[Bioperl-l] reading and writing GFF3

Fri Jun 16 19:30:23 UTC 2006

Woops, I should have said something about that.  I submitted it before I 
saw that Scott had already done the escaping in CVS.

Chris Fields wrote:
> Scott, 
>
> Looks like Robert also submitted a bug report related to this as well.
> Could you check into it (pretty-please)?  I'm still GFF3-illiterate.
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2025
>
> Chris
>
>   
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Scott Cain
>> Sent: Friday, June 16, 2006 9:18 AM
>> To: Robert Buels
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] reading and writing GFF3
>>
>> Hi Rob,
>>
>> I sympathize with your pain--writing GFF3 isn't as easy as writing GFF2,
>> but that is actually a good thing.  The tighter constraints results in a
>> better, more consistent file format.
>>
>> The reason only BSF::Annotated features are writable is that there needs
>> to be tight control on the 'type' of the feature, to insure that the
>> type is part of the Sequence Ontology.  It also makes it much easier to
>> properly write out the attributes in the ninth column, particularly the
>> ones that are 'reserved', like Parent, Dbxref, and Ontology_term.
>>
>> BTG is still usable, but the GFF3 it puts out is actually more
>> 'GFF3-like'; that is, it looks like GFF3, but because there are no
>> constraints on the type and the terms that are used in the ninth column,
>> you have to be very careful using it to produce GFF3, by making sure
>> that your feature objects conform to the standard before BTG tries to
>> write them out.  (Of course, one way to do that would be to convert your
>> feature objects to BSF::Annotated objects, but then you could use
>> BFIO::gff :-)
>>
>> [Long pause while scott goes and monkeys with Bio::Tools::GFF]
>>
>> OK, I just committed a fix Bio::Tools::GFF which produces valid GFF3 for
>> your sample data.  Conveniently, since 'nucleotide_motif' is a SO term,
>> this is completely valid.  (I even fixed the escaping the of the stray
>> '=' in 'hind_R=2046'.)  The output I get is this:
>>
>> ##gff-version 3
>> C08HBa0001K22.1 RepeatMasker    nucleotide_motif        2095    2556
>> 918     -       .       Target=Contig151 325 832
>> C08HBa0001K22.1 RepeatMasker    nucleotide_motif        2590    2736
>> 488     -       .       Target=Contig386 1 124
>> C08HBa0001K22.1 RepeatMasker    nucleotide_motif        2787    3105
>> 1718    +       .       Target=Contig358 1 311
>> C08HBa0001K22.1 RepeatMasker    nucleotide_motif        3974    4036
>> 312     -       .       Target=hind_R%3D2046 59 120
>>
>> Scott
>>
>>
>>
>> On Thu, 2006-06-15 at 18:37 -0700, Robert Buels wrote:
>>     
>>> 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.
>>>
>>> Rob
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>       
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                         cain at cshl.edu
>> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
>> Cold Spring Harbor Laboratory
>>     
>
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>   

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