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comparison getmlst.pl @ 0:c2e910327131 draft default tip

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planemo upload commit 132092ff7fe1c4810d1221054419389180b81657
author nml
date Fri, 17 Nov 2017 11:49:10 -0500
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-1:000000000000 0:c2e910327131
1 #!/usr/bin/env perl
2
3 use strict;
4 use warnings;
5 use Cwd;
6 use File::Copy;
7
8 my ($mlst_db, $mlst_defs, $species) = @ARGV;
9
10 $species =~ s/__pd__/#/ig;
11
12 my $command = "getmlst.py --species '$species'";
13
14 my $rv = system($command);
15
16 if ($rv == 0)
17 {
18 #need to find output files in the dir
19 my $cur_dir = getcwd();
20
21 foreach my $file (<$cur_dir/*>)
22 {
23 if ($file =~ /\.fasta$/)
24 {
25 move($file, $mlst_db);
26 }
27 elsif ($file =~/\.txt$/)
28 {
29 move($file, $mlst_defs);
30 }
31 }
32 }
33 $rv = $rv >> 8;
34 exit $rv;