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

Peter biopython at maubp.freeserve.co.uk
Thu Dec 3 09:20:32 EST 2009

On Thu, Dec 3, 2009 at 1:47 PM, Chris Fields <cjfields at illinois.edu> wrote:
> FASTQ parsing had undergone a major revision prior to
> 1.6.1 (the latest release in CPAN).  Basically, it now parses
> all three FASTQ variants.  However, Peter indicates there
> may still be a problem, and it's likely he's running 1.6.1.
> Peter can you confirm that?

I had BioPerl from SVN circa 1.6.1 (not sure if this was before
or after the release of 1.6.1 now):

$ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
$ perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION,"\n"'

If the tuples mean anything to you:

$ perl -MBio::Root::Version -e 'printf "%vd\n", $Bio::Root::Version::VERSION'
$ perl -MBio::SeqIO -e 'printf "%vd\n", $Bio::SeqIO::VERSION'

I just updated to revision 16435, and retested. I get the same
BioPerl version numbers, and the same extra blank line in the
sequence FASTQ output as Dan reported.


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