[Bioperl-l] [patch] getGenBank.pl

Jay Hannah jay at jays.net
Fri Sep 14 10:27:38 EDT 2007


http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/ 
examples/db/getGenBank.pl

Using this:
my $seqio = $gb->get_Stream_by_batch([ qw( 124430577 )]);

Throws this warning:
$ ./fetch.pl > 124430577.gbk
get_Stream_by_batch() is deprecated; use get_Stream_by_id() instead
STACK Bio::DB::NCBIHelper::__ANON__ /usr/lib/perl5/Bio/DB/ 
NCBIHelper.pm:261
STACK toplevel ./fetch.pl:17


Can someone with commit access please change getGenBank.pl?

24,25c24,25
< # if you want to get a bunch of sequences use the batch method
< my $seqio = $gb->get_Stream_by_batch([ qw(J00522 AF303112 2981014)]);
---
 > # feel free to pull multiple sequences
 > my $seqio = $gb->get_Stream_by_id([ qw(J00522 AF303112 2981014)]);


The tweaked version works fine for me and the warning goes away.

Thanks,

Jay Hannah
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah




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