[Bioperl-l] bp_seqfeature_load / Bio::DB::SeqFeature::Store::GFF3Loader problems augmenting Flybase annotation
MEC at stowers-institute.org
Tue Dec 19 14:57:48 EST 2006
Lincoln and fellow Bio::DB::SeqFeature travelers,
I find that using bp_seqfeature_load.PLS to load subfeatures of genes
already loaded using bp_seqfeature_load.PLS fails with
------------- EXCEPTION -------------
MSG: FBgn0017545 doesn't have a primary id
Where FBgn0017545 is the ID of a gene previously loaded.
I am unsure how to remedy my situation and welcome any advise on correct
or improved approach to my problem.
Here's some detail if it helps. I am developing a pipeline to design a
microarray probes capable of distinguishing among splice variants in
drosophila (using latest Flybase dmel_r5.1 annotation). So I
1) load a filtered selection of Flybase annotation using
bp_seqfeature_load. (for testing purposes, I am using a single gene's
worth of annotation, FBgn0017545.gff, attached). This is done as
> bp_seqfeature_load.PLS --create FBgn0017545.gff
2) analyze all the genes in the database, and create GFF3 output each
feature of which has a 'Parent' that is a previously loaded gene (i.e.
FBgn0017545). (These features represent the unique introns, splice
sites, and exonic design targets. Output of this analysis,
FBgn0017545_matd.gff, is also attached)
3) load these analysis results into the same database, as follows:
> bp_seqfeature_load.PLS FBgn0017545_matd.gff
It is at this point that I get the above error.
However, I don't get any error and the data loads fine if I load the two
files together, as follows:
> bp_seqfeature_load.PLS --create <(cat FBgn0017545.gff
So, I suspect that either I am misunderstanding when/how to use
bp_seqfeature_load.PLS or else this use case has not yet arisen and must
be provided for somehow.
I am running against bioperl-live
Thanks for your thoughts and assistance,
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri
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