[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 10:50:43 EST 2012


Hi Lincoln,

Thanks very much for your suggestions. Not sure how the single quotation 
marks appeared around the $locus variable. But looks like it was only in 
the email. Fortunately did not have quotes around the variable in my 
original code.

Now, when I switch over to 'get_features_by_name()', my script does not run 
to completion.

I want to mention that this snippet of code is part of a larger CGI script 
that interfaces with the SeqFeature backend DB. When I modify the function 
call to $gff_dbh->get_features_by_name($locus), the script just runs 
indefinitely and returns absolutely nothing. I did put in a warn statement 
to see if the correct locus ID is being passed to the function (I am able 
to see the warning message in my apache error log), which seems to be fine. 
But the moment it reaches the function call step, the CGI script freezes up 
and I am unable to do anything. It just ends up as a rogue process owned by 
the 'daemon' user and continues to use up a lot of memory.

I am using the following BioPerl modules in this CGI script:
use Bio::SeqIO;
use Bio::SearchIO;
use Bio::DB::SeqFeature::Store;
use Bio::SeqFeature::Generic;
use Bio::Graphics;
use Bio::Graphics::Feature;

Could any of these be interfering with get_features_by_name()?

Thank you.
Vivek


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