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1 #!/usr/bin/perl
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2
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3 use strict;
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4 use warnings;
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5
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6 #INPUTS_
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7 # my $Result_RES = $ARGV[0];
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8 my $sequences = $ARGV[0];
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9
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10 #OUTPUT_
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11 #my $output = $ARGV[1];
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12
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13 #my @list_seq = split(/,/,$sequences);
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14 my @list_seq = @ARGV;
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15
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16 ##########################################################################################
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17
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18 #open (OUT, ">$output");
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19 print "SEQUENCE\tRESISTANCE GENES\tPLASMIDS\tVIRULENCE GENES\tMLST NUMBER\tGENE(ALLELE)\n";
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20
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21 foreach my $sequence (@list_seq) {
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22 my $Result_RES = `abricate --db resfinder $sequence > $sequence.RES.txt`; #appel système de la commande abricate avec la BDD ResFinder
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23 my $Result_PLA = `abricate --db plasmidfinder $sequence > $sequence.PLA.txt`; #appel système de la commande abricate avec la BDD PlasmidFinder
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24 my $Result_VIR = `abricate --db vfdb $sequence > $sequence.VIR.txt`;
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25 my $Result_MLST = `mlst $sequence > $sequence.MLST.txt`;
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26
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27 open (RES, "$sequence.RES.txt");
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28 print "$sequence\t";
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29
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30 while (<RES>) {
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31
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32 chomp();
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33 if ($_ !~ m/^#/) {
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34 my @infos = split(/\t/,$_);
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35 my $geneRes = $infos[5]; # resistance gene name (ancienne valeur $infos[4])
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36 my $identity = $infos[10]; # identity % (ancienne valeur $infos[9])
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37
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38 if ($identity > 90.000) {
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39 print "$geneRes;";
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40 }
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41 }
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42
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43 }
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44
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45 close (RES);
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46 print "\t";
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47
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48
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49 open (PLA, "$sequence.PLA.txt") or die "could not open $!";
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50
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51 while (<PLA>) {
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52 chomp();
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53 if ($_ !~ m/^#/) {
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54 my @infos = split(/\t/,$_);
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55 my $plasmid = $infos[5]; # plasmid name
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56 my $identity = $infos[10]; # identity %
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57
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58 if ($identity > 90.000) {
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59 print"$plasmid;";
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60 }
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61 }
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62
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63 }
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64 close (PLA);
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65 print "\t";
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66
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67 open (VIR, "$sequence.VIR.txt") or die "could not open $!";
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68
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69 while (<VIR>) {
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70 chomp();
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71
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72 if ($_ !~ m/^#/) {
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73 my @infos = split(/\t/,$_);
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74 my $geneVir = $infos[5]; # virulence gene name
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75 my $identity = $infos[10]; # identity %
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76
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77 if ($identity > 80.000) {
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78 print "$geneVir;";
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79 }
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80 }
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81
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82 }
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83 close (VIR);
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84 print "\t";
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85
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86
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87 open (MLST, "$sequence.MLST.txt") or die "could not open $!";
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88
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89 while (<MLST>) {
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90 chomp();
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91
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92 my @infos = split(/\t/,$_);
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93 my $numMLST = $infos[2];
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94 print "$numMLST\t";
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95
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96 for (my $i=3; $i <= $#infos; $i++){
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97 print "$infos[$i];";
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98 }
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99
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100 }
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101 close (MLST);
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102 print "\n";
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103 }
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104
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105 #close (OUT);
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106
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107 unlink glob ('*.VIR.txt');
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108 unlink glob ('*.PLA.txt');
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109 unlink glob ('*.RES.txt');
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110 unlink glob ('*.MLST.txt');
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111
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