Mercurial > repos > iss > eurl_vtec_wgs_pt
annotate scripts/MultifastaFromBlast.pl @ 6:20ff3dca457f draft default tip
planemo upload commit 6857c749c21f580c828aba3543e294b69d32b662
author | iss |
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date | Mon, 23 Oct 2023 11:45:36 +0000 |
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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 } |