Mercurial > repos > dereeper > pgap
view PGAP_wrapper2.pl @ 0:83e62a1aeeeb draft
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author | dereeper |
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date | Thu, 24 Jun 2021 13:51:52 +0000 (2021-06-24) |
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children | 6d3580552457 |
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#!/usr/bin/perl use strict; use Getopt::Long; use Bio::SeqIO; use File::Basename; my $dirname = dirname(__FILE__); use Cwd qw(cwd); my $dir = cwd; my $usage = qq~Usage:$0 <args> [<opts>] where <args> are: -g, --genes <list of gene fasta files. Comma separated list> -p, --proteins <list of protein fasta files. Comma separated list> -o, --order <list of samples in the same order. Comma separated list> -o, --out <output name> ~; $usage .= "\n"; my ($genes,$proteins,$out,$order); GetOptions( "genes=s" => \$genes, "proteins=s" => \$proteins, "out=s" => \$out, "order=s" => \$order ); die $usage if ( !$proteins || !$genes || !$out || !$order); my @names = split(",",$order); my @list; mkdir("tmpdir$$"); my @gene_files = split(/,/,$genes); my $n = 0; foreach my $gene_file(@gene_files){ my $particule = $names[$i]; system("cp $gene_file tmpdir$$/$particule.nuc"); $n++; } $n = 0; my @protein_files = split(/,/,$proteins); foreach my $protein_file(@protein_files){ my $particule = $names[0]; system("cp $protein_file tmpdir$$/$particule.pep"); open(F,"$protein_file"); open(F2,">tmpdir$$/$particule.function"); while(<F>){ if (/>(.*)/){ print F2 "$1 - unknown\n"; } } close(F); close(F2); $n++; } #chdir("$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"; system($cmd); system("cp -rf outdir/1.Orthologs_Cluster.txt $out");