sanger-pathogens · andrewjpage · Apr 30, 2013 · Apr 30, 2013
diff --git a/lib/Bio/PanGenome.pm b/lib/Bio/PanGenome.pm
@@ -17,10 +17,12 @@ use Bio::PanGenome::InflateClusters;
 use Bio::PanGenome::AnalyseGroups;
 use Bio::PanGenome::GroupLabels;
 use Bio::PanGenome::AnnotateGroups;
+use Bio::PanGenome::Output::OneGenePerGroupFasta;
 
 has 'fasta_files'      => ( is => 'rw', isa => 'ArrayRef', required => 1 );
 has 'input_files'      => ( is => 'rw', isa => 'ArrayRef', required => 1 );
 has 'output_filename'  => ( is => 'rw', isa => 'Str', default => 'clustered_proteins' );
+has 'output_pan_geneome_filename'  => ( is => 'rw', isa => 'Str', default => 'pan_genome.fa' );
 has 'job_runner'       => ( is => 'rw', isa => 'Str', default => 'LSF' );
 has 'makeblastdb_exec' => ( is => 'rw', isa => 'Str', default => 'makeblastdb' );
 has 'blastp_exec'      => ( is => 'rw', isa => 'Str', default => 'blastp' );
@@ -92,13 +94,21 @@ sub run {
       groups_filename   => $output_group_labels_filename,
     );
     $annotate_groups->reannotate;
+
+    my $one_gene_per_fasta = Bio::PanGenome::Output::OneGenePerGroupFasta->new(
+        analyse_groups  => $analyse_groups_obj,
+        output_filename => $self->output_pan_geneome_filename
+    );
+    $one_gene_per_fasta->create_file();
 
     unlink($output_blast_results_filename);
     unlink($output_combined_filename);
     unlink($output_cd_hit_filename );
     unlink($output_mcl_filename );
     unlink($output_inflate_clusters_filename);
     unlink($output_group_labels_filename);
+    unlink($output_cd_hit_filename.'.clstr');
+    unlink($output_cd_hit_filename.'.bak.clstr');
 }
 
 no Moose;

diff --git a/lib/Bio/PanGenome/CommandLine/CreatePanGenome.pm b/lib/Bio/PanGenome/CommandLine/CreatePanGenome.pm
@@ -23,8 +23,8 @@ has 'output_filename'   => ( is => 'rw', isa => 'Str', default => 'clustered_pro
 has 'job_runner'        => ( is => 'rw', isa => 'Str', default => 'LSF' );
 has 'makeblastdb_exec'  => ( is => 'rw', isa => 'Str', default => 'makeblastdb' );
 has 'blastp_exec'       => ( is => 'rw', isa => 'Str', default => 'blastp' );
-has 'mcxdeblast_exec'   => ( is => 'ro', isa => 'Str', default => 'mcxdeblast' );
-has 'mcl_exec'          => ( is => 'ro', isa => 'Str', default => 'mcl' );
+has 'mcxdeblast_exec'   => ( is => 'rw', isa => 'Str', default => 'mcxdeblast' );
+has 'mcl_exec'          => ( is => 'rw', isa => 'Str', default => 'mcl' );
 
 has '_error_message'    => ( is => 'rw', isa => 'Str' );
 
@@ -39,8 +39,8 @@ sub BUILD {
         'j|job_runner=s'       => \$job_runner,
         'm|makeblastdb_exec=s' => \$makeblastdb_exec,
         'b|blastp_exec=s'      => \$blastp_exec,
-        'd|mcxdeblast_exec'    => \$mcxdeblast_exec,
-        'c|mcl_exec'           => \$mcl_exec,
+        'd|mcxdeblast_exec=s'    => \$mcxdeblast_exec,
+        'c|mcl_exec=s'           => \$mcl_exec,
         'h|help'               => \$help,
     );
 

diff --git a/lib/Bio/PanGenome/ExtractProteomeFromGFF.pm b/lib/Bio/PanGenome/ExtractProteomeFromGFF.pm
@@ -38,9 +38,8 @@ sub _build__working_directory_name {
 }
 
 sub _gff_parser {
-    my ( $self, $filename ) = @_;
-    # $self->_awk_filter .
-    open( my $fh, '-|',  "cat  " . $filename ) or die "Couldnt open GFF file";
+    my ( $self, $filename ) = @_; 
+    open( my $fh, '-|',  $self->_awk_filter . $filename ) or die "Couldnt open GFF file";
     my $gff_parser = Bio::Tools::GFF->new( -fh => $fh, gff_version => 3 );
     return $gff_parser;
 }

diff --git a/lib/Bio/PanGenome/Output/GroupMultifasta.pm b/lib/Bio/PanGenome/Output/GroupMultifasta.pm
@@ -42,7 +42,7 @@ sub _build__genes {
 
