAAAGG 13 | TCATGGAACTCCACAAGAGCTACAAGGGGATGACACCTGGGGAAGCAGAG 14 | ATGCACTTCCTGGAAAATGCCAAGAAGCTGTCCATGTACGGCGTTGATCT 15 | CCACCACGCTAAGGACTCTGAGGGAGTTGAGATCATGCTGGGAGTTTGCT 16 | CGAGCGGCCTGCTTATCTACAGAGACAGGTTGCGGATCAACAGGTTTGCT 17 | TGGCCTAAAATACTCAAGATTTCTTACAAGAGGAATAACTTCTACATCAA 18 | AATCCGTCCGGGCGAGTTTGAGCAGTTTGAGAGCACGATCGGTTTCAAGC 19 | TTCCCAATCATCGTGCTGCCAAAAGGCTCTGGAAGGTCTGTGTGGAGCAT 20 | CACACCTTCTTCAGGCAAGTCATGAAGGAGGTGCTGGGGCTAGTGTCTCC 21 | TGAGGCGCCTCCAAAGAAGTTCCTGAGTCTTGGCTCTAAGTTTCGCTACA 22 | GTGGCAGAACGCAGGCTCAGACCCGACGGGCCAGCTCTCAGATCATTAGA 23 | CCTGCTCCGTTCTTTGAGCGTTCCTCCAGCAAACGCTACAACATGTCCCG 24 | TAGTTTAGATGGAGACAGCTCTGCTGATGGAGTGGCTCGAGTTAAGGGAA 25 | ATATCATCACCACTGTAACTCCAGAGAGAAAAGCAGAAGAAGAGAACGGA 26 | GAGCAGGAGGATGCCAAGAACGATGCGGCAGACAAGCCAGACCCTGCTGC 27 | TTCCAGCCCTCTCCACCAAGAAACAAAGGTAACACTAGACGATCCCCTCC 28 | GCTCTGAGCTCTCTCTCCCCTCATCTCCTATCTCATTCACTAAAATACGG 29 | CGGAGGCGCAGGGAGAACGCACATAAGCGAGCCTCCTCAGTCAGTCCAGG 30 | CAAGAGCAGCACAGGGCGTTGCCGCCGTCAGGCCCTTGCTGATCGCAAAG 31 | CTGCGCTGCTAGATGAGCAAGCCTTGCTGCTCGTGGCACGAAAGCAGAGA 32 | CTGGAGCAGGGCAGGAATCATGGCGGCACACTCTTCTCCTTCTCCCTGCA 33 | CCTGCCCGACCTGTCCTCTGTCTTGGACGAAGACGGTTACATCACCTTCC 34 | CCGATCTGTCCAAAATGCGCTTCCTCCCTGAGTGTGCGCAGAACTTCCTG 35 | CCCATCAAGTCACCTTATCTTTGCTCGCTGCTACTTTTCACTCTCTTCAC 36 | CTTCTTTTTTCTTTGTCTACTAAATTCTCTTCACCTCTCCTCTTTCGCTG 37 | TCAGTCGGAAGCAGACGAGGAATCTGAAATACAGACTCAGGTACACTGGG 38 | CTCACTTTTATCGATCGGCCCTGCTCGATGCATCAAATCCTTGACATCCT 39 | CACAAGATGCCCCGAGCCATCGGCATCCACCATCAGTCACTTTGCTGTCT 40 | CCATCTTGGCTTACTGCTTCTCTGAGGTGGTCAAACACCAGACCAACATC 41 | AGCGAACTGAAGCGCTCCTTCCTGGAGACGGGTGATGGCACGCAAGGCCC 42 | GACCGAATGGGAGAAGAGGCTGTCCTCGTCTCCCATGTGCTCACCAAGAT 43 | TTGATGAGGCACCGATGATTGAGCCGCTGGATGTAAGCGTCGATGAGCGA 44 | ACCTCTGACTCCCAGGAGGACGTGTCGGAGAGGTCAATGTTGAAGGTCAG 45 | CCCCAGAGCTGTTACACAGGAAGTGTCGCAGGCCATCAGTGACAAGAAGG 46 | GAAGGCTTATTATCTTGAAAGATGCTGAACATAAAGAGGAGGACGAAGAA 47 | CCCGGAGAGGCTGAAGGCGTGGAGAAGGAATTGCCTCCATCAAAAGAGAA 48 | AGAAATGGTTAAAGAAGACGCCGCTGATGTTCTGGCCTCTATAACAAGGG 49 | AAATCAAGAAGCAGCATCCGAAGGTGGAAATAAAAACTAACGGCACGCAA 50 | CAGATTAACGGTAGTGACTCGCCTAAAAAGGCCATGGTGTCGTGGATCTC 51 | TGAGGAGGTGAAGACTGTCGCGACAAAGGAAGTAAGTGAGGGAGAGAGCG 52 | TTGAAGCGCCGCAGCAAACGGCGGAGATCTTCACCTTTGAAGAGGAGCAG 53 | TCAAAGTCCAGCCCGACCCAGATCACAGTTTCTGAATCTTCAGCTTCTTT 54 | TGCGGTGGTACATCTTGACACCACTGATGCTGGAACCAAAGAGATGCCCG 55 | TGATCCACACAGAGACAAAAACTATCACCTACGAGTCTGCAGAGGTTGAC 56 | ACTAATGGTGACTTGGACCCCGGTGTTCTCCTGAGTGCTCAGACCATCAC 57 | TTCAGAAATTACCAGCACCACCACAACCACACACATCACAAAGATGGTGA 58 | AAGGAGGGATTTCAGAAACAAGAATCGAGAAAAGGATCGTCATCTCAGGA 59 | GATGCAGACATCGATCACGATCAGGCTCTGGCTCAGGCCATAAAAGAGGC 60 | TAAAGAACAGCATCCTGACATGTCAGTGACCAAAGTAGTGGTACATAAAG 61 | AGACAGAGATCACGCCAGAAGAGGGGGAGGAC 62 | -------------------------------------------------------------------------------- /t/data/fastalib.fa: -------------------------------------------------------------------------------- 1 | >SINFRUT00000067802 2 | CTGGACGAGGACCAGTTATCCCATAGCAGCAGTCGTCTCTCCAGGTCTCC 3 | CCTGAAAGGAGTCAAGAAAGCGAAGATAATGCAGTGTAAAGTCACATTGC 4 | TGGACAACTCCGACTACACAATTGATGTAGAGAAAGGAGCCAGGGGCCAA 5 | ATGCTCTTTGATAAAGTATGTGAGCATCTAAATTTACTCGAGAGAGACTA 6 | CTTTGGCATCACATATAGAGACGTTGAGAATCAGAAGAATTGGCTGGATC 7 | CTTCTAAAGAGCTGAAAAAGCAGATCCGGACTGGTCCCTGGAACTTTGCC 8 | TTCAATGTCAAGTTTTACCCTCCAGATCCTGTCCAGCTGGCTGAGGACAT 9 | CACAAGGTACTATTTGTGTCTGCAGCTGAGAGATGATGTGGTTTCGGGCC 10 | GTCTGCCCTGCTCTTTTGCCACCCACACAGTTCTAGGCTCTTACACGGTG 11 | CAGTCTGAACTGGGAGACTATGACCATGAGGAGCTGGGCAGCGACTACCT 12 | CAGTGAGCTGCGCCTTGCACCCAACCAGACCAAAGAGCTTGAGGAAAAGG 13 | TCATGGAACTCCACAAGAGCTACAAGGGGATGACACCTGGGGAAGCAGAG 14 | ATGCACTTCCTGGAAAATGCCAAGAAGCTGTCCATGTACGGCGTTGATCT 15 | CCACCACGCTAAGGACTCTGAGGGAGTTGAGATCATGCTGGGAGTTTGCT 16 | CGAGCGGCCTGCTTATCTACAGAGACAGGTTGCGGATCAACAGGTTTGCT 17 | TGGCCTAAAATACTCAAGATTTCTTACAAGAGGAATAACTTCTACATCAA 18 | AATCCGTCCGGGCGAGTTTGAGCAGTTTGAGAGCACGATCGGTTTCAAGC 19 | TTCCCAATCATCGTGCTGCCAAAAGGCTCTGGAAGGTCTGTGTGGAGCAT 20 | CACACCTTCTTCAGGCAAGTCATGAAGGAGGTGCTGGGGCTAGTGTCTCC 21 | TGAGGCGCCTCCAAAGAAGTTCCTGAGTCTTGGCTCTAAGTTTCGCTACA 22 | GTGGCAGAACGCAGGCTCAGACCCGACGGGCCAGCTCTCAGATCATTAGA 23 | CCTGCTCCGTTCTTTGAGCGTTCCTCCAGCAAACGCTACAACATGTCCCG 24 | TAGTTTAGATGGAGACAGCTCTGCTGATGGAGTGGCTCGAGTTAAGGGAA 25 | ATATCATCACCACTGTAACTCCAGAGAGAAAAGCAGAAGAAGAGAACGGA 26 | GAGCAGGAGGATGCCAAGAACGATGCGGCAGACAAGCCAGACCCTGCTGC 27 | TTCCAGCCCTCTCCACCAAGAAACAAAGGTAACACTAGACGATCCCCTCC 28 | GCTCTGAGCTCTCTCTCCCCTCATCTCCTATCTCATTCACTAAAATACGG 29 | CGGAGGCGCAGGGAGAACGCACATAAGCGAGCCTCCTCAGTCAGTCCAGG 30 | CAAGAGCAGCACAGGGCGTTGCCGCCGTCAGGCCCTTGCTGATCGCAAAG 31 | CTGCGCTGCTAGATGAGCAAGCCTTGCTGCTCGTGGCACGAAAGCAGAGA 32 | CTGGAGCAGGGCAGGAATCATGGCGGCACACTCTTCTCCTTCTCCCTGCA 33 | CCTGCCCGACCTGTCCTCTGTCTTGGACGAAGACGGTTACATCACCTTCC 34 | CCGATCTGTCCAAAATGCGCTTCCTCCCTGAGTGTGCGCAGAACTTCCTG 35 | CCCATCAAGTCACCTTATCTTTGCTCGCTGCTACTTTTCACTCTCTTCAC 36 | CTTCTTTTTTCTTTGTCTACTAAATTCTCTTCACCTCTCCTCTTTCGCTG 37 | TCAGTCGGAAGCAGACGAGGAATCTGAAATACAGACTCAGGTACACTGGG 38 | CTCACTTTTATCGATCGGCCCTGCTCGATGCATCAAATCCTTGACATCCT 39 | CACAAGATGCCCCGAGCCATCGGCATCCACCATCAGTCACTTTGCTGTCT 40 | CCATCTTGGCTTACTGCTTCTCTGAGGTGGTCAAACACCAGACCAACATC 41 | AGCGAACTGAAGCGCTCCTTCCTGGAGACGGGTGATGGCACGCAAGGCCC 42 | GACCGAATGGGAGAAGAGGCTGTCCTCGTCTCCCATGTGCTCACCAAGAT 43 | TTGATGAGGCACCGATGATTGAGCCGCTGGATGTAAGCGTCGATGAGCGA 44 | ACCTCTGACTCCCAGGAGGACGTGTCGGAGAGGTCAATGTTGAAGGTCAG 45 | CCCCAGAGCTGTTACACAGGAAGTGTCGCAGGCCATCAGTGACAAGAAGG 46 | GAAGGCTTATTATCTTGAAAGATGCTGAACATAAAGAGGAGGACGAAGAA 47 | CCCGGAGAGGCTGAAGGCGTGGAGAAGGAATTGCCTCCATCAAAAGAGAA 48 | AGAAATGGTTAAAGAAGACGCCGCTGATGTTCTGGCCTCTATAACAAGGG 49 | AAATCAAGAAGCAGCATCCGAAGGTGGAAATAAAAACTAACGGCACGCAA 50 | CAGATTAACGGTAGTGACTCGCCTAAAAAGGCCATGGTGTCGTGGATCTC 51 | TGAGGAGGTGAAGACTGTCGCGACAAAGGAAGTAAGTGAGGGAGAGAGCG 52 | TTGAAGCGCCGCAGCAAACGGCGGAGATCTTCACCTTTGAAGAGGAGCAG 53 | TCAAAGTCCAGCCCGACCCAGATCACAGTTTCTGAATCTTCAGCTTCTTT 54 | TGCGGTGGTACATCTTGACACCACTGATGCTGGAACCAAAGAGATGCCCG 55 | TGATCCACACAGAGACAAAAACTATCACCTACGAGTCTGCAGAGGTTGAC 56 | ACTAATGGTGACTTGGACCCCGGTGTTCTCCTGAGTGCTCAGACCATCAC 57 | TTCAGAAATTACCAGCACCACCACAACCACACACATCACAAAGATGGTGA 58 | AAGGAGGGATTTCAGAAACAAGAATCGAGAAAAGGATCGTCATCTCAGGA 59 | GATGCAGACATCGATCACGATCAGGCTCTGGCTCAGGCCATAAAAGAGGC 60 | TAAAGAACAGCATCCTGACATGTCAGTGACCAAAGTAGTGGTACATAAAG 61 | AGACAGAGATCACGCCAGAAGAGGGGGAGGAC 62 | -------------------------------------------------------------------------------- /t/data/fastaprot.fa: -------------------------------------------------------------------------------- 1 | >SINFRUP00000067802 2 | LDEDQLSHSSSRLSRSPLKGVKKAKIMQCKVTLLDNSDYTIDVEKGARGQMLFDKVCEHLNLLERDYFGI 3 | TYRDVENQKNWLDPSKELKKQIRTGPWNFAFNVKFYPPDPVQLAEDITRYYLCLQLRDDVVSGRLPCSFA 4 | THTVLGSYTVQSELGDYDHEELGSDYLSELRLAPNQTKELEEKVMELHKSYKGMTPGEAEMHFLENAKKL 5 | SMYGVDLHHAKDSEGVEIMLGVCSSGLLIYRDRLRINRFAWPKILKISYKRNNFYIKIRPGEFEQFESTI 6 | GFKLPNHRAAKRLWKVCVEHHTFFRQVMKEVLGLVSPEAPPKKFLSLGSKFRYSGRTQAQTRRASSQIIR 7 | PAPFFERSSSKRYNMSRSLDGDSSADGVARVKGNIITTVTPERKAEEENGEQEDAKNDAADKPDPAASSP 8 | LHQETKVTLDDPLRSELSLPSSPISFTKIRRRRRENAHKRASSVSPGKSSTGRCRRQALADRKAALLDEQ 9 | ALLLVARKQRLEQGRNHGGTLFSFSLHLPDLSSVLDEDGYITFPDLSKMRFLPECAQNFLPIKSPYLCSL 10 | LLFTLFTFFFLCLLNSLHLSSFAVSRKQTRNLKYRLRYTGLTFIDRPCSMHQILDILTRCPEPSASTISH 11 | FAVSILAYCFSEVVKHQTNISELKRSFLETGDGTQGPTEWEKRLSSSPMCSPRFDEAPMIEPLDVSVDER 12 | TSDSQEDVSERSMLKVSPRAVTQEVSQAISDKKGRLIILKDAEHKEEDEEPGEAEGVEKELPPSKEKEMV 13 | KEDAADVLASITREIKKQHPKVEIKTNGTQQINGSDSPKKAMVSWISEEVKTVATKEVSEGESVEAPQQT 14 | AEIFTFEEEQSKSSPTQITVSESSASFAVVHLDTTDAGTKEMPVIHTETKTITYESAEVDTNGDLDPGVL 15 | LSAQTITSEITSTTTTTHITKMVKGGISETRIEKRIVISGDADIDHDQALAQAIKEAKEQHPDMSVTKVV 16 | VHKETEITPEEGED 17 | -------------------------------------------------------------------------------- /t/data/gerp/ENr111.gerp.tree: -------------------------------------------------------------------------------- 1 | (platypus:0.13,monodelphis:0.152013,((elephant:0.05,tenrec:0.085):0.02,(armadillo:0.063747,((shrew:0.088,(rfbat:0.047,(dog:0.049162,cow:0.045317):0.000798):0.001802):0.004810,((rabbit:0.057760,(mouse:0.029443,rat:0.032846):0.085321):0.011253,(galago:0.044986,(marmoset:0.021531,((baboon:0.002469,macaque:0.002468):0.013886,(chimp:0.002271,human:0.002259):0.006817):0.005489):0.018117):0.004605):0.004931):0.011979):0.01):0.07); 2 | -------------------------------------------------------------------------------- /t/data/gerp/ENr111.mfa.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioperl/bioperl-run/f9a864a1214361f281d31e9b8baaf70f760f6687/t/data/gerp/ENr111.mfa.gz -------------------------------------------------------------------------------- /t/data/gumby/hmrd.tree: -------------------------------------------------------------------------------- 1 | ((human, (mouse, rat)), dog); 2 | -------------------------------------------------------------------------------- /t/data/gumby/human.gff: -------------------------------------------------------------------------------- 1 | human supported_mRNA exon 17826 17994 . + . Sequence "SCL" 2 | human supported_mRNA exon 18272 18313 . + . Sequence "SCL" 3 | human supported_mRNA exon 19120 19251 . + . Sequence "SCL" 4 | human supported_mRNA exon 20390 20507 . + . Sequence "SCL" 5 | human supported_mRNA exon 20810 20965 . + . Sequence "SCL" 6 | human supported_mRNA exon 24272 24718 . + . Sequence "SCL" 7 | human supported_mRNA exon 26056 26150 . + . Sequence "SCL" 8 | human supported_mRNA exon 29980 33863 . + . Sequence "SCL" 9 | human supported_mRNA CDS 24272 24718 . + . Sequence "SCL" 10 | human supported_mRNA CDS 26056 26150 . + . Sequence "SCL" 11 | human supported_mRNA CDS 29980 30440 . + . Sequence "SCL" 12 | human alignment_with_mmscl HSS 8146 8637 . + . Equivalent of murine -9 HSS 13 | human alignment_with_mmscl HSS 8806 9545 . + . Equivalent of murine -8 HSS 14 | human alignment_with_mmscl HSS 14215 14804 . + . Equivalent of murine -4 HSS 15 | human alignment_with_mmscl HSS 17492 17878 . + . Equivalent of murine Pr1a HSS 16 | human alignment_with_mmscl HSS 18107 18300 . + . Equivalent of murine Pr1b HSS 17 | human alignment_with_mmscl HSS 18603 18903 . + . Equivalent of murine +1 HSS 18 | human alignment_with_mmscl HSS 20634 20844 . + . Equivalent of murine +3 HSS 19 | human alignment_with_mmscl HSS 24257 24697 . + . Equivalent of murine +7 HSS 20 | human alignment_with_mmscl HSS 37126 37454 . + . Equivalent of murine +18 HSS 21 | human alignment_with_mmscl HSS 37873 38182 . + . Equivalent of murine +19 HSS 22 | human alignment_with_mmscl enhancer 40125 41807 . + . Equivalent of murine +23 region 23 | -------------------------------------------------------------------------------- /t/data/gumby/readme.txt: -------------------------------------------------------------------------------- 1 | Data in this folder is that which is included with the gumby distribution, modified by Prabhakar et al. from data from: 2 | 3 | Chapman M.A., Donaldson I.J., Gilbert J., Grafham D., Rogers J., Green A.R., G?ttgens B. (2004). "Analysis of multiple genomic sequence 4 | alignments - a web resource, online tools, and lessons learned from analysis of four mammalian SCL loci". Genome Research. 14: 313-318. 5 | 6 | Re-distributed with permission. 7 | 8 | -------------------------------------------------------------------------------- /t/data/hmmpfam_protein_input: -------------------------------------------------------------------------------- 1 | >protein_input 2 | KSHTGARLFICETCGKAFNTNSILKVHIRCHTGERPYLCKTCGKAFKQSSALSYHIRVHTGERPDVCKTCGKSFQRSEELKFHVRDHTGERPYVCKICGKAFKRNKELKTHFRVHTGERPYLCKTCGKAFKQNSQLYVHMRIHKDERPCLCKTCGKAFKRNEELKTHLRVHTGERPYLCKTCGKTFKQKSALNVHMRVHTDERPYVCETCGETFSQNCELVQH 3 | -------------------------------------------------------------------------------- /t/data/hyphy1.fasta: -------------------------------------------------------------------------------- 1 | >Alfa 2 | ---GTGCCGAGGATTGTGAACCCTCTGGATGAGATGCTCTTTAAGGAGGTCCTGAAGGAG 3 | CAGCAGAGGATAAGGGTCTACGTGGAGAGGGCCCGCTACGGCAAGCTCAAGACCATAATC 4 | GAGGGCATAGACGAGAAGGAGTTCGACCTTGAGGACATCGCAAAAAAGCTTAAGGCGAAG 5 | CTGGCATGCGGCGGAACGGCAAAGAACGGAAGGATAGAACTGCAGGGAGACCACAGAGAC 6 | AGGGTCAAGAAGTTGCTGGCAGAGCTTGGATTTTCAGAGGAGCTCATAGAGGTCGAG 7 | >Beta 8 | TTGGTGCCTAGGATAGTAAATCCGTTGGATGAAATGCTCTTTAAAGAAGTCCTAAAGGAG 9 | CAACAGAGAATTAAGGTATACATAGAAAGGGCAAGGTACGGAAAAGTCAAGACAATAATC 10 | GAGGGGATCGATGAGAAAGAGTTTGATCTGGAGGAAATAGCAAAGAAGCTCAAGGCGAAG 11 | TTGGCATGCGGCGGAACAGCAAAGAACGGAAGAATAGAGCTACAAGGAGATCACAGGGAT 12 | CGTATCAAGAAATTATTGGCAGAACTTGGATTTTCAGAGGAGCTCATAGAGGTAGAG 13 | >Gamma 14 | ---GTGCCCAGGATTGTAAACCCCTTGGATGAAATGCTATTTAAGGAGGTACTAAAGGAG 15 | CAGCAGAGGATTAGAGTCTACACAGAAAGGGCAAGATACGGAAAGATAAAGACTATAATT 16 | GAAGGAATTGATGAAAAAGAGTTTGACCTCGAGGAGATAGCAAAGAAACTCAAGGCGAAG 17 | TTAGCATGTGGAGGAACAGCGAAGAACGGGAGAATAGAACTTCAGGGAGATCACAGGGAT 18 | CGTATCAAGAAATTATTGGTAGAACTTGGATTTTCAGAGGAGCTCATAGAGGTAGAG 19 | >Delta 20 | TTGGTGCCGAGGATAGTAAACCCGTTGGATGAAATGCTCTTTAAGGAGGTCCTCAAGGAG 21 | CAGCAGAGAATTAGGGTGTACACAGAGAGGGCAAGGTACGGAAAGATAAAGACAATAATC 22 | GAAGGAATAGACGAAAAAGAGTTCGATCTCGAGGAGATAGCAAAGAAGTTGAAGGCGAAG 23 | CTAGCATGCGGAGGAACGGCAAAGAACGGAAGGATAGAACTTCAGGGGGATCACAGAGAC 24 | CGTATCAAGAAATTGTTGGCAGAACTTGGATTTTCAGAGGATCTCATAGAGGTAGAG 25 | -------------------------------------------------------------------------------- /t/data/hyphy1.tree: -------------------------------------------------------------------------------- 1 | (Alfa:3.920036,Gamma:1.492971,(Delta:1.117458,Beta:1.362452)Node4:0.871056); 2 | -------------------------------------------------------------------------------- /t/data/lagan_dna.fa: -------------------------------------------------------------------------------- 1 | >sequence_10 2 | CAATGCACATGAACACATACATTTATTAAATTATCGAACGCATCTGTATGATGAATAATGTGGCATTTCACTGAATAATT 3 | AAAGCGCCGGCGTTTAAAGTTCCGTTTTAACGACGTGAATTAATTGAGTTGATCTTGTTTGCAAATATATATAACAAGCT 4 | GTTTGTGGACCGCTACTTTATCCGTATCACTTTCTTGGCCCTACAGCACGCGCTACAAACAACTATCACAGGTGCAAATA 5 | TAGACGACCGCGCACAAGTAAACACATAGCAGACATCAAACAAAGGGAAGGCGAAGGTCGGATTGAGATTCCACAACGAA 6 | TCGAAATATTCGCCATTGTCGGTCTCGGATTACACAATGACGGGCAATAAAACAGTCATTTTTTGTAAATATTTTATAAC 7 | GATTAAAACTTCATGTTCCGCTTTCAAAGGGCGTTTTTTTAATAATAATAACACATAGGAGAAAATCGTAGTGGGATAGA 8 | AGTTAGACTAGACATTAAAACGTGGGAAAAGTAGTTAATTTCCTTTACAATGCTAAGCGACACGACTTCTTTTTCGTTGC 9 | CAAAGCTAATTGCCGTGCCGAAGCGGAACTGATGTCGCGCAGTTGTTAGGAACCGGTTATTACAAAGCGGACGCGCGTGT 10 | CGCAACACTAGGCATTATTCTTCAGCGCTTCATCGCTGTACATTGAAATGTGCGGCATGAATTATTATAACTTGAAGTTA 11 | GCCGCAGCAAAGGGATATCCTGGCTGCGGTGGCGCGTTTATCTGATAAACGGGACAATTATCCAAATTACCATAGAAGCT 12 | CACACCTGCGCGACTGGAAATTATTTTGAAATTACTTTTTTTCAGAAACACGGAGTGGGTTGCAGGTTACAAATTATTTT 13 | GTTTGCTTTTTGATTAAAATACCACTACTACATGTTGCAACATGGTGCTGTATTATTACAGTTTGGGTGTGATGTTTTTC 14 | AAATGTGAATTCGACTTATTGGCGGTTTGATTTTGACAGAACACTTAGACCTGTCAGTTCCAGTTTAAAGTTATTAGTTA 15 | ATATTGACAGATTTATTAGGCATTAGTGACAAGCGAAGACGAAGTTTTCACGTCCTTTTAACCATCAAATCTCCGATAAA 16 | CCGGATCTTCTCGGTTTATCGGAGATTTGATGTACTGCCGTGACGCACGACGTTGTTGAAATAAAACCAATACGCTGCTA 17 | ACAATGCTGCAAAAACTCAGTGTCTAGTTTTCCGTGTTTCTGAAGAACGCATTTGTAACGAAGTAAAGACTGCAGATTAA 18 | TTTGGTGATGCACAAATATGCCCAAGTATCTGACACATCAGCACTTTTACATAGCATAGTGCACAACCAATTGACAATGT 19 | TAAAATAACACATTTATAAGTTTACTAGTGCATTAAAGGTGAAACGCCCCTACAAATCATAACCCCCCAACAAAATCTTA 20 | ATTGATTCATCGAGTAACACTATGCTCGCGGGTTTGAGCTTTCACGAACCTTACATATAGATATGTAAGCAAAACTACTA 21 | CGGTCACGCCCGCGATCAGCCAAGCGATTCAATCTATAAATACAAACACCGCGAGTTAGCTCACACAGGTATGTCTTGGC 22 | AAAGGGGAGTTCCCTTGGTCTAACCGTCGAGTAACCCGAAGACTTATCATGATTGGGATGTTGCCGTGGTCGGTAGATAA 23 | AACTCCGGGACAATGTAAGACAGATGTAAATCGTCAAGGTGGTTCAGTTACTCCCTGTTTACAATGTCAAAACTGGGGTA 24 | AGTGTGAACTGAATG 25 | -------------------------------------------------------------------------------- /t/data/lvb.fa: -------------------------------------------------------------------------------- 1 | >Sp._1_____ 2 | ACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 3 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 4 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN- 5 | >Species_2_ 6 | ACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 7 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 8 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN- 9 | >Sp_______3 10 | ACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 11 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 12 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT 13 | >Species_4_ 14 | TCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 15 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 16 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT 17 | >Species_5_ 18 | TCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 19 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 20 | NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT 21 | -------------------------------------------------------------------------------- /t/data/lvb_sequential.phy: -------------------------------------------------------------------------------- 1 | 5 7 2 | Sp. 1 RACNN 3 | GA 4 | Species_2_RACNN 5 | GA 6 | Sp_______3RACNN 7 | GA 8 | Species 4 RUCNN 9 | GU 10 | Species 5 RUCNN 11 | GU 12 | -------------------------------------------------------------------------------- /t/data/neighbor.dist: -------------------------------------------------------------------------------- 1 | 3 2 | SINFRUP001 0.00000 0.16316 0.28603 3 | SINFRUP002 0.16316 0.00000 0.27995 4 | ENSP000002 0.28603 0.27995 0.00000 5 | -------------------------------------------------------------------------------- /t/data/new_pep.fa: -------------------------------------------------------------------------------- 1 | >SINFRUP00000067802 2 | LDEDQLSHSSSRLSRSPLKGVKKAKIMQCKVTLLDNSDYTIDVEKGARGQMLFDKVCEHLNLLERDYFGI 3 | TYRDVENQKNWLDPSKELKKQIRTGPWNFAFNVKFYPPDPVQLAEDITRYYLCLQLRDDVVSGRLPCSFA 4 | THTVLGSYTVQSELGDYDHEELGSDYLSELRLAPNQTKELEEKVMELHKSYKGMTPGEAEMHFLENAKKL 5 | SMYGVDLHHAKDSEGVEIMLGVCSSGLLIYRDRLRINRFAWPKILKISYKRNNFYIKIRPGEFEQFESTI 6 | GFKLPNHRAAKRLWKVCVEHHTFFRQVMKEVLGLVSPEAPPKKFLSLGSKFRYSGRTQAQTRRASSQIIR 7 | PAPFFERSSSKRYNMSRSLDGDSSADGVARVKGNIITTVTPERKAEEENGEQEDAKNDAADKPDPAASSP 8 | LHQETKVTLDDPLRSELSLPSSPISFTKIRRRRRENAHKRASSVSPGKSSTGRCRRQALADRKAALLDEQ 9 | ALLLVARKQRLEQGRNHGGTLFSFSLHLPDLSSVLDEDGYITFPDLSKMRFLPECAQNFLPIKSPYLCSL 10 | LLFTLFTFFFLCLLNSLHLSSFAVSRKQTRNLKYRLRYTGLTFIDRPCSMHQILDILTRCPEPSASTISH 11 | FAVSILAYCFSEVVKHQTNISELKRSFLETGDGTQGPTEWEKRLSSSPMCSPRFDEAPMIEPLDVSVDER 12 | TSDSQEDVSERSMLKVSPRAVTQEVSQAISDKKGRLIILKDAEHKEEDEEPGEAEGVEKELPPSKEKEMV 13 | KEDAADVLASITREIKKQHPKVEIKTNGTQQINGSDSPKKAMVSWISEEVKTVATKEVSEGESVEAPQQT 14 | AEIFTFEEEQSKSSPTQITVSESSASFAVVHLDTTDAGTKEMPVIHTETKTITYESAEVDTNGDLDPGVL 15 | LSAQTITSEITSTTTTTHITKMVKGGISETRIEKRIVISGDADIDHDQALAQAIKEAKEQHPDMSVTKVV 16 | VHKETEITPEEGED 17 | 18 | -------------------------------------------------------------------------------- /t/data/pal2nal.aln: -------------------------------------------------------------------------------- 1 | CLUSTAL W (1.82) multiple sequence alignment 2 | 3 | 4 | BC070280 MVGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFS 5 | pseudogene ----LNCIVNDSQKMGIIRNGDLP*PQLKNKF2-FQRMTTPSSAEGKENLVFLIRKNWFS 6 | 7 | 8 | BC070280 IPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMLWIVGGSS 9 | pseudogene ITEKNQPLKYIINLVVSRESKEPPQRPPFLD*SLGDALKRIEQLKLANKQDVFFTVGGSS 10 | 11 | 12 | BC070280 VYKEAMNHPGHLKLFVTRIMQDFESDTFF-PEIDLEKYKLLPEYP-GVLSDVQEEKGIKY 13 | pseudogene VYKESMN*-DHFKLFVTWIMQDFQSDTFFS4EGDLEKYKLLPEYPQGVVSDVEEEKGIKY 14 | 15 | 16 | BC070280 KFEVYEKND 17 | pseudogene KFEVYEKND 18 | 19 | 20 | -------------------------------------------------------------------------------- /t/data/pal2nal.nuc: -------------------------------------------------------------------------------- 1 | >BC0700280 2 | TGTAACGAGCGGGCTCGGAGGTCCTCCCGCTGCTGTCATGGTTGGTTCGCTAAACTGCAT 3 | CGTCGCTGTGTCCCAGAACATGGGCATCGGCAAGAACGGGGACCTGCCCTGGCCACCGCT 4 | CAGGAATGAATTCAGATATTTCCAGAGAATGACCACAACCTCTTCAGTAGAAGGTAAACA 5 | GAATCTGGTGATTATGGGTAAGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCTTT 6 | AAAGGGTAGAATTAATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCTCA 7 | TTTTCTTTCCAGAAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAA 8 | TAAAGTAGACATGCTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAATCA 9 | CCCAGGCCATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTGACACGTT 10 | TTTTCCAGAAATTGATTTGGAGAAATATAAACTTCTGCCAGAATACCCAGGTGTTCTCTC 11 | TGATGTCCAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAGAAGAATGATTA 12 | ATATGAAGGTGTTTTCTAGTTTAAGTTGTTCCCCCTCCCTCTGAAAAAAGTATGTATTTT 13 | TACATTAGAAAAGGTTTTTTGTTGACTTTAGATCTATAATTATTTCTAAGCAACTTGTTT 14 | TTATTCCCCACTACTCTTGTCTCTATCAGATACCATTTATGAGACATTCTTGCTATAACT 15 | AAGTGCTTCTCCAAGACCCCAACTGAGTCCCCAGCACCTGCTACAGTGAGCTGCCATTCC 16 | ACACCCATCACATGTGGCACTCTTGCCAGTCCTTGACATTGTCGGGCTTTTCACATGTTG 17 | GTAATATTTATTAAAGATGAAGATCCACATACCCTTCAAAAAAAAAAAAAAAAAAAAAAA 18 | AAAAAAA 19 | >pseudogene 20 | CTAAACTGCATTGTCAATGATTCCCAGAAGATGGGCATCATCAGGAATGGGGACCTGCCC 21 | TGACCTCAGCTCAAAAATAAATTCGATTCCAAAGAATGACCACACCCTCTTCAGCAGAGG 22 | GTAAAGAAAATTTAGTATTTTTAATTAGGAAGAACTGGTTCTCGATTACTGAGAAGAATC 23 | AACCTTTAAAGTATATAATTAATTTAGTTGTCAGTAGAGAATCCAAGGAACCACCGCAAA 24 | GACCTCCTTTTCTTGACTAAAGTCTGGGTGATGCCTTAAAACGTATTGAGCAACTAAAAT 25 | TAGCAAATAAACAAGACGTGTTTTTTACAGTGGGAGGCAGTTCTGTTTATAAGGAATCCA 26 | TGAATTGAGACCATTTTAAACTATTTGTGACATGGATCATGCAGGACTTTCAAAGTGACA 27 | CGTTTTTTTCCCCTAGAAGGTGATTTAGAGAAATATAAACTTCTCCCAGAATACCCACAA 28 | GGTGTTGTCTCTGATGTGGAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAA 29 | AAGAATGAT 30 | -------------------------------------------------------------------------------- /t/data/primate_query.fa: -------------------------------------------------------------------------------- 1 | >E1 2 | TATTTCTAC 3 | >E2 4 | TTCAC 5 | >E3 6 | TGCACAGAG 7 | >E4 8 | CTGTTA 9 | >E5 10 | TTGCAC 11 | >VM1 12 | TTTCTA 13 | >E1T 14 | GTGGTGGT 15 | >E3T 16 | CTAACTCT 17 | >E4T 18 | CATTTTC 19 | >E5T 20 | TGTGTG 21 | 22 | -------------------------------------------------------------------------------- /t/data/primate_target.fa: -------------------------------------------------------------------------------- 1 | >AOULE15-H12 2 | TTCACTTCACTTCACTTCACTTCACTATTTCTACTATTTCTACTTCGGCACGAGGAAAAGAGGCTTCACTTTGGAGTTTAGTGCTACTTTGTATCACTAGTCGTTTATGTGCTGCAAATACTTCTTTACAAAGTAAAGAAGTGTTCCAATGGCCTGAACAACATCTGTTGGGTTTGGGTGTGAGAGAGCTACCATCTATTTCTACTCAAGCAGAACCTGTTCAGAAGTGTGATGTGCAAGATGAGGATAAGGTGCAGTGTGGAGAGCCTGGCATTTCTCCTGAAGACTGTAATGTTTTAAACTGCTGTTTTGATGGAAAACAGTGCTACTATGGCAATAC AGTAACTGTCCAGTGTACAAGAGATGGGCAGTTTGTTGTTGTGGCCTTGAGAGATGCAACTATTCCAAGAATAAGCTTGGAGTCCATCAGCCTTTTGGGAGGAAGTGATCCTCCTTGTGCCCCCGTTGATGCCACTAAAGCTTT TGCCATCTACCAGTTCCCTGTCACTGCTTGTGGCACCACAGTGATGGNGGAAGATGACTTCCTAATCTATGAAAACAGAATGACATCTGTATATGAAGGAAATGNTGGACCTCTAGGCTCTATCACAAGAGATAGCCATTATGA GCTCCTCTTCCAGGGTAATATTCACGCAGCAGTTTTGAAGCGCTGGTTGTTTGAAGCCAACCCTGTTCCCCNCCCTCTTCCTGTGGGCTGCNCTTGGACCTCTTAGAGTGGAGCTTAAACTGGTTAACGGGCAGTGTTTTCTTA AGGGAGGTATTTCTACGGTGGAANAAGNCNAGCATTTCTTCNGACTNTGGGGAGGCTGAGAATCTATTTCTACCTGGGANNNAAAGGCCGGCGGGTATTTCTACGGC 3 | -------------------------------------------------------------------------------- /t/data/profile_prot.FastA: -------------------------------------------------------------------------------- 1 | >91252 2 | ALVFGVLLIVVIICGNLLVCLSVLTEKALKTTTNYFIVSLAVADLMLAVLVLPLFVYSEFQDGVWPLSSTICDYLMTMDVMLCTASIFNLCAISVDRFIAVLIPLNYNRKHVDLRQAVLLSATWILALAVASPIIFGINNMPGRDPRECKLENNDYVLYSSVCSFFIPCPIMLLLYCGMFRGLRRWEEARKAKLRNSIQACRKLQEAAATLPPLASLPPPLPPIIEREPTETLDEMSNFPSPEPPFPSSEYRAPVPAVSFAEIQFNPDPRRRKRAKINSRERKAMKVLPVVVGAFLFCWTPFFVLHTLRARCEDCQIPAALMSVVTWLGYVNSALNPVIYTIFNTEFRNLFKKLLHRCC 3 | -------------------------------------------------------------------------------- /t/data/purine.1.sto: -------------------------------------------------------------------------------- 1 | # STOCKHOLM 1.0 2 | #=GF ID Purine 3 | #=GF AU Boese B, Barrick JE, Breaker RR 4 | 5 | Purine1 AAAAUUGAAUAUCGUUUUACUUGUUUAUGUCGUGAAUUGGCACGACGUUU 6 | #=GC SS_cons .................<<<<<<<<...<<<<<<......>>>>>>.... 7 | 8 | Purine1 CUACAAGGUGCCGGAACACCUAACAAUAAGUAAGUCAGCAGUGAGAU 9 | #=GC SS_cons ....<<<<<<......>>>>>>..>>>>>>>>............... 