pybedtools.helpers.chromsizes

pybedtools.helpers.chromsizes(genome)

Looks for a genome already included in the genome registry; if not found it first tries to look it up via genomepy. If genomepy is not installed, or if this lookup fails then it looks it up on UCSC. Returns the dictionary of chromsize tuples where each tuple has (start,stop).

Chromsizes are described as (start, stop) tuples to allow randomization within specified regions; e. g., you can make a chromsizes dictionary that represents the extent of a tiling array.

Example usage:

>>> dm3_chromsizes = chromsizes('dm3')
>>> for i in sorted(dm3_chromsizes.items()):
...     print(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))