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bbcf / bbcflib

Internal utility modules for the BBCF
http://bbcf.epfl.ch/bbcflib
GNU General Public License v3.0
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Instead of a chromosome file, use GenRep #3

Closed xapple closed 13 years ago

xapple commented 13 years ago

Currently, any text-file type track (like bed or wig) needs an associated chromosome file specifying the lengths of each chromosome for the particular specie/assembly. This variable is passed to the Track object creator.

It would be nice to replace this variable with a "NR assembly id", that would then be used to query GenRep.

xapple commented 13 years ago

Done. You can use it like this:

from bbcflib.track import Track
with Track('tracks/yeast_genes.bed', chrmeta='sacCer2') as yeast:
    data = yeast.read('chrIV')