fastq_to_fasta

#!/usr/bin/perl

# convert fastq to fastq
#
# reads from stdin writes to stdout
# assume 4-line fastq 
#
# Mark Stenglein, July 11, 2012

use strict;

my $line_count = 0;

while (<>)
{
   $line_count += 1;

   if ($line_count == 1)
   {
      # sanity check on fastq input format
      if (!/^@/)
      {
         die ("error - was expecting 4-line fastq input.\nline = $_\n");
      }
      tr/@/>/;
      print "$_";
   }
   elsif ($line_count == 2)
   {
      print "$_";
   }
   elsif ($line_count == 4)
   {
      $line_count = 0;
   }
}