10 | // 11 | -------------------------------------------------------------------------------- /t/data/purine.added.fa: -------------------------------------------------------------------------------- 1 | >Purine2 2 | AAAAUUUAAUAAGAAGCACUCAUAUAAUCCcGAGAAUaUGGCUCgGGAGU 3 | CUCUACCGAACAaCCGUAAauUGUUCGACUAUGAGUGAAAGUGUACCUAG 4 | GG 5 | >Purine3 6 | UGGCAGUAACUAGCGUCACUUCGUAUAACCCCAGUGAUAUGGAUUGGGGG 7 | UCUCUACCAGGAACCAAUAAAUCCUGAUUACGAAGAGUUUAGUGCUUUAG 8 | U 9 | -------------------------------------------------------------------------------- /t/data/purine.all.fa: -------------------------------------------------------------------------------- 1 | >Purine2 2 | AAAAUUUAAUAAGAAGCACUCAUAUAAUCCcGAGAAUaUGGCUCgGGAGU 3 | CUCUACCGAACAaCCGUAAauUGUUCGACUAUGAGUGAAAGUGUACCUAG 4 | GG 5 | >Purine3 6 | UGGCAGUAACUAGCGUCACUUCGUAUAACCCCAGUGAUAUGGAUUGGGGG 7 | UCUCUACCAGGAACCAAUAAAUCCUGAUUACGAAGAGUUUAGUGCUUUAG 8 | U 9 | -------------------------------------------------------------------------------- /t/data/repeatmasker.fa: -------------------------------------------------------------------------------- 1 | >contig11600 2 | ATTAACAGCTTATTTTAATTAAAAACAACCACAGGTGCAGTTTGAAACTAAAAACAATGGCTTAAAAATGGTCAATAAAGAATAAAGATGTTGCTCAGACATTATGAAACAATAAATAGATGTTCTTTGATCTTTAGTCAGCACTCCTCACACACACCCTTTCATCCTTATCCTGGACATGAAAGCACATCAGTACTTTGATGCTTTCTTGTCTCTTCTCCATATAAACATTGAAGCCAGCTCATTAAGAACCAACGAATCTGGTCTCCATATTTGTTAAACATGTCCTGGAAAAGCCTGCTTCCCTCCCCACAACTGTACGTATCTCCTGACATTAAGATTTGTGATTTATTTCAGAATACGTGTTGAGGCCTCCAGATTGAATCTACGCCACTGTGGTTGATGGGTGAAACACGTTTGTTTTGCTTTTTTTCAATGCTAATGTGTCATGTGACCGGTGTGTGTCCTGCTCAAGTCATTCTGCTGTGGAAGCGGACGGAGATTCTCCGTTCCTCACGTACGAGGTGAAGGGGTTGCTGGGGAAGGGCACTTATGGCAAAGTGCTCAAATGCACCCATATGACCACCAACGTGACCGTGGCCATTAAGATGATGAAAAATGAAGGCTTTTATCGGATCAGTTTGCATCAGAGGTAAGCAAAAAGGTCAGATATGTCATAATCAGGGGTGTCCAAAGCCAGGACATGGGGCCGCAATCCAACCGCGTTCTCTGATCTACCGGGTAAACGACTCTCCCACTTGTCTTGTCAACGCCATTTTCTGCCTGGGACAGAAAACATGGATGGATTTTGGCCCTGGAGGACTGGGTTTTGGTACCCCTGGCCTAAATCCATCCCATCAATCACCAGGTGTATATGCTGCGCAAACTGAGAAGGCACGGCTCCAGCGAACACAACATCGTTAACTTCTACGACAGCTTTTCCGACAGTAGACATCACTTCCTCGTGTTTGAGCAGCTGGACAAAAGTCTGAAAGACTTCTTGGATGAGAGGAAATGGCAGCGTGTGCCTTTGAGGGACATCAGACCCATTCTTCTGCAGGTGTTAGCTGCTCTATACAAACATTCTCTAATGTCAGGCACGTGTAACAGCAGCTCATTTGCAAACATTACAGATGGCTACAGCCCTGGATTTCCTGAAGGTTCGGAGGTTCATGCACTCCGACATCAAGCTCGAGAACGTGATGTTGGTGAACCACCAGAAAGAACCTTTCAGAGTCAAACTGAATGACTCTGGTCTGGCTGATAAGATCTCGAGAGTTGAAAAGGGGCGAACCCTTCAGACCCTTCCATACAGGTCAGCAACTGGACTTGAGTAAGGGTTAGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGTTAGGGTTAGGTTAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAGGTTAGGGTTAGGTTAGGGGTAGGGGTATGGTTAGGTTAGGGTTAGGTTAGGGTCAGGGTTAGGTTATGGTTCGGGTTAGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGTTAGGGTTAGGTTAGGTTAGGTTAGGTTAGGGTTAGGTTAGGGGTAGGGGTATGGTTAGGTTAGGGTTAGGTTAGGGTTAGGTTAGGGGTAGGGGTATGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGTTAGGGTTAGGGTTAGGTTAGGTTAGGTTAGGGTTAGGTTAGGGGTAGGGGTAGGGGTATGGTTAGGTTAGGGTTAGGTTAGGTTAGGTTAGGTTAGGGTTAGGTTAGGGTTAGGTTAGGGGTAGGGGTATGGTTAGGTTAGGGTTAGGGTTAGGGTTAGGTTAGGTTAGGGTTAGGGTCAGGGTTAGGTTATGGTTCGGGTTGGGTTAGGGTTCGGGTTAGGTTTCGGGTTAGGTTAGGGTTCGGGTTAGGGTTCGGGTTAGGGTTAGGGTCACAAGTAAGGGCTCGCTGCCATCATGTGTCCTCATGTGTCCTCGTGGGTCCTCATGTGTCCTCATGTGTCCTCGTGGGTCCTCATGTGTCCTCGTGTGTCCTTGTGTGTCCTCATGGGTCCTCATGTATCCTCGTGTGTCCACATGGGTCCTCATGTGTCCTCGTGTGTCCTCA 3 | -------------------------------------------------------------------------------- /t/data/road.pep: -------------------------------------------------------------------------------- 1 | >roa1_drome 2 | MVNSNQNQNGNSNGHDDDFPQDSITEPEHMRKLFIGGLDYRTTDENLKAH 3 | FEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRV 4 | VEPKRAVPRQDIDSPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVD 5 | INIVIDKETGKKRGFAFVEFDDYDPVDKVVLQKQHQLNGKMVDVKKALPK 6 | QNDQQGGGGGRGGPGGRAGGNRGNMGGGNYGNQNGGGNWNNGGNNWGNNR 7 | GGNDNWGNNSFGGGGGGGGGYGGGNNSWGNNNPWDNGNGGGNFGGGGNNW 8 | NNGGNDFGGYQQNYGGGPQRGGGNFNNNRMQPYQGGGGFKAGGGNQGNYG 9 | GNNQGFNNGGNNRRY 10 | -------------------------------------------------------------------------------- /t/data/semphy.seq: -------------------------------------------------------------------------------- 1 | >Semnopithecus_entellus 2 | KIFERCELARTLKKLGLDGYKGVSLANWVCLAKWESGYNTEATNYNPGDESTDYGIFQINSRYWCNNGKPGAVDACHISCSALLQNNIADAVACAKRVVSDQGIRAWVAWRNHCQNKDVSQYVKGCGV 3 | >Baboon 4 | KIFERCELARTLKRLGLDGYRGISLANWVCLAKWESDYNTQATNYNPGDQSTDYGIFQINSHYWCNDGKPGAVNACHISCNALLQDNITDAVACAKRVVSDQGIRAWVAWRNHCQNRDVSQYVQGCGV 5 | >Human 6 | KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKPGAVNACHLSCSALLQDNIADAVACAKRVVRDQGIRAWVAWRNRCQNRDVRQYVQGCGV 7 | >Rat 8 | KTYERCEFARTLKRNGMSGYYGVSLADWVCLAQHESNYNTQARNYDPGDQSTDYGIFQINSRYWCNDGKPRAKNACGIPCSALLQDDITQAIQCAKRVVRDQGIRAWVAWQRHCKNRDLSGYIRNCGV 9 | >Cow 10 | KVFERCELARTLKKLGLDGYKGVSLANWLCLTKWESSYNTKATNYNPSSESTDYGIFQINSKWWCNDGKPNAVDGCHVSCSELMENDIAKAVACAKKIVSEQGITAWVAWKSHCRDHDVSSYVEGCTL 11 | >Horse 12 | KVFSKCELAHKLKAQEMDGFGGYSLANWVCMAEYESNFNTRAFNGKNANGSSDYGLFQLNNKWWCKDNKRSSSNACNIMCSKLLDENIDDDISCAKRVVRDKGMSAWKAWVKHCKDKDLSEYLASCNL 13 | -------------------------------------------------------------------------------- /t/data/semphy.tree: -------------------------------------------------------------------------------- 1 | (((Semnopithecus_entellus:0.081,Baboon:0.033):0.021,Human:0.064):0.01,Rat:0.288,(Cow:0.240,Horse:0.63):0.106); 2 | -------------------------------------------------------------------------------- /t/data/signalp_input_protein: -------------------------------------------------------------------------------- 1 | >signalp_protein 2 | MRYQRILTYLRIFGTTMFGISLLVGISTAYIMGYQFFTTAGHHLSFGLYGAILVIHLLIQSLFALLEHRNMRRSLETPIKLNKSLALCIAAYQEDPNYLRKCLVSVKRLTYPGIKVIMVIDGNTEDDNYMMDIFKEVMGRDKVASYVWRSNFHHRAPEETDESYAESIQHIYKLVLNNKCMCIMQKWGGKREVMYTPFKALGKSVDYVQVCDSDTMLDPASSVEMVKVLEEDHMVGGVGGDVQILNKYESWISFLSSVRYWMAFNIERACQSYFGCVQCISGPLGMYRNSLLNEFLEDWYNQTFMGSHCSFGDDRHLTNRVLSLGYATKYTARSKCLTETPITYLRWLNQQTRWSKSYFREWLYNSMWFHKHHLWMTYEAVITGFFPFFLIATAIQLFYQGRLWNILLFLLIVQAVALIKSSFASCLRGNIVMIFMSFYSVLYMSSLLPAKMFAIATINKSGWGTSGRKTIVVNFIGLIPISVWFTILFFGIIYTIVQQTRKPFPETEKIVLIVGAVVYASYWVILLTLYTVLINKCGKRKKESHYDMVLDV 3 | -------------------------------------------------------------------------------- /t/data/sim4_cdna.fa: -------------------------------------------------------------------------------- 1 | >MUSSPSYN Mouse spermidine synthase mRNA, complete cds. 2 | CGGGTTGTGCTGGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCG 3 | GCCCGCCCGCCCGCCATGGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCC 4 | ATCCGTGAGGGCTGGTTCCGAGAGACCTGCAGCCTGTGGCCCGGCCAGGCCCTGTCGCTG 5 | CAAGTGGAGCAGCTGCTTCACCACCGGCGATCGCGGTACCAAGACATCCTCGTCTTCCGC 6 | AGTAAAACCTACGGCAACGTGCTGGTTCTGGATGGCGTCATCCAGTGTACTGAGAGGGAT 7 | GAGTTCTCCTACCAGGAGATGATCGCCAACCTGCCGCTCTGCAGCCACCCCAACCCGCGG 8 | AAGGTGCTGATCATCGGGGGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCC 