diff pmlst.pl @ 0:cfab64885f66 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pmlst.pl	Mon Sep 06 18:27:45 2021 +0000
@@ -0,0 +1,29 @@
+#!/usr/bin/perl -w
+use strict;
+use warnings;   
+
+my $STpmlst = "";
+
+my $path = $ARGV[0];
+my $seq = $ARGV[1];
+my $scheme = $ARGV[2];
+
+
+open PMLST, "python3 $path/pmlst/pmlst.py -i $seq -s $scheme -p $path/pmlst/pmlst_db/ -mp $path/blastn |";
+while (<PMLST>) {
+     chomp ($_);
+    if ($_ =~ "sequence_type") {
+        #print "ST:$_ \n";
+        my @table = split (/:/,$_);
+        $STpmlst = $table [1];
+        #chomp ($STpmlst); $STpmlst = chop($STpmlst);
+        $STpmlst =~ s/\s+//;
+        $STpmlst = substr($STpmlst,1);
+	my @table2 = split (/'/,$STpmlst);
+	$STpmlst = $table2[0];
+        #print "$STpmlst\n" ;
+    }
+}
+
+#print "Sequence\tSequence Type (pMLST)\n" ;
+print "pMLST for $seq:\t$STpmlst\n" ;