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

Brian Osborne brian_osborne at cognia.com
Mon Mar 29 11:50:35 EST 2004


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?

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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