[Bioperl-l] BioPerl and undefined value

[Scott Cain]

next unless $ID;


On Mon, Jun 13, 2011 at 5:40 PM, Flora Fan <fanx0038 at umn.edu> wrote:
> Hi,
> I am trying to retrieve UTR for a list of RefSeq IDs using get_sequence.
> However, because some of my identifiers were removed from the most current
> DB, BioPerl stopped when it first encounters an undefined ID , and gave the
> following error message:
> ------------- EXCEPTION  -------------
> MSG: acc does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /project/ccbioinf/Software/Ensembl/ensembl_55/bioperl-live/Bio/DB/WebDBSeqI.
> pm:177
> STACK Bio::DB::GenBank::get_Seq_by_acc
> /project/ccbioinf/Software/Ensembl/ensembl_55/bioperl-live/Bio/DB/GenBank.pm
> :216
> STACK Bio::Perl::get_sequence
> /project/ccbioinf/Software/Ensembl/ensembl_55/bioperl-live/Bio/Perl.pm:510
> STACK main::BEGIN test_retrieve_UTR.pl:11
> STACK (eval) test_retrieve_UTR.pl:11
> STACK toplevel test_retrieve_UTR.pl:11
>
> Does anybody know how to let the script move on to the next ID, and skip
> those undefined values? Œif (defined get_sequence('Genbank',$ID)) {}¹
> doesn¹t work....
>
> Thank you very much.
> -Flora
>
> --
> Flora Danhua Fan, Ph.D
> Biostatistics and Bioinformatics
> Masonic Cancer Center, University of Minnesota
> 425 Delaware St SE MMC 806, Minneapolis, MN 55455
> Office: 2-152 Moos Tower
> Phone: 612-625-3648
> http://www.cancer.umn.edu/research/cores/biostats/bioinformatics.html
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research