[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

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

$ 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

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

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

More information about the Bioperl-l mailing list