[Bioperl-l] OSX, NCBI blast 2.2.8, blast parsers

[Jason Stajich]

Strict BLAST parsers are going to fall over on ncbi blast 2.2.8 produced
reports.

You can see what happens on you system by doing this is the bioperl
directory:

$ blastpgp -d  $BLASTDB/swissprot  -i t/data/amino.fa -j 2 | grep "total letters"
  U79 sequences; E27 total letters
$ blastall -p blastn -i t/data/test.txt -d $BLASTDB/ecoli.nt | grep "total letters"
 400 sequences; N39 total letters

The parser expects numbers in those spots not a combination.  This is
using
ftp://ftp.ncbi.nih.gov/blast/executables/blast-2.2.8-powerpc-macosx.tar.gz

This does not appear on linux ia32 distribution so I assume it is an OSX
specific issue or compilation related issue.

This was found per bug #1598
http://bugzilla.open-bio.org/show_bug.cgi?id=1598

-jason
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu