[Bioperl-l] [patch] getGenBank.pl

Chris Fields cjfields at uiuc.edu
Fri Sep 14 12:36:56 EDT 2007


Done.  Thanks for the heads up!

chris

On Sep 14, 2007, at 9:27 AM, Jay Hannah wrote:

> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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