[Bioperl-l] passing multiple databases to blastall
anunberg at oriongenomics.com
Wed Jun 4 11:39:46 EDT 2003
Yes this does work but only if the
$Bio::Tools::StandAloneBlast::DATADIR variable is undefined;
otherwise what happens is that the string is prepended with the path.
A possible fix is to actually look at what is being passed to see if
its multiple db or just a single one..
On Saturday, May 31, 2003, at 11:39 AM, James Wasmuth wrote:
> Place the databases into a variable. The below works for me..
> my $est_db = '"/dba/BMC.fsa /dba/ALC.fsa /dba/HCC.fsa"';
> my @params_est = ('d' => "$est_db" , 'program' => "$est_blast_meth" ,
> 'e' => "$e" , 'F' => "$mask_status" , '_READMETHOD' => "Blast" ,
> 'outfile' => "$dir/est.bls");
> Andrew Nunberg wrote:
>> in blast you can pass multiple databases to blastall (-d "db1 db2
>> db3"), the quotes are required.
>> In bioperl-1.2 if i pass the option to the blast factory,
>> $factory->d('"db1 db2"');
>> the result is not the expected behavior. The first db is seen but
>> not the second.
>> any ideas?
>> Andy Nunberg
>> Orion Genomics
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
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