[Bioperl-l] does BLAST parsing working in (forthcoming) 0.7 on

Mike Reith michael.reith@nrc.ca
Fri, 23 Feb 2001 17:18:40 -0400

Jonathan Epstein wrote:
> ... it doesn't work under 0.6, and this has been a showstopper for my

In my hands, the current version of Blast.pm in bioperl-live seems to
work pretty well on Win98, at least for parsing Blast reports.  A few
caveats - blast.t will undoubtedly fail, mostly due to attempts at
compressing and uncompressing files (tests 25 - 29 I think).  It also
still uses `ls -lga` to get the file date in Bio::Root::Utilities and
thus will flash a "Bad command or filename" message during test 1.  I
haven't thoroughly tested all the functionality of the module (eg.
running Blasts, parsing HTML formatted Blast reports, etc.) but for
parsing of plain BLAST reports, it seems to do the trick.

Mike Reith

Michael Reith
Senior Research Officer
NRC Institute for Marine Biosciences
1411 Oxford St.
Halifax, Nova Scotia  B3H 3Z1

email:    michael.reith@nrc.ca
phone:    (902) 426-8276