Main goal: providing a python (instead of CLI) interface to convert coordinates
pip3 install git+https://github.com/klaasg/CrossMap.git
if you want pip freeze to contain this github link instead of just 'CrossMap', use
pip3 install -e git+https://github.com/klaasg/CrossMap.git#egg=CrossMap
>>> import crossmap as cm
>>>
>>> (mapping, t, s) = cm.read_chain_file("/path/to/chain/file")
>>> cm.convert_coordinate_tuples(mapping, [("X", 10000, 20000), ("Y", 15000, 25000)])
([('X', 20000, 30000), ('Y', 25000, 35000)], [])
# Result is a tuple of 1) a list of coordinates and 2) a list of errors
>>> cm.convert_coordinates(mapping, ["X", "Y"], [10000, 15000], [20000, 25000])
(['X', 'Y'], [20000, 25000], [30000, 35000], [])
# Result is a tuple with lists of chromosomes, start positions, end positions and errorsSee original documentation on where to download chain files
Original README:
pip3 install git+https://github.com/liguowang/CrossMap.git or pip3 install CrossMap #Install CrossMap supporting Python3
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