pygros 0.3.0

A python package for finding genomic range overlaps

a python library for finding genomic range overlaps based on cgranges.

Installation

pygros is available on PyPi, to install it:

pip install pygros

Usage

>>> 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)]

API reference

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 index

overlap(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