Mercurial > repos > dereeper > pangenome_explorer
comparison PanExplorer_workflow/Perl/generateConfig.pl @ 1:032f6b3806a3 draft
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author | dereeper |
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date | Thu, 30 May 2024 11:16:08 +0000 |
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0:3cbb01081cde | 1:032f6b3806a3 |
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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); |