[Bioperl-l] BioPerl and undefined value

Flora Fan fanx0038 at umn.edu
Mon Jun 13 21:40:36 UTC 2011


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







More information about the Bioperl-l mailing list