 sub _lookup_sequence {
     my ( $self, $gene, $filename ) = @_;
-
+    return undef if(! defined($filename));
     open(my $fh, '-|', 'fasta_grep -f '.$filename. ' '.$gene);
     my $fasta_obj = Bio::SeqIO->new( -fh => $fh, -format => 'Fasta' );
     while ( my $seq = $fasta_obj->next_seq() ) {

diff --git a/t/Bio/PanGenome/CommandLine/CreatePanGenome.t b/t/Bio/PanGenome/CommandLine/CreatePanGenome.t
@@ -0,0 +1,30 @@
+#!/usr/bin/env perl
+use Moose;
+use Data::Dumper;
+use File::Slurp;
+use Cwd;
+
+BEGIN { unshift( @INC, './lib' ) }
+BEGIN { unshift( @INC, './t/lib' ) }
+with 'TestHelper';
+
+BEGIN {
+    use Test::Most;
+    use_ok('Bio::PanGenome::CommandLine::CreatePanGenome');
+}
+my $script_name = 'Bio::PanGenome::CommandLine::CreatePanGenome';
+my $cwd = getcwd();
+
+
+my %scripts_and_expected_files = (
+      ' -j Local t/data/example_1.faa t/data/example_2.faa t/data/example_3.faa' =>
+        [ 'clustered_proteins', 't/data/expected_clustered_proteins' ],
+        ' -j Local t/data/example_1.faa t/data/example_2.faa t/data/example_3.faa' =>
+          [ 'pan_genome.fa', 't/data/expected_create_pan_genome.fa' ],
+);
+
+unlink('freq_of_genes.png');
+
+mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
+
+done_testing();
diff --git a/t/data/example_3.faa b/t/data/example_3.faa
@@ -0,0 +1,43 @@
+>3333#10_00016 hypothetical protein
+MKVTHSCLEFDSIEGLIDFAREFETGSMIRFLSPIEDNSGNVLVKEEVQVKESTLARLKD
+IKGQYTPKFEVKLNKELLEQIQNILAIKIVNQLKVTDMKFLKFMYENTNYNFKGIIRNSL
+LSKKTTLTLLKVYNQNLNFFKYISELGLLSLGIVMIPDTMRFRLLRRYAFTAGILMDVPR
+IGVDKFTKLPSDDNEKVRVAHKCSDILQKLDLIEFTYGSISNHMPLGMIEDSTSSDKAAP
+GENIDETFLDDIISNDGESDSKVDGSREDAIPEKSYDIFQALLTDALKLARYIANVSHNA
+VDKDYVMEELVYYIAYNTSKKYFDELLANPLVATFKEFEVNVKRLRKIAEVEMKCVYPPS
+AWAYPKPKSSQVLCKNKVWDCPNIVMGWDIHVITAQEAFGWVGTSLPVDNYPKCRLEEEL
+DEIMVEPEKPKKK*
+>3333#10_00018 putative lipoprotein
+MDFSFNLVDNNGTVMRSTFSPIRFFTFSFLWILIDCSSVQKIENFNSVLQEPTFKSLKEE
+EAILGGSSDSDYKIRKTGNTIPVFVLSPIQTPEGMDSKLAAFLSDEVRLIWAKVKGKQVR
+IQEMSWKNPSQLSQELKRLNVDAVIKTDIREVSGKWVVNQKITDPVKEIVYGSVDGSFQS
+PKIEDELQANQAYYLKHGSGVLALDAKSSLVPIWEKSLSSGEIDSILKKSIQGYLSFSAS
+SADTEVLFQGEKIGIASFRNYPLPEGLQQIQITRPGQKDISKSLQIRSGQTISIYQEWKE
+DRTLGGVRILSFPEALQVALDGLKMGETPFYRSNLTPGAMQLELVRETENGPLVYYEGQL
+IVDADKITEIALPYKTDNLISEPEFWKLSGEKGFQAFSGKTLDFQNVSSLPPGWYGVFSA
+PFVPENMELEGIIPITAESDSGIVAISFHTSKKTISLEYEKERLSVYSFPSNGNNVGTYK
+FKKEDKEDGRPFRIITDVKEGTIRLYLGYSKVLEDRLDVSGVWRISILTRGENFSKRSPL