9 | TCTGTGGAGTCGGTGGTCCAGTGCGAGATTGATGAGGATGTCATTGAAGTCTCTAAGAAG 10 | TTCCTGCCTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGGGCGAT 11 | GGCTTTGAGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCCTCA 12 | GACCCCATGGGCCCTGCTGAGAGCCTCTTCAAGGAGTCCTATTACCAGCTCATGAAGACA 13 | GCACTCAAAGAAGATGGCATCCTGTGCTGCCAGGGTGAGTGCCAGTGGCTGCACCTGGAC 14 | CTCATCAAGGAGATGAGGCACTTCTGCAAATCTCTCTTCCCCGTGGTGGACTACGCCTAC 15 | TGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGCTTCATGCTGTGTAGCAAAAACCCG 16 | AGCACCAACTTCCGGGAGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAG 17 | CTGAAATACTATAACTCGGACATGCACCGTGCCGCCTTCGTACTGCCTGAGTTCACCCGG 18 | AAGGCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACCACCCGAGACCTCAA 19 | TCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCTGGACCAGACTCC 20 | CAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCATGATGCTGCCTGGCCTGGCC 21 | TGGCCTGGCCTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGTCTATCTCT 22 | GTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTGTGACCC 23 | AACAAAATACATGTGTATTCCG 24 | -------------------------------------------------------------------------------- /t/data/sim4_database.fa: -------------------------------------------------------------------------------- 1 | >MUSSPSYN Mouse spermidine synthase mRNA, complete cds. 2 | CGGGTTGTGCTGGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCG 3 | GCCCGCCCGCCCGCCATGGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCC 4 | ATCCGTGAGGGCTGGTTCCGAGAGACCTGCAGCCTGTGGCCCGGCCAGGCCCTGTCGCTG 5 | CAAGTGGAGCAGCTGCTTCACCACCGGCGATCGCGGTACCAAGACATCCTCGTCTTCCGC 6 | AGTAAAACCTACGGCAACGTGCTGGTTCTGGATGGCGTCATCCAGTGTACTGAGAGGGAT 7 | GAGTTCTCCTACCAGGAGATGATCGCCAACCTGCCGCTCTGCAGCCACCCCAACCCGCGG 8 | AAGGTGCTGATCATCGGGGGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCC 9 | TCTGTGGAGTCGGTGGTCCAGTGCGAGATTGATGAGGATGTCATTGAAGTCTCTAAGAAG 10 | TTCCTGCCTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGGGCGAT 11 | GGCTTTGAGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCCTCA 12 | GACCCCATGGGCCCTGCTGAGAGCCTCTTCAAGGAGTCCTATTACCAGCTCATGAAGACA 13 | GCACTCAAAGAAGATGGCATCCTGTGCTGCCAGGGTGAGTGCCAGTGGCTGCACCTGGAC 14 | CTCATCAAGGAGATGAGGCACTTCTGCAAATCTCTCTTCCCCGTGGTGGACTACGCCTAC 15 | TGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGCTTCATGCTGTGTAGCAAAAACCCG 16 | AGCACCAACTTCCGGGAGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAG 17 | CTGAAATACTATAACTCGGACATGCACCGTGCCGCCTTCGTACTGCCTGAGTTCACCCGG 18 | AAGGCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACCACCCGAGACCTCAA 19 | TCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCTGGACCAGACTCC 20 | CAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCATGATGCTGCCTGGCCTGGCC 21 | TGGCCTGGCCTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGTCTATCTCT 22 | GTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTGTGACCC 23 | AACAAAATACATGTGTATTCCG 24 | >MUSSPSYN Mouse spermidine synthase mRNA, complete cds. 25 | CGGGTTGTGCTGGGGGGGTCCGCGCGCCCTGCAGTCCCGAACCCGCTACGCGCTCCGTCG 26 | GCCCGCCCGCCCGCCATGGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCC 27 | ATCCGTGAGGGCTGGTTCCGAGAGACCTGCAGCCTGTGGCCCGGCCAGGCCCTGTCGCTG 28 | CAAGTGGAGCAGCTGCTTCACCACCGGCGATCGCGGTACCAAGACATCCTCGTCTTCCGC 29 | AGTAAAACCTACGGCAACGTGCTGGTTCTGGATGGCGTCATCCAGTGTACTGAGAGGGAT 30 | GAGTTCTCCTACCAGGAGATGATCGCCAACCTGCCGCTCTGCAGCCACCCCAACCCGCGG 31 | AAGGTGCTGATCATCGGGGGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCC 32 | TCTGTGGAGTCGGTGGTCCAGTGCGAGATTGATGAGGATGTCATTGAAGTCTCTAAGAAG 33 | TTCCTGCCTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGGGCGAT 34 | GGCTTTGAGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCCTCA 35 | GACCCCATGGGCCCTGCTGAGAGCCTCTTCAAGGAGTCCTATTACCAGCTCATGAAGACA 36 | GCACTCAAAGAAGATGGCATCCTGTGCTGCCAGGGTGAGTGCCAGTGGCTGCACCTGGAC 37 | CTCATCAAGGAGATGAGGCACTTCTGCAAATCTCTCTTCCCCGTGGTGGACTACGCCTAC 38 | TGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGCTTCATGCTGTGTAGCAAAAACCCG 39 | AGCACCAACTTCCGGGAGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAG 40 | CTGAAATACTATAACTCGGACATGCACCGTGCCGCCTTCGTACTGCCTGAGTTCACCCGG 41 | AAGGCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACCACCCGAGACCTCAA 42 | TCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCTGGACCAGACTCC 43 | CAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCATGATGCTGCCTGGCCTGGCC 44 | TGGCCTGGCCTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGTCTATCTCT 45 | GTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTGTGACCC 46 | AACAAAATACATGTGTATTCCG 47 | -------------------------------------------------------------------------------- /t/data/sim4_genomic.fa: -------------------------------------------------------------------------------- 1 | >4.143962167-143965267 Slice, no description 2 | GGCGCGGGCAGCGGGCAGAGCTGGTCACGTTGTGCTGGGGGGGGTCCGCGCGCCCTGCAG 3 | TCCCGAACCCGCTACGCGCTCCGTCGGCCCGCCCGCCCGCCATGGAGCCTGGCCCCGACG 4 | GCCCAGCCGCGCCCGGCCCCGCCGCCATCCGTGAGGGCTGGTTCCGAGAGACCTGCAGCC 5 | TGTGGCCCGGCCAGGCCCTGTCGCTGCAAGTGGAGCAGCTGCTTCACCACCGGCGATCGC 6 | GGTACCAAGACATCCTCGTCTTCCGCAGGTATGGCCCGCCGCGCGCCGGTGCAGCTGTCA 7 | GAAGTTCTGCGCTGGGCCCGGCCCTGCGTCCACGTGTCACTATCGGGACACGTCAGCCGA 8 | GGGGACCCCGGGACCCACCCAGCCCCCACACGTGGCTCGCCTGCCACGTGTCACCCCGAA 9 | TGCCCACCCCTGGACCCCATGGCGGCCACGTGCACGCCCAGGGAGGACAGGGACCTAACC 10 | TCCCAGTGTCCCAGGACCCACGTCCCCGACTGTCTCTGCCCGCAGTAAAACCTACGGCAA 11 | CGTGCTGGTTCTGGATGGCGTCATCCAGTGTACTGAGAGGGATGAGTTCTCCTACCAGGA 12 | GATGATCGCCAACCTGCCGCTCTGCAGCCACCCCAACCCGCGGAAGGTACCGCATTGCCC 13 | CTGGGTTCAGCCCTGAGCTCGGGGTCCTAGAAAAGCATGTCGGGCTGACACTAGGTGAGG 14 | ATGTTTGGGGGCAGATGCTACCCAGATGACTGTCAGAAAATGCGGGTCGGTCAGGATGAA 15 | TAGAGCTCCTGGGAGAGCTGGTCTCCTTAGAAGCCCCGAGAGGGGAACCCAGGCTGCCAG 16 | GAAGGACCCCGTGGCACAGAAGCGTTCTGGAGAGTAGAGAATGACTCAGAGTCCTGTAGC 17 | TGGGAAGATCAGGTTCTGTGGGAGTGGGCCTGCTCAGTCCTGACTTGTCCTTCCCTGGCC 18 | CAGGTGCTGATCATCGGGGGTGGAGATGGGGGCGTCCTACGGGAAGTGGTGAAGCACCCC 19 | TCTGTGGAGTCGGTGGTCCAGTGCGAGATTGATGAGGTGGGTGCAGTCCAGGAGGCCTGG 20 | ATTTGAGTCACCAGAGTCAGCTCTGTCCCATCCTGACTCTGCACCCCGAGGCGCAATGTT 21 | CTTACCATCCCTGCCCTGTTTCCTCAGTCTGAAAAGAGGGTTCAGTAGGAAAACCAGATT 22 | GTTAAGGCCTGGCACACACCACACCATGGATGTTAACTCTTAGTGCTTTCAGAGCCCAGG 23 | CAGAGCCAGAGAGCTCAACAACTTATGGCATCTCCCCTTGAGACCCAGCATGGTTTTAGT 