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

Jason Stajich jason at cgt.duhs.duke.edu
Tue Mar 9 21:25:53 EST 2004


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


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