Mercurial > repos > dereeper > pgap

comparison PGAP_wrapper2.pl @ 5:d8c5bea1cce2 draft

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Uploaded
author dereeper
date Thu, 24 Jun 2021 17:56:22 +0000
parents 041355b97140
children 1085c917d850
comparison
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4:70b7a5270968 5:d8c5bea1cce2
30 30
31 31
32 die $usage 32 die $usage
33 if ( !$proteins || !$genes || !$out || !$order); 33 if ( !$proteins || !$genes || !$out || !$order);
34 34
35 if ($order =~/^,(.*)$/){
36 $order = $1;
37 }
35 my @names = split(",",$order); 38 my @names = split(",",$order);
36 my @list;
37 mkdir("tmpdir$$"); 39 mkdir("tmpdir$$");
38 my @gene_files = split(/,/,$genes); 40 my @gene_files = split(/,/,$genes);
39 my $n = 0; 41 my $n = 0;
40 foreach my $gene_file(@gene_files){ 42 foreach my $gene_file(@gene_files){
41 my $particule = $names[$n]; 43 my $particule = $names[$n];
43 $n++; 45 $n++;
44 } 46 }
45 $n = 0; 47 $n = 0;
46 my @protein_files = split(/,/,$proteins); 48 my @protein_files = split(/,/,$proteins);
47 foreach my $protein_file(@protein_files){ 49 foreach my $protein_file(@protein_files){
48 my $particule = $names[0]; 50 my $particule = $names[$n];
49 system("cp $protein_file tmpdir$$/$particule.pep"); 51 system("cp $protein_file tmpdir$$/$particule.pep");
50 open(F,"$protein_file"); 52 open(F,"$protein_file");
51 open(F2,">tmpdir$$/$particule.function"); 53 open(F2,">tmpdir$$/$particule.function");
52 while(<F>){ 54 while(<F>){
53 if (/>(.*)/){ 55 if (/>(.*)/){
58 close(F2); 60 close(F2);
59 $n++; 61 $n++;
60 } 62 }
61 63
62 #chdir("$dirname/PGAP-1.2.1"); 64 #chdir("$dirname/PGAP-1.2.1");
63 my $cmd = "perl $dirname/PGAP-1.2.1/PGAP.pl --input tmpdir$$ --output outdir --cluster --pangenome --variation --evolution --function --strains ".join("+",@list)." --method GF"; 65 my $cmd = "perl $dirname/PGAP-1.2.1/PGAP.pl --input tmpdir$$ --output outdir --cluster --pangenome --variation --evolution --function --strains ".join("+",@names)." --method GF";
64 system($cmd); 66 system($cmd);
65 system("cp -rf outdir/1.Orthologs_Cluster.txt $out"); 67 system("cp -rf outdir/1.Orthologs_Cluster.txt $out");