[Bioperl-l] Bio::DB::GenBank problem?

[wxu]

Thanks, James, I reinstalled v1.2.2, and it works fine now.

Wayne
--


Wayne Xu
Computational Genomics Specialist  www.msi.umn.edu/user_support/compgen

Supercomputing Institute
550 Walter Library
117 Pleasant Street SE
University of Minnesota
Minneapolis, Minnesota 55455
email: wxu at msi.umn.edu        help email:  help at msi.umn.edu
phone: 612-624-1447           help phone:  612-626-0802
fax:   612-624-8861


-----Original Message-----
From: James Wasmuth [mailto:james.wasmuth at ed.ac.uk]
Sent: Tuesday, September 09, 2003 4:04 AM
To: wxu
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Bio::DB::GenBank problem?


Hi Wayne,

I identified this a few months back, and from what I can remember Heikki
fixed it and is now in the CVS.

james

wxu wrote:

>Hello,
>I wrote a simple bioperl program to retrieve genBank sequences by genBank
>accession numbers using $gb->get_Stream_by_id function.
>But it seems to me it can only work on GI number, not work on accession
>numbers. I use $gb->get_Stream_by_acc, the result is the same. In my
>following code, it only give me 2981014 sequences. I search NCBI web
>manually, all "J00522","AF303112","2981014","BG065024","BG065143" work.
>And I tried $gb->get_Seq_by_acc("J00522"); It complains "No such acc
error".
>
>What is the problem?
>Your help would be greatly appreciated.
>
>Wayne
>--
>
>----------------------------------------------------------
>#!/usr/local/bin/perl
>use lib "/usr/local/bioperl/bioperl-1.2";
>use lib qw(/home/wxu/bioperl);
>
>use Bio::Perl;
>use Bio::DB::GenBank;
>use Bio::SeqIO;
>my $gb = new Bio::DB::GenBank();
>
>my $seqio =
>$gb->get_Stream_by_id(["J00522","AF303112","2981014","BG065024","BG065143"]
)
>;
>
>while( my $seq =  $seqio->next_seq ) {
>    #print "seq length is ", $seq->length,"\n";
>    write_sequence('>>outputfile', 'fasta', $seq)
>  }
>---------------------------------------------------------------------------
-
>--
>Wayne Xu
>Computational Genomics Specialist  www.msi.umn.edu/user_support/compgen
>
>Supercomputing Institute
>550 Walter Library
>117 Pleasant Street SE
>University of Minnesota
>Minneapolis, Minnesota 55455
>email: wxu at msi.umn.edu        help email:  help at msi.umn.edu
>phone: 612-624-1447           help phone:  612-626-0802
>fax:   612-624-8861
>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>

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