20251125

99.scripts/trinity_utils/util/support_scripts/revcomp_fasta.pl

@@ -0,0 +1,21 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+local $/ = ">";
+while(<>){
+	chomp;
+	my $lineSepPos = index($_, "\n");
+	my $header = substr($_,0,$lineSepPos);
+	if($header){
+		print(">", $header, "\n");
+		my $sequence = reverse(substr($_,$lineSepPos));
+		# see http://shootout.alioth.debian.org/u32/performance.php?test=revcomp#about
+		# for ambiguity codes and translation
+		$sequence =~ tr/ACGTUMRWSYKVHDBNacgtumrwsykvhdbn\n/TGCAAKYWSRMBDHVNtgcaakywsrmbdhvn/d;
+		for(my $pos = 0; $pos < length($sequence);$pos += 60){
+			print(substr($sequence, $pos, 60),"\n");
+		}
+	}
+}