+RNLKIEYKGYK*
+>3333#10_00001 nudix hydrolase
+MSKHGFFQITQKLFLRKGDELLILRDRKSGLGDLPGGRMNENEFFEDWSLSMQREIEEEL
+GSQVQIRVSTKPLFIHKHKVNEGNFPCIIIAYHADYLGGDIILSDEHDYISWEKVQTYEP
+SPLFTEYMLDAVNLYLKEYAPLVH*
+>3333#10_00003 hypothetical protein
+VKTTLSGEIEKLRYEVAVKIVNLQGEVLDLRAEMKINFSEVNSKILKLQFEFEMAKIRKE
+LKTEIADLRAETKTDFLELQKSIVDIYKTISTQTRWILGVATLFAAIGKVIN*
+>3333#10_00005 imidazoleglycerol-phosphate dehydratase or histidinol-phosphatase
+LTDKLIGFYDPVRMKAERKTSETEIKLEMNLRGTGQYQFDTEIPFFEHMLSHISKHGLID
+LNLWLRGDIEIDCHHSVEDTAILMGATIHKQLGDKAGIFRYGHFTLTMDEVLTTVAVDLG
+GRYFFKYTGPELTGKFGIYDAELSLEFLQKLALNAKMNLHVVVHYGDNKHHVHESIFKAL
+GKALRMAIAQDSAAAGAIPSTKGVLE*
+>3333#10_00006 imidazole glycerol phosphate synthase subunit HisH
+MIAILDYGMGNIHSCLKAVSLYTKDFVFTKDHSTIENSKALILPGDGHFDKAMENLNSTG
+LRKTIDKHVTSGKPLFGICIGFQILFESSEEIAQGSKKEQIEGLGYIKGKIKKFHGKDFK
+VPHIGWNRLQIRRKDKSVLLKGIGDQSFFYFIHSYRPTDAEGNAITGLCDYYQEKFPAVV
+EKNNIFGTQFHPEKSHTHGLKLLENFIRFI*
+>3333#10_00007 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
+MIVIPAIDLFDNCAVRLFKGNYEEKKIYSSEPWKLAESFAKNGATLLHLVDLNGARNQLG
+VNEDSILKIRETTSLKVQLGGGIRDKEKLAYYDKIGINRFILGTAAVTNPDLLKYALDNY
+GKERVVVAVDARDGIVKIAGWEKDSGIHYRDLLERLVKAGIEHIVFTDIAQDGTLAGPNL
+EAYREILNSYPFQVIASGGIASLKDLMDLSSLKTKISLYGVITGKALYEGKLDLAKAISS
+I*
diff --git a/t/data/expected_clustered_proteins b/t/data/expected_clustered_proteins
@@ -0,0 +1,9 @@
+group_5: 1234#10_00006	3333#10_00006
+group_1: 1234#10_00001	3333#10_00001
+group_6: 1234#10_00007	3333#10_00007
+group_9: 1234#10_00018	3333#10_00018
+group_3: 1234#10_00003	3333#10_00003
+group_7: 1234#10_00016	3333#10_00016
+group_4: 1234#10_00005	3333#10_00005
+group_8: 1234#10_00017
+group_2: 1234#10_00002
diff --git a/t/data/expected_create_pan_genome.fa b/t/data/expected_create_pan_genome.fa
@@ -0,0 +1,56 @@
+>1234#10_00001 nudix hydrolase
+MSKHGFFQITQKLFLRKGDELLILRDRKSGLGDLPGGRMNENEFFEDWSLSMQREIEEEL
+GSQVQIRVSTKPLFIHKHKVNEGNFPCIIIAYHADYLGGDIILSDEHDYISWEKVQTYEP
+SPLFTEYMLDAVNLYLKEYAPLVH*
+>1234#10_00002 intramembrane serine protease
+MIIKLKIILNSYLIYYFLRGQNTLIRTLLFEFPLTTFFVFLMVATFFIVNVFLPEHLIRQ
+YFLNHPGQIQPLSWIGAVFYHGNLIHLFGNMFYLFFLGRAVEYKAGKGRWLLFFFMAALI
+SSLLDSFIRGVILHDPTPVVGASGAISGIAAVAALLSPFSLRFNQRNIPFPVFLVAWIMV
+YSDITNVFTEDGVARWAHLGGFISVIFAAYFLKPTERKQLHSGFILNLIFIILTLILAFF
+YSNRS*
+>1234#10_00003 hypothetical protein
+VKTTLSGEIEKLRYEVAVKIVNLQGEVLDLRAEMKINFSEVNSKILKLQFEFEMAKIRKE
