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Perl script to run in parellel !

  • Public
By LEGE 1886 days ago
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::SeqIO; my ($sequence_data_ref) = parse_genome_files($ARGV[0]); my %genome=%{$sequence_data_ref}; my $n_processes = 4; my $pm = Parallel::ForkManager->new( $n_processes ); for my $i ( 1 .. $n_processes ) { $pm->start and next; my $count = 0; foreach my $chr_set (keys %genome) { $count++; if ( ( $count % $i ) == 0 ) { if ( !output_exists($genome{$chr_set}{name}) ) { start_new_XFOIL_instance($genome{$chr_set}{name}, $genome{$chr_set}{nuc_seq}); } } } $pm->finish; } $pm->wait_all_children; sub output_exists { my $chr_set = shift; return ( -f "$chr_set.out" ); } sub start_new_XFOIL_instance { my ($chr_set, $chr_seq) = @_; print "starting XFOIL instance with parameters $chr_set!\n"; touch( "$chr_set.out", $chr_seq ); print "finished run with parameters $chr_set!\n"; } sub touch { my ($fn, $seq) = @_; open FILE, ">$fn" or die $!; system ("augustus --species=caenorhabditis --outfile=$fn $seq --AUGUSTUS_CONFIG_PATH=/home/urbe/Tools/Alienomics_v1.1/augustus.2.5.5/config"); close FILE or die $!; } sub parse_genome_files { my $file=shift; my (%sequence_data); my $file_content = new Bio::SeqIO(-format => 'fasta',-file => "$file"); my $out_content = Bio::SeqIO->newFh(-format => 'fasta', ,-file => ">genomeRES.fa"); while (my $gene_info = $file_content->next_seq()) { my $sequence = $gene_info->seq(); my $accession_number = $gene_info->display_id; my $len = $gene_info->length; my $GCcount = $sequence =~ tr/GC|gc//; my $GCcontent = ($GCcount / $len) * 100; $sequence_data{$accession_number}{status} = "OK"; #everybody starts fine $sequence_data{$accession_number}{problem_desc} = "-"; #everybody starts fine if ($sequence_data{$accession_number}{status} eq "OK") { # Add check points here <<<<<< $sequence_data{$accession_number}{nuc_seq} = $sequence; $sequence_data{$accession_number}{len} = $len; $sequence_data{$accession_number}{gc} = $GCcontent; $sequence_data{$accession_number}{name} = $accession_number; print $out_content $gene_info; } } return (\%sequence_data); }