[Bioperl-l] [bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy?

John Anderson genehack at genehack.org
Sun Jul 25 14:06:55 EDT 2010

(This is in reference to:


; sorry I'm not responding to the original message but I wasn't on the list at that point.)

There are really two issues being reported here. First, bp_seqfeature_gff3.PLS throws the following error when used with Bio::SeqFeature::Store::DBI::SQLite:

> Can't locate object method "gff3_string" via package "Bio::SeqFeature::Generic" at /Users/jhannah/src/bioperl-live/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS line 58.

Second, when called on a database that's been built with '$db->no_blobs(1)', the output doesn't actually include any features.

I've got a fix for the first bug in <http://github.com/genehack/bioperl-live/tree/topic/bug-3120>. (I've submitted a pull request for that branch to the 'bioperl' user.) Basically, when looping over the feature objects in bp_seqfeature_gff3.PLS, we introspect each one to find out if it supports the gff3_string() or gff_string() methods, and either call the appropriate one or throw an exception.

(I considered just calling gff_string() instead of doing the introspection, since (a) that's the interface documented in SeqFeatureI and (b) SeqFeature::Lite, which is the only thing that currently implements gff3_string() _also_ implements gff_string(), which recalls gff3_string() when appropriate, but in the end decided that this way preserves the original intent of the script as much as possible...)

I'm working on something that may be a fix for the second issue as well, but thought I'd throw this first bit out for comments, being as this is the first change I've contributed back to the project. 


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