[Bioperl-l] Merging separate sequence and quality files to FASTQ ?

[Peter]

On Thu, Dec 3, 2009 at 2:39 PM, Chris Fields <cjfields at illinois.edu> wrote:
> Okay I will try to look into it today (it should be an easy fix).  There are two issues, correct?
>
> 1) extra blank line.

Which seems to be a bug in BioPerl SeqIO itself.

> 2) missing description

This is just a trivial bug/omission in the wiki example,
http://www.bioperl.org/wiki/Merging_separate_sequence_and_quality_files_to_FASTQ

You just need to replace this:

  my $bsq_obj =
    Bio::Seq::Quality->
	new( -id   => $seq_obj->id,
	     -seq  => $seq_obj->seq,
	     -qual => $qual_obj->qual,
	   );

With:

  my $bsq_obj =
    Bio::Seq::Quality->
	new( -id   => $seq_obj->id,
	     -description => $seq_obj->description,
             -seq  => $seq_obj->seq,
	     -qual => $qual_obj->qual,
	   );

Look - I seem to be learning Perl by osmosis ;)

Peter