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1 #!/usr/bin/perl -w
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2 use strict;
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3 use warnings;
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4
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5 my $STpmlst = "";
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6
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7 my $path = $ARGV[0];
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8 my $seq = $ARGV[1];
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9 my $scheme = $ARGV[2];
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10
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11
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12 open PMLST, "python3 $path/pmlst/pmlst.py -i $seq -s $scheme -p $path/pmlst/pmlst_db/ -mp $path/blastn |";
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13 while (<PMLST>) {
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14 chomp ($_);
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15 if ($_ =~ "sequence_type") {
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16 #print "ST:$_ \n";
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17 my @table = split (/:/,$_);
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18 $STpmlst = $table [1];
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19 #chomp ($STpmlst); $STpmlst = chop($STpmlst);
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20 $STpmlst =~ s/\s+//;
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21 $STpmlst = substr($STpmlst,1);
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22 my @table2 = split (/'/,$STpmlst);
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23 $STpmlst = $table2[0];
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24 #print "$STpmlst\n" ;
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25 }
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26 }
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27
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28 #print "Sequence\tSequence Type (pMLST)\n" ;
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29 print "pMLST for $seq:\t$STpmlst\n" ;
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