[Bioperl-l] reading and writing GFF3

Robert Buels rmb32 at cornell.edu
Thu Jun 15 21:37:03 EDT 2006

There is stuff in bioperl for reading and writing GFF3.  There's 
Bio::Tools::GFF.  There's Bio::FeatureIO::gff.  Are there more?  Which 
is the 'best' one to use?

Neither of these is working very well for me.

My proximate use case is reading in a RepeatMasker report with 
Bio::Tools::RepeatMasker, which spits out FeaturePair objects, then 
writing those out to a GFF3 file.

Bio::Tools::GFF will take these things and write out something that 
closely resembles GFF3, but with Target attributes that don't seem to 
comply with Lincoln's GFF3 spec, since its coordinates are join()ed with 
commas instead of spaces.  I'm attaching a little script that 
illustrates this.

Bio::FeatureIO::gff refuses to take these FeaturePairs or either of the 
features contained in them, throwing 'only Bio::SeqFeature::Annotated 
objects are writeable'.  This seems a bit silly, since one of the whole 
points of Bioperl is using polymorphism to make it easy to connect 
things together.  I've attached a little script to illustrate this one too.

So my questions are:  what _should_ I be doing here?  Is Bio::Tools::GFF 
deprecated?  Why does Bio::FeatureIO::gff only accept 
Bio::SeqFeature::Annotated objects?

Thanks in advance.


Robert Buels
SGN Bioinformatics Analyst
252A Emerson Hall, Cornell University
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu

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