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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 my $res = 90.00;
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17 my $plas = 90.00;
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18 my $vf = 80.00;
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19
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20 my $percentage = "ident"; # other possibility is "cov"
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21 my $columPerc = 10; # other possibility is 9
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22
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23
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24
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25 #Other parameters
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26 for (my $i = 0; $i <= $#ARGV; $i++) {
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27 if ($ARGV[$i]=~/-percent/i or $ARGV[$i]=~/-perc/i) {
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28 $percentage = $ARGV[$i+1];
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29 }
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30 elsif ($ARGV[$i]=~/-res/i) {
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31 $res = $ARGV[$i+1];
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32 }
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33 elsif ($ARGV[$i]=~/-plas/i) {
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34 $plas = $ARGV[$i+1];
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35 }
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36 elsif ($ARGV[$i]=~/-vf/i) {
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37 $vf = $ARGV[$i+1];
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38 }
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39 }
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40
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41 ##########################################################################################
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42
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43 if ($percentage eq "ident"){
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44 $columPerc = 10;
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45 }
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46 elsif ($percentage eq "cov"){
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47 $columPerc = 9;
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48 }
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49
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50
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51 #open (OUT, ">$output");
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52 print "Sequence\tResistance genes\tPlasmids\tVirulence genes\tST (MLST)\tAlleles (MLST)\n";
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53
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54 foreach my $sequence (@list_seq) {
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55 my $Result_RES = `abricate --db resfinder $sequence > $sequence.RES.txt`; #appel système de la commande abricate avec la BDD ResFinder
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56 my $Result_PLA = `abricate --db plasmidfinder $sequence > $sequence.PLA.txt`; #appel système de la commande abricate avec la BDD PlasmidFinder
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57 my $Result_VIR = `abricate --db vfdb $sequence > $sequence.VIR.txt`;
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58 my $Result_MLST = `mlst $sequence > $sequence.MLST.txt`;
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59
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60 open (RES, "$sequence.RES.txt");
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61 print "$sequence\t";
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62
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63 while (<RES>) {
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64
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65 chomp();
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66 if ($_ !~ m/^#/) {
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67 my @infos = split(/\t/,$_);
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68 my $geneRes = $infos[5]; # resistance gene name (ancienne valeur $infos[4])
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69 my $identity = $infos[$columPerc]; # identity % (ancienne valeur $infos[9])
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70
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71 if ($identity > $res) {
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72 print "$geneRes;";
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73 }
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74 }
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75
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76 }
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77
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78 close (RES);
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79 print "\t";
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80
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81
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82 open (PLA, "$sequence.PLA.txt") or die "could not open $!";
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83
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84 while (<PLA>) {
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85 chomp();
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86 if ($_ !~ m/^#/) {
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87 my @infos = split(/\t/,$_);
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88 my $plasmid = $infos[5]; # plasmid name
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89 my $identity = $infos[$columPerc]; # identity %
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90
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91 if ($identity > $plas) {
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92 print"$plasmid;";
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93 }
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94 }
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95
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96 }
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97 close (PLA);
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98 print "\t";
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99
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100 open (VIR, "$sequence.VIR.txt") or die "could not open $!";
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101
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102 while (<VIR>) {
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103 chomp();
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104
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105 if ($_ !~ m/^#/) {
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106 my @infos = split(/\t/,$_);
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107 my $geneVir = $infos[5]; # virulence gene name
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108 my $identity = $infos[$columPerc]; # identity %
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109
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110 if ($identity > $vf) {
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111 print "$geneVir;";
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112 }
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113 }
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114
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115 }
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116 close (VIR);
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117 print "\t";
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118
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119
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120 open (MLST, "$sequence.MLST.txt") or die "could not open $!";
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121
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122 while (<MLST>) {
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123 chomp();
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124
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125 my @infos = split(/\t/,$_);
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126 my $numMLST = $infos[2];
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127 print "$numMLST\t";
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128
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129 for (my $i=3; $i <= $#infos; $i++){
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130 print "$infos[$i];";
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131 }
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132
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133 }
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134 close (MLST);
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135 print "\n";
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136 }
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137
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138 #close (OUT);
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139
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140 unlink glob ('*.VIR.txt');
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141 unlink glob ('*.PLA.txt');
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142 unlink glob ('*.RES.txt');
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143 unlink glob ('*.MLST.txt');
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144
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