pybedtools.helpers.get_chromsizes_from_ucsc

pybedtools.helpers.get_chromsizes_from_ucsc(genome, saveas=None, mysql='mysql', timeout=None)[source]

Download chrom size info for genome from UCSC and returns the dictionary.

If you need the file, then specify a filename with saveas (the dictionary will still be returned as well).

If mysql is not on your path, specify where to find it with mysql=<path to mysql executable>.

timeout is how long to wait for a response; mostly used for testing.

Example usage:

>>> dm3_chromsizes = get_chromsizes_from_ucsc('dm3')
>>> for i in sorted(dm3_chromsizes.items()):
...     print('{0}: {1}'.format(*i))
chr2L: (0, 23011544)
chr2LHet: (0, 368872)
chr2R: (0, 21146708)
chr2RHet: (0, 3288761)
chr3L: (0, 24543557)
chr3LHet: (0, 2555491)
chr3R: (0, 27905053)
chr3RHet: (0, 2517507)
chr4: (0, 1351857)
chrM: (0, 19517)
chrU: (0, 10049037)
chrUextra: (0, 29004656)
chrX: (0, 22422827)
chrXHet: (0, 204112)
chrYHet: (0, 347038)