[Bioperl-l] `get_feature_by_name` not working after migrating to Bio::DB::SeqFeature::Store from a Bio::DB::GFF backend
vivekkrishnakumar at gmail.com
Wed Feb 1 10:50:43 EST 2012
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
Now, when I switch over to 'get_features_by_name()', my script does not run
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:
Could any of these be interfering with get_features_by_name()?
More information about the Bioperl-l