Mercurial > repos > mgarnier > catchsequence
view catchsequence/catchsequence.pl @ 0:c30eb2050ef5 draft default tip
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author | mgarnier |
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date | Thu, 26 Aug 2021 13:41:33 +0000 |
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#!/usr/bin/perl use strict; use warnings; #INPUTS_ # my $Result_RES = $ARGV[0]; my $sequences = $ARGV[0]; #OUTPUT_ #my $output = $ARGV[1]; #my @list_seq = split(/,/,$sequences); my @list_seq = @ARGV; ########################################################################################## #open (OUT, ">$output"); print "SEQUENCE\tRESISTANCE GENES\tPLASMIDS\tVIRULENCE GENES\tMLST NUMBER\tGENE(ALLELE)\n"; foreach my $sequence (@list_seq) { my $Result_RES = `abricate --db resfinder $sequence > $sequence.RES.txt`; #appel système de la commande abricate avec la BDD ResFinder my $Result_PLA = `abricate --db plasmidfinder $sequence > $sequence.PLA.txt`; #appel système de la commande abricate avec la BDD PlasmidFinder my $Result_VIR = `abricate --db vfdb $sequence > $sequence.VIR.txt`; my $Result_MLST = `mlst $sequence > $sequence.MLST.txt`; open (RES, "$sequence.RES.txt"); print "$sequence\t"; while (<RES>) { chomp(); if ($_ !~ m/^#/) { my @infos = split(/\t/,$_); my $geneRes = $infos[5]; # resistance gene name (ancienne valeur $infos[4]) my $identity = $infos[10]; # identity % (ancienne valeur $infos[9]) if ($identity > 90.000) { print "$geneRes;"; } } } close (RES); print "\t"; open (PLA, "$sequence.PLA.txt") or die "could not open $!"; while (<PLA>) { chomp(); if ($_ !~ m/^#/) { my @infos = split(/\t/,$_); my $plasmid = $infos[5]; # plasmid name my $identity = $infos[10]; # identity % if ($identity > 90.000) { print"$plasmid;"; } } } close (PLA); print "\t"; open (VIR, "$sequence.VIR.txt") or die "could not open $!"; while (<VIR>) { chomp(); if ($_ !~ m/^#/) { my @infos = split(/\t/,$_); my $geneVir = $infos[5]; # virulence gene name my $identity = $infos[10]; # identity % if ($identity > 80.000) { print "$geneVir;"; } } } close (VIR); print "\t"; open (MLST, "$sequence.MLST.txt") or die "could not open $!"; while (<MLST>) { chomp(); my @infos = split(/\t/,$_); my $numMLST = $infos[2]; print "$numMLST\t"; for (my $i=3; $i <= $#infos; $i++){ print "$infos[$i];"; } } close (MLST); print "\n"; } #close (OUT); unlink glob ('*.VIR.txt'); unlink glob ('*.PLA.txt'); unlink glob ('*.RES.txt'); unlink glob ('*.MLST.txt');