added reverse-complement script

fastx-rc.pl

@@ -0,0 +1,74 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+
+## fastx-rc -- reverse complement a sequence
+
+use Getopt::Long qw(:config auto_help pass_through);
+
+my $quiet = 0;
+
+sub rc {
+  my ($seq) = @_;
+  $seq =~ tr/ACGTUYRSWMKDVHBXN-/TGCAARYSWKMHBDVXN-/;
+  # work on masked sequences as well
+  $seq =~ tr/acgtuyrswmkdvhbxn/tgcaaryswkmhbdvxn/;
+  return(scalar(reverse($seq)));
+}
+
+GetOptions("quiet!" => \$quiet) or
+  die("Error in command line arguments");
+
+# unknown commands are treated as identifiers
+my @files = ();
+while(@ARGV){
+  my $arg = shift(@ARGV);
+  if(-f $arg){
+    push(@files, $arg);
+  }
+}
+@ARGV = @files;
+
+my $inQual = 0; # false
+my $seqID = "";
+my $qualID = "";
+my $seq = "";
+my $qual = "";
+while(<>){
+  chomp;
+  chomp;
+  if(!$inQual){
+    if(/^(>|@)((.+?)( .*?\s*)?)$/){
+      my $newSeqID = $2;
+      my $newShortID = $3;
+      if($seqID){
+        if($qual){
+          printf("@%s [RC]\n%s\n+\n%s\n", $seqID, rc($seq), scalar(reverse($qual)));
+        } else {
+          printf(">%s [RC]\n%s\n", $seqID, rc($seq));
+        }
+      }
+      $seq = "";
+      $qual = "";
+      $seqID = $newSeqID;
+    } elsif(/^\+(.*)$/) {
+      $inQual = 1; # true
+      $qualID = $1;
+    } else {
+      $seq .= $_;
+    }
+  } else {
+    $qual .= $_;
+    if(length($qual) >= length($seq)){
+      $inQual = 0; # false
+    }
+  }
+}
+
+if($seqID){
+  if($qual){
+    printf("@%s [rc]\n%s\n+\n%s\n", $seqID, rc($seq), scalar(reverse($qual)));
+  } else {
+    printf(">%s [rc]\n%s\n", $seqID, rc($seq));
+  }
+}