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comparison pmlst.pl @ 0:cfab64885f66 draft default tip

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author dcouvin
date Mon, 06 Sep 2021 18:27:45 +0000
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1 #!/usr/bin/perl -w
2 use strict;
3 use warnings;
4
5 my $STpmlst = "";
6
7 my $path = $ARGV[0];
8 my $seq = $ARGV[1];
9 my $scheme = $ARGV[2];
10
11
12 open PMLST, "python3 $path/pmlst/pmlst.py -i $seq -s $scheme -p $path/pmlst/pmlst_db/ -mp $path/blastn |";
13 while (<PMLST>) {
14 chomp ($_);
15 if ($_ =~ "sequence_type") {
16 #print "ST:$_ \n";
17 my @table = split (/:/,$_);
18 $STpmlst = $table [1];
19 #chomp ($STpmlst); $STpmlst = chop($STpmlst);
20 $STpmlst =~ s/\s+//;
21 $STpmlst = substr($STpmlst,1);
22 my @table2 = split (/'/,$STpmlst);
23 $STpmlst = $table2[0];
24 #print "$STpmlst\n" ;
25 }
26 }
27
28 #print "Sequence\tSequence Type (pMLST)\n" ;
29 print "pMLST for $seq:\t$STpmlst\n" ;