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

Mark Johnson mjohnson at watson.wustl.edu
Mon Mar 29 11:39:35 EST 2004

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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