[Bioperl-l] Bio::Index::Fasta, Bio::Index::Qual

Mark Johnson mjohnson at watson.wustl.edu
Mon Mar 29 15:45:16 EST 2004

Done.  Thanks!

> Mark,
> If there are no objections you can submit this as a "bug" to our Bugzilla
> with the attached file - I'd be happy to add it to the distribution for
> you.
> Brian O.
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Mark Johnson
> Sent: Monday, March 29, 2004 11:40 AM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] Bio::Index::Fasta, Bio::Index::Qual
> Bio::Index::Fasta is great, but there is no corresponding
> Bio::Index::Qual...I created one via subsitution various permutations of
> 'qual' for 'fasta' on Bio::Index::Fasta.
> Unless I'm the only person that thinks Bio::Index::Qual might be useful,
> is there a chance of getting such a thing into the next release?
> Motivation:
> I maintain a piece of a makeshift submission pipeline for sending BAC end
> reads to the NCBI trace archive (http://www.ncbi.nlm.nih.gov/Traces).  I
> process files containing nucleotide sequence and quality values...the
> nucleotide sequence being in a seperate file from the quality values.  The
> access pattern is random with respect to the ordering of the sequences
> within the individual files.  So Bio::Index::Fasta is very handy, as is my
> cobbled together Bio::Index::Qual.  Which works fine...I just don't like
> maintaining a seperate local module...
> Thoughts, suggestions, comments, rotten fruit?
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