Add a GFF/GTF parser - Githubissues

bbcf / bbcflib

Internal utility modules for the BBCF

http://bbcf.epfl.ch/bbcflib

GNU General Public License v3.0

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Add a GFF/GTF parser #18

Closed xapple closed 12 years ago

xapple commented 13 years ago

Amongst the list of currently supported formats (sql, bed, wig, bedGraph, bigWig) it is necessary to add a GFF/GTF parser for use in pygdv.

The UCSC format definition is found here: http://genome.ucsc.edu/FAQ/FAQformat.html#format3
A summary parser exists in bbcfutils/Python/parse_gtf.py.
Some work has been done in biopython here: https://github.com/chapmanb/bcbb/blob/master/gff/BCBio/GFF/GFFParser.py

yjarosz commented 13 years ago

Perhaps it also need the parsers to be refactored in a way that they are simple and easy to use. That's not the case for the moment as they're embeded in the bbcflib.track package and they're not really parse a file as they should do ( parse the file without any modifications).

xapple commented 13 years ago

Yes, I agree. This should be done at the same time with ticket 16 when the library is largely refactored.