+LKTEIADLRAETKTDFLELQKSIVDIYKTISTQTRWILGVATLFAAIGKVIN*
+>1234#10_00005 imidazoleglycerol-phosphate dehydratase or histidinol-phosphatase
+LTDKLIGFYDPVRMKAERKTSETEIKLEMNLRGTGQYQFDTEIPFFEHMLSHISKHGLID
+LNLWLRGDIEIDCHHSVEDTAILMGATIHKQLGDKAGIFRYGHFTLTMDEVLTTVAVDLG
+GRYFFKYTGPELTGKFGIYDAELSLEFLQKLALNAKMNLHVVVHYGDNKHHVHESIFKAL
+GKALRMAIAQDSAAAGAIPSTKGVLE*
+>1234#10_00006 imidazole glycerol phosphate synthase subunit HisH
+MIAILDYGMGNIHSCLKAVSLYTKDFVFTKDHSTIENSKALILPGDGHFDKAMENLNSTG
+LRKTIDKHVTSGKPLFGICIGFQILFESSEEIAQGSKKEQIEGLGYIKGKIKKFHGKDFK
+VPHIGWNRLQIRRKDKSVLLKGIGDQSFFYFIHSYRPTDAEGNAITGLCDYYQEKFPAVV
+EKNNIFGTQFHPEKSHTHGLKLLENFIRFI*
+>1234#10_00007 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
+MIVIPAIDLFDNCAVRLFKGNYEEKKIYSSEPWKLAESFAKNGATLLHLVDLNGARNQLG
+VNEDSILKIRETTSLKVQLGGGIRDKEKLAYYDKIGINRFILGTAAVTNPDLLKYALDNY
+GKERVVVAVDARDGIVKIAGWEKDSGIHYRDLLERLVKAGIEHIVFTDIAQDGTLAGPNL
+EAYREILNSYPFQVIASGGIASLKDLMDLSSLKTKISLYGVITGKALYEGKLDLAKAISS
+I*
+>1234#10_00016 hypothetical protein
+MKVTHSCLEFDSIEGLIDFAREFETGSMIRFLSPIEDNSGNVLVKEEVQVKESTLARLKD
+IKGQYTPKFEVKLNKELLEQIQNILAIKIVNQLKVTDMKFLKFMYENTNYNFKGIIRNSL
+LSKKTTLTLLKVYNQNLNFFKYISELGLLSLGIVMIPDTMRFRLLRRYAFTAGILMDVPR
+IGVDKFTKLPSDDNEKVRVAHKCSDILQKLDLIEFTYGSISNHMPLGMIEDSTSSDKAAP
+GENIDETFLDDIISNDGESDSKVDGSREDAIPEKSYDIFQALLTDALKLARYIANVSHNA
+VDKDYVMEELVYYIAYNTSKKYFDELLANPLVATFKEFEVNVKRLRKIAEVEMKCVYPPS
+AWAYPKPKSSQVLCKNKVWDCPNIVMGWDIHVITAQEAFGWVGTSLPVDNYPKCRLEEEL
+DEIMVEPEKPKKK*
+>1234#10_00017 LipL45-like lipoprotein
+MKRYLSIVILCTFAMLLLVCSTNKSSGSDQVKTESNATSARIVWLLGDVKILSDSGEKKA
+ELGASLSSTDRVVTGPNGGAEIMVADSGIIKMSKNSDIEISSLMNPNGSDTNVQVNYGKI
+VTMVKKGQKTTEFTVSTPTALAGVRGTSFLTSVESPEGSKINCAKANCTVRFAVIEGTIA
+VSKKGESSEVILSKNRELRIEKNQKLTDKLIRSLQNDSLSEMKELIVLHKNETFEYGKLV
+EELKSSSEELKILSQSGSVEEVKAAFQKREADRNNADEITKTAKAVNETKYVQQDVQKEK
+LKLNPKETF*
+>1234#10_00018 putative lipoprotein
+MDFSFNLVDNNGTVMRSTFSPIRFFTFSFLWILIDCSSVQKIENFNSVLQEPTFKSLKEE
+EAILGGSSDSDYKIRKTGNTIPVFVLSPIQTPEGMDSKLAAFLSDEVRLIWAKVKGKQVR
+IQEMSWKNPSQLSQELKRLNVDAVIKTDIREVSGKWVVNQKITDPVKEIVYGSVDGSFQS
+PKIEDELQANQAYYLKHGSGVLALDAKSSLVPIWEKSLSSGEIDSILKKSIQGYLSFSAS
+SADTEVLFQGEKIGIASFRNYPLPEGLQQIQITRPGQKDISKSLQIRSGQTISIYQEWKE
+DRTLGGVRILSFPEALQVALDGLKMGETPFYRSNLTPGAMQLELVRETENGPLVYYEGQL
+IVDADKITEIALPYKTDNLISEPEFWKLSGEKGFQAFSGKTLDFQNVSSLPPGWYGVFSA
+PFVPENMELEGIIPITAESDSGIVAISFHTSKKTISLEYEKERLSVYSFPSNGNNVGTYK
+FKKEDKEDGRPFRIITDVKEGTIRLYLGYSKVLEDRLDVSGVWRISILTRGENFSKRSPL
+RNLKIEYKGYK*