[Bioperl-l] Bio::index::Fasta- where's the indexed file?
zhihua li
lzhtom at hotmail.com
Fri Feb 2 03:27:39 UTC 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!
_________________________________________________________________
与联机的朋友进行交流,请使用 MSN Messenger: http://messenger.msn.com/cn
More information about the Bioperl-l
mailing list