Memory Usage in SeqIO

kevin richard thornton krthornt@midway.uchicago.edu
Wed, 5 Apr 2000 18:26:00 -0500 (CDT)


I'm not sure if this qualifies as a bug or if its more of a design issue,
but here goes.  I'm dealing with Drosophila genome sequences, which come
in FASTA format of around 20-30 megabases each.  When using input streams
in the standard way (i.e. basically copy-pasting from the documentation),
the RAM usage is 387MB per sequence.  I'm just starting to look at the
code, but if I could get more verbal info on how sequences are handled,
I'd be very grateful (my OO skills are lacking in Perl).

Other than that, 0.6 is a great release, and I've trimmed 100's of lines
of code this week using your interfaces.  Gook work!

--Kevin

_______________________
Kevin Thornton
Committee on Genetics
Long Lab
University of Chicago
k-thornton@uchicago.edu


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