[Bioperl-l] Unable to retrieve genebank file with GI number

Brian Osborne brian_osborne at cognia.com
Mon Sep 27 07:52:24 EDT 2004


If you're using GI numbers you want to do something like this:

my $db = new Bio::DB::GenBank;
my $seqobj = $db->get_Seq_by_id(24585102);

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 Rambabu Gudavalli
Sent: Monday, September 27, 2004 7:04 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] Unable to retrieve genebank file with GI number

Dear Sirs,

        i am trying to connect the genbank  remotely  with GI number   using
the bioperl
in this link, they are telling we can connect genbank remotely using GI
i am retrieving the data using the Accession numbers but not with GI
with GI number,  is not connecting and it is giving warning like this

-------------------- WARNING ---------------------
MSG: acc (gb|24585102) does not exist
Use of uninitialized value in length at /Library/Perl/5.8.1/Bio/Perl.pm
line 271.
Use of uninitialized value in concatenation (.) or string at
/Library/Perl/5.8.1/Bio/Perl.pm line 283.
You have a non object [] passed to write_sequence. It maybe that you
want to use new_sequence to make this string into a sequence object? at
/Library/Perl/5.8.1/Bio/Perl.pm line 283
         Bio::Perl::write_sequence('>x.fasta','fasta','undef') called at
ConnectGenbak1.pl line 14

any help,

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