[Bioperl-l] Bio::index::Fasta- where's the indexed file?

Jason Stajich jason at bioperl.org
Fri Feb 2 01:24:44 EST 2007


I don't think BIOPERL_INDEX does anything in the module so that  
documentation is not quite right.  the env variable is used in the  
scripts/index/bp_index and bp_fetch scripts so maybe a cut+paste job  
went bad somewhere.

you need to specify the full path you want with -filename - you can  
just prepen the BIOPERL_INDEX to the filename like.
-filename => $ENV{BIOPERL_INDEX}."/$index"

-jason
On Feb 1, 2007, at 7:27 PM, zhihua li wrote:

> Sorry guys, the former empty mail was sent out by mistake.
>
> I'm using Bio::index::Fasta to index a file containing lots of  
> sequences in fasta format. All is fine except one thing.
>
> According to the bioperl tutorial and the documents, the following  
> code will make a indexed file:
>
> my $inx = Bio::Index::Fasta->new(-filename => "test.fasta.idx",
>                                     -write_flag => 1);
>    $inx->make_index("test.fasta");
>
> And in another script I can access the indexed file by sayinig
>
> $ENV{BIOPERL_INDEX} = "."; # find index in current directory
> my $inx = Bio::Index::Fasta->new(-filename => "test.fasta.idx");
> my $seq=$inx->fetch("ent1001");        #fetch the sequence named  
> ent1001
>
> However, after running the first script, I cannot find a new file  
> test.fasta.idx in my current directory. And not surprisingly, when  
> I ran the second script, perl told me it couldn't find  
> "test.fasta.idx".
>
> What's going on here?
>
> Thanks a lot!
>
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--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html
http://fungalgenomes.org/




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