24 | GAGCACTTACTGTATGCTGAGTGTTACCCAAGGTGCTGGGTTGATACGGCCATGGACAGG 25 | TGAGCCCCTGAGTGTAGAGCTGGTGTTTGGGTTGGAGAAGACACCATAACACAGCATGAC 26 | ATGATGAGGCCAGACAGGGATAAAAGATATGGAGAACACAGGCTGATAGGAAGTGTGCAG 27 | CCACGCATGCTTACAGCCCCAGCACTTGGGTAGAAGCAGGACGATCAAGAGTTTGAGGCC 28 | AGCGTGAGTTATCTGAGACCATCTCTCAAAAATGCAGAAGCTCAGATGGGACTTGGTCTG 29 | CAGGGAGTTGAGGCCTGAAAACCATGAAGAGCTGAGGTGGTGTAGATCTGGGGGAAAGGG 30 | TTTTCAAAAGAGAAGACTTGTCCAAAGAAACCCCACCAGGAGTCCCCAGCCTCTAGTCCA 31 | GCCCAGCCCTTCCTCTCCCCCCTCTTCAGGATGTCATTGAAGTCTCTAAGAAGTTCCTGC 32 | CTGGCATGGCCGTTGGCTTCTCCAGCTCAAAGCTGACTCTCCACGTGGGCGATGGCTTTG 33 | AGTTCATGAAACAGAACCAAGATGCCTTTGACGTCATCATCACCGACTCCTCAGACCCCA 34 | TGGGTGAGCCAGGGCACGCGCGTCCTGCAGCACACAGCAGCCCCAGACTAGAGCCATGTG 35 | ATGATGGAGGCCTGAGGACGGTGGGGGTCTAGCCTTGGTCCATAGTGACCTCTGCTTCCT 36 | CTTTGGCTTCTTCCCTGTGCTTGTTGGCCAGCATCCGGGTGTGCTATGGTGCAGTGGGGG 37 | AGGGTTTGAATGCAGGGCCTCCCAGGTGCTAAGGCAGTAGGGGGCCACATCCCACAAACA 38 | TGGGTCCAGCACCTGCTTTGCCACTGAGCTGCTGTGGGTGACTGTGGCCTGGAGGTCTCA 39 | GGCAGGATGGCCATGCTCTACCCCTCTAGGCCCTGCTGAGAGCCTCTTCAAGGAGTCCTA 40 | TTACCAGCTCATGAAGACAGCACTCAAAGAAGATGGCATCCTGTGCTGCCAGGGTGAGTG 41 | CCAGTGGCTGCACCTGGACCTCATCAAGGAGATGAGGCACTTCTGCAAATCTCTCTTCCC 42 | CGTGGTGGACTACGCCTACTGTAGCATTCCTACCTATCCCAGCGGCCAGATCGGCTTCAT 43 | GCTGTGTAGCAAAAACCCGGTGAGCTGGGGGTGACTGCCTGCAGGGTGGGGCGAGGGCAG 44 | GCACTAAGAGCCCCATCTTGATGCTCTTTGTCCCTGGTTCCCAGAGCACCAACTTCCGGG 45 | AGCCAGTGCAGCAGTTGACACAGGCCCAGGTGGAGCAGATGCAGCTGAAATACTATAACT 46 | CGGACATGCACCGTGCCGCCTTCGTACTGCCCGAGTTCACCCGGAAGGTGAGTGGCCTGC 47 | CAGGCTCCCTGCTGGGCCTCATCCTGCACAGCTTGCACATCCTCCTGACTGCCTTCATGT 48 | CCCACCAGGCCCTCAATGACATAAGCTGAATCCAGGTGCCACTGTGACACCACCCGAGAC 49 | CTCAATCGGATTGGACCAAGGATCTTCCAAGTTGTCTGGGGACCACCAGTCCTGGACCAG 50 | ACTCCCAGATGACTCTTGCCCACCAACCAAGTGTTACAGGCCCCACGATGCTGCCTGGCC 51 | TGGCCTGGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTCTGTCTATCTCTGTGGC 52 | GTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCGCCTATGCCCTGTGACCCAACAA 53 | AATACATGTGTATTTATAACAAGCTCAGTCATGACCTCTGA 54 | -------------------------------------------------------------------------------- /t/data/simprot_tree.nh: -------------------------------------------------------------------------------- 1 | ((((((((((human:0.003731,chimp:0.005784):0.010784,(macaque:0.010132,baboon:0.005298):0.020022):0.008086,marmoset:0.031742):0.027926,galago:0.059928):0.008603,((rat:0.033689,mouse:0.028067):0.090631,rabbit:0.083641):0.009613):0.012552,(((dog:0.04844,cow:0.073628):0.005271,rfbat:0.063326):0.003432,shrew:0.122568):0.035539):0.012172,armadillo:0.094907):0.009802,(elephant:0.052481,tenrec:0.113618):0.034246):0.1028,monodelphi:0.179185):0.120801,platypus:0.120801); 2 | -------------------------------------------------------------------------------- /t/data/species_tree_njtree.nh: -------------------------------------------------------------------------------- 1 | ((ORYSA*-4530.rice,ARATH*-3702)Magnoliophyta-3398,(SCHPO*-4896.S_pombe,YEAST*-4932)Ascomycota-4890,((((((((((((HUMAN*-9606,PANTR*-9598.chimpanzee)Homo/Pan/Gorilla-207598,MACMU*-9544.monkey)Catarrhini-9526,OTOGA-*30611.galago)Primates-9443,((MOUSE*-10090,RAT*-10116)Murinae-39107,RABIT-9986)Glires-314147)Euarchontoglires-314146,((BOVIN*-9913.cow,PIG-*9823)Cetartiodactyla-91561,(CANFA*-9615.dog,FELCA-*9685.cat)Carnivora-33554,SORAR-*42254.shrew,MYOLU-*59463.bat)Laurasiatheria-314145,(ECHTE-9371.tenrec,LOXAF-9785.elephant)Afrotheria-311790,DASNO-9361.armadillo)Eutheria-9347,MONDO*-13616.opossum)Theria-32525,ORNAN-*9258.platypus)Mammalia-40674,CHICK*-9031)Amniota-32524,XENTR*-8364.frog)Tetrapoda-32523,(BRARE*-7955.zebrafish,((TETNG*-99883.pufferfish,FUGRU*-31033.pufferfish)Tetraodontidae-31031,(GASAC-*69293.stickleback,ORYLA-*8090.ricefish)Smegmamorpha-129949)Percomorpha-32485)Clupeocephala-186625)Euteleostomi-117571,(CIOIN*-7719,CIOSA-*51511)Ciona-7718)Chordata-7711,(((DROME*-7227.fly,DROPS*-7237.fly)Sophophora-32341,(AEDAE-*7159.mosquito,ANOGA*-7165.mosquito)Culicidae-7157)Diptera-7147,APIME-*7460.honeybee)Endopterygota-33392,SCHMA*-6183.fluke,(CAEEL*-6239.worm,CAEBR*-6238.worm,CAERE*-31234.worm)Caenorhabditis-6237)Bilateria-33213)Eukaryota-2759; 2 | -------------------------------------------------------------------------------- /t/data/test-query.fas: -------------------------------------------------------------------------------- 1 | >SA009 query 2 | GACGATCCTTCGGTGAGCAAAGAAATTTTAGCAGAAGCTAAAAAGCTAAACGATGCTCAAGCACCAAAAG 3 | -------------------------------------------------------------------------------- /t/data/test.txt: -------------------------------------------------------------------------------- 1 | >Test 2 | AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC 3 | TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA 4 | TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC 5 | ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG 6 | CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA 7 | GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC 8 | AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG 9 | AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT -------------------------------------------------------------------------------- /t/data/test_prot.FastA: -------------------------------------------------------------------------------- 1 | >test_prot 2 | MHSAVDCNGVVSLVDGRSALMLPNGQLLPEVIIDKATSDDSGTTNQIHKKRRCSSYLLSEDMLNDPNLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHKFLIWNCSPYWIKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGNLVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVLVSLTSNLSSGIQKVGYGNSHMVLNLFLALLLSSFSSDNLTAIEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFSKKPKISREIRQAEDLNTKKENYISNHTLAEMSKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFIHNPSLTVTVPIAPGESDLENMNAEELSSDSDSEYSKV 3 | -------------------------------------------------------------------------------- /t/data/testaln.phylip: -------------------------------------------------------------------------------- 1 | 4 50 2 | Homo_sapie AGTCGAGTC---GCAGAAACGCATGAC-GACC 3 | Pan_panisc AGTCGCGTCG--GCAGAAACGCATGACGGACC 4 | Gorilla_go AGTCGCGTCG--GCAGATACGCATCACGGAC- 5 | Pongo_pigm AGTCGCGTCGAAGCAGA--CGCATGACGGACC 6 | 7 | ACATTTT-CCTTGCAAAG 8 | ACATCAT-CCTTGCAAAG 9 | ACATCATCCCTCGCAGAG 10 | ACATCATCCCTTGCAGAG 11 | -------------------------------------------------------------------------------- /t/data/transfac.dat: -------------------------------------------------------------------------------- 1 | VV TRANSFAC MATRIX TABLE, Release 6.4 - licensed - 2002-12-02, (C) Biobase GmbH 2 | XX 3 | // 4 | AC M00001 5 | XX 6 | ID V$MYOD_01 7 | XX 8 | DT 19.10.1992 (created); ewi. 9 | DT 22.10.1997 (updated); dbo. 10 | CO Copyright (C), Biobase GmbH. 11 | XX 12 | NA MyoD 13 | XX 14 | DE myoblast determination gene product 15 | XX 16 | BF T00526; MyoD; Species: mouse, Mus musculus. 