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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
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1 #!/usr/bin/env perl
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2 ## A wrapper script to collect patho_typing.py output
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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 English;
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7 use File::Copy;
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8 use File::Basename;
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9
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10 # Parse arguments
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11 my ($python) = @ARGV;
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12
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13 # Run program
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14 runPathoTyping();
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15 collectOutput();
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16 exit 0;
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17
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18 # Run patho_typing
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19 sub runPathoTyping {
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20 my $abs_path = Cwd::abs_path($PROGRAM_NAME);
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21 my $scriptdir = dirname($abs_path);
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22 my $rematchdir = "$scriptdir/ReMatCh";
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23 my $newpath = "PATH=$ENV{PATH}:$rematchdir";
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24 `$newpath; $python`;
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25 return 0;
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26 }
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27
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28 sub collectOutput{
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29 my $patho_type = "";
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30 open(my $fh, '<', 'output_dir/rematch/rematchModule_report.txt') || die "Could not open file 'output_dir/rematch/rematchModule_report.txt' $!";
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31 my @rematch_lines = <$fh>;
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32 close($fh);
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33 my @rematch_table = "";
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34 my @rematch_total_table = "";
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35 my $highest_coverage = 0;
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36 foreach(@rematch_lines) {
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37 if ($_ =~ m/\t/) { # Only table lines
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38 my @elems = split('\t', $_);
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39 if ($_ =~ m/#/) { # First line
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40 s/_/ /g for @elems;
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41 push(@rematch_table,join("\t", @elems[0,1,2,5]));
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42 push(@rematch_total_table,join("\t", @elems[0,1,2,5]));
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43 }
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44 else {
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45 push(@rematch_total_table,join("\t", @elems[0,1,2,5]));
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46 if ($elems[1] > 90.0) { # Only genes with over 90% coverage in report table
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47 push(@rematch_table,join("\t", @elems[0,1,2,5]));
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48 }
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49 }
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50 }
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51 }
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52 open($fh, '>', 'pathotyper_rep_tab') || die "Could not open file 'pathotyper_rep_tab' $!";
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53 print $fh @rematch_table;
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54 close($fh);
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55 open($fh, '>', 'pathotyper_rep_tot_tab') || die "Could not open file 'pathotyper_rep_tot_tab' $!";
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56 print $fh @rematch_total_table;
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57 close($fh);
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58
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59 return 0;
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60 }