Mercurial > repos > iss > eurl_vtec_wgs_pt

annotate scripts/MultifastaFromBlast.pl @ 1:444b0421bbdc draft

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"planemo upload commit c8533b93fb2816db37887244489cbd6e919fc155"
author iss
date Tue, 22 Mar 2022 08:39:10 +0000
parents c6bab5103a14
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env perl
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2 use strict;
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3 use warnings;
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4 use English;
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5
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6 # Parse arguments
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7 my ($inputs, $output) = @ARGV;
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8 # Run program
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9 unlink $output;
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10 my @infiles = split( /,/, $inputs );
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11 foreach(@infiles) {
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12 transformFileContent($_, $output);
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13 }
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14
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15 # read input file and write multifasta with sequence (forward or reverse complement)
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16 sub transformFileContent {
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17 my ($infile, $outfile) = @_;
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18 open my $if, '<', $infile or die "Cannot open : $infile!";
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19 open my $of, '>>', $outfile or die "Cannot open : $outfile!";
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20 my @lines = <$if>;
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21 close $if;
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22 foreach(@lines) {
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23 my @elems = split( /\t/, $_ );
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24 print $of ">$elems[0]\n";
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25 chomp $elems[2];
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26 if ($elems[1] == 1) {
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27 print $of "$elems[2]\n";
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28 }
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29 else {
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30 my $revcomp = reverseComplement($elems[2]);
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31 print $of "$revcomp\n";
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32 }
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33 }
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34 close $of;
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35 return 0;
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36 }
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37
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38 # calculate reverse complement
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39 sub reverseComplement {
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40 my ($DNA) = @_;
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41 my $revcom = reverse $DNA;
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42 $revcom =~ tr/ACGTacgt/TGCAtgca/;
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43 return $revcom;
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44 }