Mercurial > repos > cstrittmatter > test_galtrakr_eurl_vtec_wgs_pt_23

comparison scripts/MultifastaFromBlast.pl @ 0:8be2feb96994

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"planemo upload commit cb65588391944306ff3cb32a23e1c28f65122014"
author cstrittmatter
date Fri, 11 Mar 2022 15:50:35 -0500
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-1:000000000000 0:8be2feb96994
1 #!/usr/bin/env perl
2 use strict;
3 use warnings;
4 use English;
5
6 # Parse arguments
7 my ($inputs, $output) = @ARGV;
8 # Run program
9 unlink $output;
10 my @infiles = split( /,/, $inputs );
11 foreach(@infiles) {
12 transformFileContent($_, $output);
13 }
14
15 # read input file and write multifasta with sequence (forward or reverse complement)
16 sub transformFileContent {
17 my ($infile, $outfile) = @_;
18 open my $if, '<', $infile or die "Cannot open : $infile!";
19 open my $of, '>>', $outfile or die "Cannot open : $outfile!";
20 my @lines = <$if>;
21 close $if;
22 foreach(@lines) {
23 my @elems = split( /\t/, $_ );
24 print $of ">$elems[0]\n";
25 chomp $elems[2];
26 if ($elems[1] == 1) {
27 print $of "$elems[2]\n";
28 }
29 else {
30 my $revcomp = reverseComplement($elems[2]);
31 print $of "$revcomp\n";
32 }
33 }
34 close $of;
35 return 0;
36 }
37
38 # calculate reverse complement
39 sub reverseComplement {
40 my ($DNA) = @_;
41 my $revcom = reverse $DNA;
42 $revcom =~ tr/ACGTacgt/TGCAtgca/;
43 return $revcom;
44 }