[Bioperl-l] passing multiple databases to blastall

[Andrew Nunberg]

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..

Andy
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");
>
>
> J
>
>
>
>
> Andrew Nunberg wrote:
>
>> Hi,
>> 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
>>
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>
>
>