[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.
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