[Bioperl-l] Merging separate sequence and quality files to FASTQ ?
Peter
biopython at maubp.freeserve.co.uk
Thu Dec 3 14:56:39 UTC 2009
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
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