[Bioperl-l] `get_feature_by_name` not working after migrating to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend

Vivek Krishnakumar vivekkrishnakumar at gmail.com
Wed Feb 1 13:15:17 EST 2012


Hi Lincoln,

This exception was NOT generated by the $gff_dbh->get_features_by_name() 
call.

It was later on in the script by the $gff_dbh->segment() call.
And the reason was because I was trying to get the reference seq_id by 
using $locus_obj->refseq, which seems to be deprecated in DB::SeqFeature. 
When I switched to $locus_obj->seq_id, everything worked fine.

Thanks again and sorry for the confusion.
Vivek


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