diff scripts/MultifastaFromBlast.pl @ 0:c6bab5103a14 draft

"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/MultifastaFromBlast.pl	Mon Mar 21 15:23:09 2022 +0000
@@ -0,0 +1,44 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use English;
+
+# Parse arguments
+my ($inputs, $output) = @ARGV;
+# Run program
+unlink $output;
+my @infiles = split( /,/, $inputs );
+foreach(@infiles) {
+  transformFileContent($_, $output);
+}
+
+# read input file and write multifasta with sequence (forward or reverse complement)
+sub transformFileContent {
+  my ($infile, $outfile) = @_;
+  open my $if, '<', $infile or die "Cannot open : $infile!";
+  open my $of, '>>', $outfile or die "Cannot open : $outfile!";
+  my @lines = <$if>;
+  close $if;
+  foreach(@lines) {
+    my @elems = split( /\t/, $_ );
+    print $of ">$elems[0]\n";
+    chomp $elems[2];
+    if ($elems[1] == 1) {
+      print $of "$elems[2]\n";
+    }
+    else {
+	  my $revcomp = reverseComplement($elems[2]);
+      print $of "$revcomp\n";
+    }
+  }
+  close $of;
+  return 0;
+}
+
+# calculate reverse complement
+sub reverseComplement {
+  my ($DNA) = @_;
+  my $revcom = reverse $DNA;
+  $revcom =~ tr/ACGTacgt/TGCAtgca/;
+  return $revcom;
+}