[Bioperl-l] Bio::DB::GenPept

[Brian Osborne]

Neil,

Perhaps I've misunderstood your question, but this works:

~/programming/perl/examples>perl -e 'use Bio::DB::GenPept; @arr =
qw(131470); $d
b = new Bio::DB::GenPept; $seqio = $db->get_Stream_by_id(\@arr); $seqobj =
$seqi
o->next_seq ; print $seqobj->seq ; '
MVRWFHRDLSGPDAETLLKGRGVPGSFLARPSRKNQGDFSLSVRVDDQVTHIRIQNSGDFYDLYGGEKFATLTELV
EYYT
QQQGILQDRDGTIIHLKYPLNCSDPTSERWYHGHISGGQAESLLQAKGEPWTFLVRESLSQPGDFVLSVLNDQPKA
GPGS
PLRVTHIKVMCEGGRYTVGGSETFDSLTDLVEHFKKTGIEEASGAFVYLRQPYYATRVNAADIENRVLELNKKQES
EDTR
KAGFWEEFESLQKQEVKNLHQRLEGQRPENKSKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYVKNQLLGPDE
NSKT
YIASQGCLDATVNDFWQMAWQENTRVIVMTTREVEKGRNKCVPYWPEVGTQRVYGLYSVTNSREHDTAEYKLRTLQ
ISPL
DNGDLVREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHCSAGIGRTGTIIVIDMLMESISTK
GLDC
DIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEIIQSQKGQESEYGNITYPPAVRSAHAKASRTS
SKHK
EEVYENVHSKSQKEEKVKKQRSADKEKNKGSLKRK

Just as you suggested.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Neil Saunders
Sent: Friday, January 31, 2003 1:34 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Bio::DB::GenPept

I'm having a bit of trouble using Bio::DB::GenPept, specifically the
get_Stream_by_id method.

Something like:  get_Stream_by_id([27904502,23813659])

works fine.  However, I have an array of uids that I would like to use.
The documentation says:

Args    : $ref : a reference to an array of unique identifiers for
                 the desired sequence entries

Does this mean literally a Perl reference, e.g. $ref=\@my_array?

I have tried various arguments (arrays, references, constructing
strings) but am not having much joy.  Would greatly appreciate a code
snippet showing how to use an array of uids.

thanks,
Neil Saunders
--
 School of Biotechnology and Biomolecular Sciences,
 The University of New South Wales,
 Sydney 2052,
 Australia

http://psychro.bioinformatics.unsw.edu.au/neil/index.php
_______________________________________________
Bioperl-l mailing list
Bioperl-l at bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-l