fasta_qual_to_fasta.pl

#!/usr/bin/perl -w
 
use strict;
 
use Bio::SeqIO;
use Bio::Seq::Quality;
 
use Getopt::Long;
 
die "pass a fasta and a fasta-quality file\n"
    unless @ARGV;
 
 
my ($seq_infile,$qual_infile)
    = (scalar @ARGV == 1) ?($ARGV[0], "$ARGV[0].qual") : @ARGV;
 
## Create input objects for both a seq (fasta) and qual file
 
my $in_seq_obj =
    Bio::SeqIO->new( -file   => $seq_infile,
		        -format => 'fasta',
    );
 
my $in_qual_obj =
    Bio::SeqIO->new( -file   => $qual_infile,
		        -format => 'qual',
    );
 
my $out_fastq_obj =
    Bio::SeqIO->new( -format => 'fastq'
    );
 
while (1){
  ## create objects for both a seq and its associated qual
    my $seq_obj  = $in_seq_obj->next_seq || last;
    my $qual_obj = $in_qual_obj->next_seq;
 
  die "foo!\n"
    unless
      $seq_obj->id eq
      $qual_obj->id;
 
  ## Here we use seq and qual object methods feed info for new BSQ
  ## object.
  my $bsq_obj =
      Bio::Seq::Quality->
      new( -id   => $seq_obj->id,
	        -seq  => $seq_obj->seq,
	        -qual => $qual_obj->qual,
      );
 
  ## and print it out.
    $out_fastq_obj->write_fastq($bsq_obj);
}