[Bioperl-l] Bio::Index sequence fetching

Brian Osborne brian_osborne at cognia.com
Wed Aug 18 10:16:23 EDT 2004


You need to use the "net::" suffix, the default is local, not remote.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Sucheta Tripathy
Sent: Tuesday, August 10, 2004 8:15 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Bio::Index sequence fetching

I am sorry for posting it again.. I did it yesterday without a subject line.

I am trying to retrieve records from a genbank index file that I had
created using bp_index.pl. I have set the environment variables as

While fetching records I use the following syntax:

bp_fetch.pl -fmt genbank genbank:50355994 where 50355994 is the GI number
of one of the sequences.

But I don't get any results.

It says sequence 50355994 in database genbank not present.

Can anyone please comment where I may be going wrong.



Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
Fax:  (540) 231-2606
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