[Bioperl-l] blast database paths and Blast.pm parsing

[Kim Brugger]

Hi

I am trying to blast against several databases, using the
Bio::Tools::Run::StandAloneBlast module and have sat BLASTDATADIR
according to the documentation, but when I run the query I get this error :

<snip>
[blastall] WARNING: Could not find index files for database ../databases/aero.n
[blastall] WARNING: Could not find index files for database mthe.n
[blastall] WARNING: Could not find index files for database stok.n
[blastall] WARNING:  Could not find index files for database ../databases/aero.n
[blastall] WARNING:  Could not find index files for database mthe.n
[blastall] WARNING:  Could not find index files for database stok.n
<snip>

it seems like the BLASTDATADIR is only prefixed the first database. I am
currently using bioperl-0.7.2. If no one has fixed this where do I send my
patch for this ?

And while on the matter of blast, it seems that the Bio::Tool::Blast
module does not include all the used databases if the database name string
spans more than one line.

Best

Kim Brugger

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Kim Brügger             (brugger@mermaid.molbio.ku.dk)
Department of Molecular Biology Copenhagen University
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