[Biopython-dev] [Bug 2762] New: GFF capability in SeqIO

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2762

           Summary: GFF capability in SeqIO
           Product: Biopython
           Version: 1.49b
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: lpritc at scri.sari.ac.uk


I'm increasingly coming across GFF format files, and SeqIO currently can't
handle them.  It might be useful if at some point in the future, it could. 
Also, the Bio.GFF module handles access to a database, and doesn't provide a
mechanism for importing or writing GFF format files.  I'm not sure that there
is currently any facility to handle this format in Biopython.

There are at least two variants of the GFF format that I've seen in use...

GFF2 is the one I'm working with at the moment, and its specification is here:
http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml

I've come across GFF3 in other contexts, and it is defined here:
http://www.sequenceontology.org/gff3.shtml

Note that GFF3 is similar to GenBank files in that it may explicitly describe
both sequence features, and the sequence itself (potentially for multiple
sequences).  GFF2 has the potential for this in the specification for the
Comments section, which includes a recommended syntax for defining sequences to
which the features refer, although that spec makes the reasonable assumption
that you would be able to obtain the sequence from elsewhere, knowing the
sequence ID from the GFF file.


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