[Bioperl-l] Bio::DB::Fasta

[Mark A. Jensen]

I seem to be able to do
$db = Bio::DB::Fasta->new("$tmp/test.faa");
without a problem- something in the mixing of named and unnamed parameters?
----- Original Message ----- 
From: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
To: "'Mark A. Jensen'" <maj at fortinbras.us>; "'bioperl-l'" 
<bioperl-l at bioperl.org>
Sent: Tuesday, November 24, 2009 5:21 PM
Subject: RE: [Bioperl-l] Bio::DB::Fasta


That's what I ended up doing.
Also, there's no "obvious" way to index a single file so I ended putting the 
filename in the glob parameter.

my $db = Bio::DB::Fasta->new( "$tmp", -glob => "test.faa", -reindex => 1 );

--Russell


> -----Original Message-----
> From: Mark A. Jensen [mailto:maj at fortinbras.us]
> Sent: Wednesday, 25 November 2009 11:19 a.m.
> To: Smithies, Russell; 'bioperl-l'
> Subject: Re: [Bioperl-l] Bio::DB::Fasta
>
> The code (method index_dir() ) seems to expect all the fasta files to be
> contained in that directory. Looks hairy; what about creating symlinks to
> your
> fasta files in a /tmp subdir and calling new() with that subdir?
> ----- Original Message -----
> From: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
> To: "'bioperl-l'" <bioperl-l at bioperl.org>
> Sent: Tuesday, November 24, 2009 5:04 PM
> Subject: [Bioperl-l] Bio::DB::Fasta
>
>
> > Is there any way to pass a filename to Bio::DB::Fasta for the location
> of
> > where to write the directory.index?
> > It's writing in the same dir as the fasta but I'd rather have it write
> in /tmp
> > as it's part of a web app.
> >
> > Thanx,
> >
> > Russell
> >
> >
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