cstrittmatter@0: #!/usr/bin/env perl
cstrittmatter@0: use strict;
cstrittmatter@0: use warnings;
cstrittmatter@0: use English;
cstrittmatter@0: 
cstrittmatter@0: # Parse arguments
cstrittmatter@0: my ($inputs, $output) = @ARGV;
cstrittmatter@0: # Run program
cstrittmatter@0: unlink $output;
cstrittmatter@0: my @infiles = split( /,/, $inputs );
cstrittmatter@0: foreach(@infiles) {
cstrittmatter@0:   transformFileContent($_, $output);
cstrittmatter@0: }
cstrittmatter@0: 
cstrittmatter@0: # read input file and write multifasta with sequence (forward or reverse complement)
cstrittmatter@0: sub transformFileContent {
cstrittmatter@0:   my ($infile, $outfile) = @_;
cstrittmatter@0:   open my $if, '<', $infile or die "Cannot open : $infile!";
cstrittmatter@0:   open my $of, '>>', $outfile or die "Cannot open : $outfile!";
cstrittmatter@0:   my @lines = <$if>;
cstrittmatter@0:   close $if;
cstrittmatter@0:   foreach(@lines) {
cstrittmatter@0:     my @elems = split( /\t/, $_ );
cstrittmatter@0:     print $of ">$elems[0]\n";
cstrittmatter@0:     chomp $elems[2];
cstrittmatter@0:     if ($elems[1] == 1) {
cstrittmatter@0:       print $of "$elems[2]\n";
cstrittmatter@0:     }
cstrittmatter@0:     else {
cstrittmatter@0: 	  my $revcomp = reverseComplement($elems[2]);
cstrittmatter@0:       print $of "$revcomp\n";
cstrittmatter@0:     }
cstrittmatter@0:   }
cstrittmatter@0:   close $of;
cstrittmatter@0:   return 0;
cstrittmatter@0: }
cstrittmatter@0: 
cstrittmatter@0: # calculate reverse complement
cstrittmatter@0: sub reverseComplement {
cstrittmatter@0:   my ($DNA) = @_;
cstrittmatter@0:   my $revcom = reverse $DNA;
cstrittmatter@0:   $revcom =~ tr/ACGTacgt/TGCAtgca/;
cstrittmatter@0:   return $revcom;
cstrittmatter@0: }