comparison PanExplorer_workflow/Perl/generateConfig.pl @ 1:032f6b3806a3 draft

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author dereeper
date Thu, 30 May 2024 11:16:08 +0000
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0:3cbb01081cde 1:032f6b3806a3
1 #!/usr/bin/perl
2
3 use strict;
4 use warnings;
5 use YAML qw(DumpFile);
6
7 use Cwd;
8 my $dir = getcwd;
9
10
11 my $zip = $ARGV[0];
12 my $list = $ARGV[1];
13 my $out = $ARGV[2];
14 my $zip_fasta = $ARGV[3];
15
16 $list =~s/NZ_//g;
17 my @list_ids = split(/,/,$list);
18
19 my %data = ();
20 foreach my $id(@list_ids){
21 push @{$data{"ids"}}, "$id";
22 }
23 # case fasta+gff
24 if ($zip ne "None" && $zip_fasta ne "None"){
25 system("rm -rf $zip.genomeszip");
26 mkdir("$zip.genomeszip");
27 chdir("$zip.genomeszip");
28 system("cp -rf $zip ./genomes.zip");
29 system("cp -rf $zip_fasta ./fasta_genomes.zip");
30 system("unzip fasta_genomes.zip");
31 system("unzip genomes.zip");
32 unlink("fasta_genomes.zip");
33 unlink("genomes.zip");
34 open(LS,"ls *gff |");
35 while(my $line = <LS>){
36 chomp($line);
37 my $concat = "$zip.genomeszip/".$line;
38 if ($line =~/(.*)\.gff/){
39 my $name = $1;
40 if ($concat =~/\w+/){
41 $data{"input_genomes"}{"$name"}{"gff3"} = "$concat";
42 $data{"input_genomes"}{"$name"}{"name"} = "$name";
43 }
44 }
45 }
46 close(LS);
47
48 open(LS,"ls *fasta |");
49 while(my $line = <LS>){
50 chomp($line);
51 my $concat = "$zip.genomeszip/".$line;
52 if ($line =~/(.*)\.fasta/){
53 my $name = $1;
54 if ($concat =~/\w+/){
55 $data{"input_genomes"}{"$name"}{"fasta"} = "$concat";
56 }
57 }
58 }
59 close(LS);
60
61 }
62 elsif ($zip ne "None"){
63 system("rm -rf $zip.genomeszip");
64 mkdir("$zip.genomeszip");
65 chdir("$zip.genomeszip");
66 my $head = `head -1 $zip`;
67 if ($head =~/LOCUS/){
68 push @{$data{"input_genbanks"}}, "$zip";
69 }
70 else{
71 system("cp -rf $zip ./genomes.zip");
72 system("unzip genomes.zip");
73 unlink("genomes.zip");
74 open(LS,"ls |");
75 while(my $line = <LS>){
76 chomp($line);
77 my $concat = "$zip.genomeszip/".$line;
78 if ($concat =~/\w+/){
79 push @{$data{"input_genbanks"}}, "$concat";
80 }
81 }
82 close(LS);
83 }
84 }
85 #else{
86 # push @{$data{"input_genbanks"}}, "";
87 #}
88 chdir($dir);
89
90 DumpFile($out, \%data);