[Bioperl-l] passing multiple databases to blastall

Paul Boutros pcboutro at engmail.uwaterloo.ca
Wed Jun 4 14:26:49 EDT 2003

Sorry to see this so late: I'm only skimming the list these days.  I submitted 
this as a bug a while back with a possible patch to fix the issue.  I have it 
working on my machine with 1.2.1, but I don't know how much things have changed 
in CVS.


Hope this helps,

Message: 6
Date: Wed, 4 Jun 2003 10:39:46 -0500
From: Andrew Nunberg <anunberg at oriongenomics.com>
Subject: Re: [Bioperl-l] passing multiple databases to blastall
To: James Wasmuth <james.wasmuth at ed.ac.uk>
Cc: bioperl <bioperl-l at bioperl.org>
Message-ID: <C4C2298A-96A2-11D7-9514-000A95A001EE at oriongenomics.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed

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");
> 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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