a python library for finding genomic range overlaps based on cgranges.
pygros is available on PyPi, to install it:
pip install pygros>>> import pygros
>>> ranges = pygros.Ranges()
>>> ranges.add('chr1', 10, 20)
>>> ranges.add('chr1', 30, 50)
>>> ranges.add('chr1', 25, 40)
>>> ranges.index()
>>> ranges.overlap('chr1', 30, 40)
[(25, 40, -1), (30, 50, -1)]pygros.Ranges(intervals=[])
create a Ranges object to store genomic ranges
@param intervals: a list or tuple containing multiple ranges
@return Ranges object
add(chrom, start, end, label=-1)
add genomic range into Ranges object
@param chrom: chromosome name or sequence name
@param start: start of range
@param end: end of range
@param label: an integer
index()
After add new genomic ranges, use this method to build indexoverlap(chrom, start, end)
get genomic ranges that overlapped with your given range (start, end)
@param chrom: chromosome or sequence name
@param start: start of range
@param end: end of range
@return: a list of ranges
within(chrom, start, end)
get genomic ranges within given range (start, end)
@param chrom: chromosome or sequence name
@param start: start of range
@param end: end of range
@return: a list of ranges
contain(chrom, start, end)
get genomic ranges that contained in given range (start, end)
@param chrom: chromosome or sequence name
@param start: start of range
@param end: end of range
@return: a list of ranges