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

zhihua li lzhtom at hotmail.com
Thu Feb 1 22:27:39 EST 2007


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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