[Bioperl-l] Newbie Question about Bio::DB::GenBank

[nkuipers]

Are you root on your linux machine?  If not you'll need to include a

use lib "/directory/to/bioperl/modules";

statement.  Are there any additional warnings thrown when you

use warnings;

and run

perl -c yourscript

?

Nathanael



>===== Original Message From Joseph Urban <urbanj2 at rpi.edu> =====
>Hi:
>
>I have installed BioPerl 1.2 on my linux machine, but I am having
>problems retrieving data from GenBank.  I also installed the bundle.
>During the installation of the bundle, I received a few warning about
>not having the MD5 security  package installed.  Might this be the
>source of my problem?
>
>Here is the short code that I am trying to execute:
>
>
>..
>
>use Bio::Perl;
>use Bio::DB::GenBank;
>
>my ($seqID, $protID, $gb, $seq1, $seq2);
>
>$seqID=$ARGV[0];
>$protID=$ARGV[1];
>
>$gb = new Bio::DB::GenBank();
>
>$seq1 = $gb->get_Seq_by_id($seqID);
>
>
>
>The last 2 lines were copied from the BioPerl tutorial.
>
>The last line is the one that is the source of the error.
>If this line is commented out, the program runs, which confuses me
>because I still create a Bio::DB::GenBank object.
>
>The error message is as follows:
>
>Can't locate object method "get_Seq_by_id" via package
>"Bio::DB::GenBank" (perhaps you forgot to load "Bio::DB::GenBank"?) at
>./genseq.pl line 21.
>
>I find the method get_Seq_by_id in the Bio:DB:GenBank man page...
>
>
>Any input on how to resolve this issue is greatly appreciated.
>
>Cheers,
>Joe
>
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