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