Bioperl-guts: New Blast module
Thu, 11 Mar 1999 05:50:53 -0800 (PST)
I just committed some major updates to my Bio::Tools::Blast
modules (primarily Blast.pm). What's new is the basic parsing strategy
which should solve the memory munching behavior that has plagued it in
There's also a new example script, parse_blast.pl, that replaces
parse.pl and parse_stream.pl.
It still needs more testing before it's at production quality. For
example, I haven't actually verified memory usage when parsing streams
with lots of reports of various sizes. If you can start banging on it
and report any problems, that would be great. I'm curious to see if it
behaves differently under 5.004 and 5.005 (memory-wise, that is).
There are some other changes in the distribution so cvs update at the
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