[Biopython] GFF parsing

John Reid j.reid at mail.cryst.bbk.ac.uk
Fri Feb 26 10:22:35 UTC 2010


The GFF page on the BioPython wiki
(http://www.biopython.org/wiki/GFF_Parsing) contains the following
contradictory statements:

Note: GFF parsing is not yet integrated into Biopython. This
documentation is work towards making it ready for inclusion.

Biopython provides a full featured GFF parser which will handle several
versions of GFF: GFF3, GFF2, and GTF. It supports writing GFF3, the
latest version.

As far as I can work out if I have biopython 1.53 and I want to parse
GFF, I should get the latest version of the parser from:
http://github.com/chapmanb/bcbb/tree/master/gff

I've tried using this to parse my 40Mb GFF file and it takes a long 
time. From inspecting my GFF file I thought it should be able to parse 
the records independently or does it need to parse the whole file before 
outputting the first record?

Is there a roadmap for biopython anywhere?

Thanks,
John.




More information about the Biopython mailing list