Mercurial > repos > dereeper > pgap
changeset 5:d8c5bea1cce2 draft
Uploaded
author | dereeper |
---|---|
date | Thu, 24 Jun 2021 17:56:22 +0000 (2021-06-24) |
parents | 70b7a5270968 |
children | c43a55b28d06 |
files | PGAP-1.2.1/PGAP.pl PGAP.xml PGAP_wrapper2.pl |
diffstat | 3 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/PGAP-1.2.1/PGAP.pl Thu Jun 24 16:15:34 2021 +0000 +++ b/PGAP-1.2.1/PGAP.pl Thu Jun 24 17:56:22 2021 +0000 @@ -1804,7 +1804,8 @@ system("grep '>' All.pep > genelist"); system("$formatdb -p T -i All.pep"); system("$blastall -p blastp -i All.pep -d All.pep -M BLOSUM45 -m9 -e $evalue -o All.blastp -a $thread"); - system("perl ./Blast_Filter.pl All.blastp All.pep $coverage $identity $score | $mcl - --abc -I 2.0 -o All.cluster"); + my $dircur = dirname(__FILE__); + system("perl $dircur/Blast_Filter.pl All.blastp All.pep $coverage $identity $score | $mcl - --abc -I 2.0 -o All.cluster"); &FormatCluster("All.cluster","genelist",$spnum,\@clusters); #system("rm -rf *.pep* All.blastp All.cluster genelist"); }
--- a/PGAP.xml Thu Jun 24 16:15:34 2021 +0000 +++ b/PGAP.xml Thu Jun 24 17:56:22 2021 +0000 @@ -6,7 +6,6 @@ <requirement type="package" version="14.137">mcl</requirement> <requirement type="package" version="3.697">phylip</requirement> <requirement type="package" version="1.7.2">perl-bioperl</requirement> - <requirement type="package" version="0.07">perl-statistics-linefit</requirement> </requirements> --> <command detect_errors="aggressive"><![CDATA[ #import re
--- a/PGAP_wrapper2.pl Thu Jun 24 16:15:34 2021 +0000 +++ b/PGAP_wrapper2.pl Thu Jun 24 17:56:22 2021 +0000 @@ -32,8 +32,10 @@ die $usage if ( !$proteins || !$genes || !$out || !$order); +if ($order =~/^,(.*)$/){ + $order = $1; +} my @names = split(",",$order); -my @list; mkdir("tmpdir$$"); my @gene_files = split(/,/,$genes); my $n = 0; @@ -45,7 +47,7 @@ $n = 0; my @protein_files = split(/,/,$proteins); foreach my $protein_file(@protein_files){ - my $particule = $names[0]; + my $particule = $names[$n]; system("cp $protein_file tmpdir$$/$particule.pep"); open(F,"$protein_file"); open(F2,">tmpdir$$/$particule.function"); @@ -60,6 +62,6 @@ } #chdir("$dirname/PGAP-1.2.1"); -my $cmd = "perl $dirname/PGAP-1.2.1/PGAP.pl --input tmpdir$$ --output outdir --cluster --pangenome --variation --evolution --function --strains ".join("+",@list)." --method GF"; +my $cmd = "perl $dirname/PGAP-1.2.1/PGAP.pl --input tmpdir$$ --output outdir --cluster --pangenome --variation --evolution --function --strains ".join("+",@names)." --method GF"; system($cmd); system("cp -rf outdir/1.Orthologs_Cluster.txt $out");