17 | XX 18 | P0 A C G T 19 | 01 1 2 2 0 S 20 | 02 2 1 2 0 R 21 | 03 3 0 1 1 A 22 | 04 0 5 0 0 C 23 | 05 5 0 0 0 A 24 | 06 0 0 4 1 G 25 | 07 0 1 4 0 G 26 | 08 0 0 0 5 T 27 | 09 0 0 5 0 G 28 | 10 0 1 2 2 K 29 | 11 0 2 0 3 Y 30 | 12 1 0 3 1 G 31 | XX 32 | BA 5 functional elements in 3 genes 33 | XX 34 | CC no comment 35 | XX 36 | // 37 | AC M00002 38 | XX 39 | ID V$E47_01 40 | XX 41 | DT 19.10.1992 (created); ewi. 42 | DT 18.07.2000 (updated); ewi. 43 | CO Copyright (C), Biobase GmbH. 44 | XX 45 | NA E47 46 | XX 47 | DE E47 48 | XX 49 | BF T00207; E47; Species: human, Homo sapiens. 50 | XX 51 | P0 A C G T 52 | 01 4 4 3 0 V 53 | 02 2 5 4 0 S 54 | 03 3 2 4 2 N 55 | 04 2 0 9 0 G 56 | 05 0 11 0 0 C 57 | 06 11 0 0 0 A 58 | 07 0 0 11 0 G 59 | 08 1 2 8 0 G 60 | 09 0 0 0 11 T 61 | 10 0 0 11 0 G 62 | 11 0 0 4 7 K 63 | 12 1 4 3 3 N 64 | 13 1 6 2 2 C 65 | 14 1 4 4 2 N 66 | 15 1 4 2 3 N 67 | XX 68 | BA 11 selected strong binding sites for E47, E47-MyoD, E12+MyoD and (weak) for 69 | BA E12 70 | XX 71 | BS R05108; Start: 3; Length: 15; Gaps: 17; Orientation: p. 72 | BS R05109; Start: 1; Length: 15; Gaps:; Orientation: p. 73 | BS R05110; Start: 5; Length: 15; Gaps:; Orientation: p. 74 | BS R05111; Start: 5; Length: 15; Gaps:; Orientation: p. 75 | BS R05112; Start: 8; Length: 15; Gaps:; Orientation: p. 76 | BS R05113; Start: 9; Length: 15; Gaps:; Orientation: p. 77 | BS R05114; Start: 8; Length: 15; Gaps:; Orientation: p. 78 | BS R05115; Start: 7; Length: 15; Gaps:; Orientation: p. 79 | BS R05116; Start: 11; Length: 15; Gaps:; Orientation: p. 80 | BS R05117; Start: 5; Length: 15; Gaps:; Orientation: p. 81 | BS R05118; Start: 5; Length: 15; Gaps:; Orientation: p. 82 | XX 83 | 84 | -------------------------------------------------------------------------------- /t/data/treefile.example: -------------------------------------------------------------------------------- 1 | (SINFRUP002:0.07854,ENSP000002:0.20141,SINFRUP001:0.08462); 2 | -------------------------------------------------------------------------------- /t/data/vista.gff: -------------------------------------------------------------------------------- 1 | SEQ EMBL/GenBank/SwissProt CDS 50 100 . + . gene HoxD3a; 2 | SEQ EMBL/GenBank/SwissProt CDS 120 190 . + . gene HoxD3a; 3 | SEQ EMBL/GenBank/SwissProt CDS 250 350 . + . gene HoxD3a; 4 | SEQ EMBL/GenBank/SwissProt CDS 450 900 . + . gene HoxD3a; 5 | SEQ EMBL/GenBank/SwissProt CDS 1200 1580 . + . gene HoxD3a; 6 | SEQ EMBL/GenBank/SwissProt CDS 1700 2000 . + . gene HoxD3a; 7 | -------------------------------------------------------------------------------- /t/gmap-run.t: -------------------------------------------------------------------------------- 1 | #!perl 2 | 3 | use strict; 4 | use warnings; 5 | 6 | BEGIN { 7 | use Bio::Root::Test; 8 | test_begin(-tests => 8); 9 | use_ok( 'Bio::Tools::Run::Alignment::Gmap' ); 10 | } 11 | 12 | use Bio::SeqIO; 13 | 14 | # load the slightly edited her2 sequence (don't expect exact match) 15 | my $sio = Bio::SeqIO->new(-file=>'t/data/her2-edited.fasta' ,-format=>'fasta'); 16 | my @seq; 17 | while(my $seq = $sio->next_seq()){ 18 | push @seq,$seq; 19 | } 20 | 21 | my $gmapper = Bio::Tools::Run::Alignment::Gmap->new(); 22 | 23 | SKIP: { 24 | 25 | test_skip(-tests => 7, -requires_executable => $gmapper); 26 | 27 | my $result_handle = $gmapper->run(\@seq); 28 | 29 | my $result; 30 | $result .= $_ while (<$result_handle>); 31 | 32 | like($result, qr|^>NM_004448 Homo sapiens|, 'Check query info line'); 33 | like($result, qr|md5:a7f28cc6e121f649fa8eb2d44805100e|, 'Check md5 info'); 34 | like($result, qr|1 E\t2 G\t\+17:\d+ \d+ G\tE|, 35 | 'Does it look reasonable like -f 9 output'); 36 | 37 | $result = ''; 38 | $gmapper->flags('-A -5 -e -n 100'); 39 | $result_handle = $gmapper->run(\@seq); 40 | $result .= $_ while (<$result_handle>); 41 | 42 | like($result, qr|^>NM_004448 Homo sapiens|, 'Check query info line'); 43 | like($result, qr|md5:a7f28cc6e121f649fa8eb2d44805100e|, 'Check md5 info'); 44 | like($result, qr|Paths \(\d+\)|, 'Does it look like -A output (I)'); 45 | like($result, qr|Alignment for path \d+|, 'Does it look like -A output (II)'); 46 | 47 | } 48 | -------------------------------------------------------------------------------- /t/tRNAscanSE.t: -------------------------------------------------------------------------------- 1 | #-*-Perl-*- 2 | # ## Bioperl Test Harness Script for Modules 3 | # # 4 | use strict; 5 | use vars qw($NTESTS); 6 | 7 | BEGIN { 8 | use Bio::Root::Test; 9 | $NTESTS = 12; 10 | test_begin(-tests => $NTESTS, 11 | -requires_modules => [qw(IPC::Run)]); 12 | use_ok('Bio::Tools::Run::tRNAscanSE'); 13 | use_ok('Bio::Root::IO'); 14 | use_ok('Bio::Seq'); 15 | } 16 | 17 | my $verbose = test_debug(); 18 | 19 | my $fasta_file = test_input_file('H_pylori_J99.fasta'); 20 | 21 | my $factory = Bio::Tools::Run::tRNAscanSE->new(-program => 'tRNAscan-SE'); 22 | isa_ok $factory, 'Bio::Tools::Run::tRNAscanSE'; 23 | 24 | my $seqstream = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta'); 25 | my $seq = $seqstream->next_seq(); 26 | 27 | SKIP: { 28 | test_skip(-requires_executable => $factory, 29 | -tests => 8); 30 | 31 | my $tRNAscanSE = $factory->run($seq); 32 | isa_ok $tRNAscanSE, 'Bio::Tools::tRNAscanSE'; 33 | 34 | while (my $gene = $tRNAscanSE->next_prediction()) { 35 | isa_ok $gene, 'Bio::SeqFeature::Generic'; 36 | } 37 | } 38 | 39 | 1; 40 | --------------------------------------------------------------------------------