Mercurial > repos > dereeper > pangenome_explorer
view Perl/generateConfig.pl @ 6:35d71348e81e draft
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author | dereeper |
---|---|
date | Thu, 30 May 2024 12:12:30 +0000 |
parents | e42d30da7a74 |
children | 5a5c9a6b047b |
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#!/usr/bin/perl use strict; use warnings; use YAML qw(DumpFile); use Cwd; my $dir = getcwd; my $zip = $ARGV[0]; my $list = $ARGV[1]; my $out = $ARGV[2]; my $zip_fasta = $ARGV[3]; $list =~s/NZ_//g; my @list_ids = split(/,/,$list); my %data = (); foreach my $id(@list_ids){ push @{$data{"ids"}}, "$id"; } # case fasta+gff if ($zip ne "None" && $zip_fasta ne "None"){ system("rm -rf $zip.genomeszip"); mkdir("$zip.genomeszip"); chdir("$zip.genomeszip"); system("cp -rf $zip ./genomes.zip"); system("cp -rf $zip_fasta ./fasta_genomes.zip"); system("unzip fasta_genomes.zip"); system("unzip genomes.zip"); unlink("fasta_genomes.zip"); unlink("genomes.zip"); open(LS,"ls *gff |"); while(my $line = <LS>){ chomp($line); my $concat = "$zip.genomeszip/".$line; if ($line =~/(.*)\.gff/){ my $name = $1; if ($concat =~/\w+/){ $data{"input_genomes"}{"$name"}{"gff3"} = "$concat"; $data{"input_genomes"}{"$name"}{"name"} = "$name"; } } } close(LS); open(LS,"ls *fasta |"); while(my $line = <LS>){ chomp($line); my $concat = "$zip.genomeszip/".$line; if ($line =~/(.*)\.fasta/){ my $name = $1; if ($concat =~/\w+/){ $data{"input_genomes"}{"$name"}{"fasta"} = "$concat"; } } } close(LS); } elsif ($zip ne "None"){ system("rm -rf $zip.genomeszip"); mkdir("$zip.genomeszip"); chdir("$zip.genomeszip"); my $head = `head -1 $zip`; if ($head =~/LOCUS/){ push @{$data{"input_genbanks"}}, "$zip"; } else{ system("cp -rf $zip ./genomes.zip"); system("unzip genomes.zip"); unlink("genomes.zip"); open(LS,"ls |"); while(my $line = <LS>){ chomp($line); my $concat = "$zip.genomeszip/".$line; if ($concat =~/\w+/){ push @{$data{"input_genbanks"}}, "$concat"; } } close(LS); } } #else{ # push @{$data{"input_genbanks"}}, ""; #} chdir($dir); DumpFile($out, \%data);