pygros
======
a python library for finding genomic range overlaps based on `cgranges <https://github.com/lh3/cgranges>`_.
Installation
------------
``pygros`` is available on `PyPi <https://pypi.org>`_, to install it:
.. code:: bash
pip install pygros
Usage
-----
.. code:: python
>>> 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
Raw data
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"description": "pygros\n======\n\na python library for finding genomic range overlaps based on `cgranges <https://github.com/lh3/cgranges>`_.\n\nInstallation\n------------\n\n``pygros`` is available on `PyPi <https://pypi.org>`_, to install it:\n\n.. code:: bash\n\n\tpip install pygros\n\nUsage\n-----\n\n.. code:: python\n\n\t>>> import pygros\n\t>>> ranges = pygros.Ranges()\n\t>>> ranges.add('chr1', 10, 20)\n\t>>> ranges.add('chr1', 30, 50)\n\t>>> ranges.add('chr1', 25, 40)\n\t>>> ranges.index()\n\t>>> ranges.overlap('chr1', 30, 40)\n\t[(25, 40, -1), (30, 50, -1)]\n\nAPI reference\n-------------\n\npygros.Ranges(intervals=[])\n\n\tcreate a Ranges object to store genomic ranges\n\n\t@param intervals: a list or tuple containing multiple ranges\n\n\t@return Ranges object\n\n\tadd(chrom, start, end, label=-1)\n\n\t\tadd genomic range into Ranges object\n\n\t\t@param chrom: chromosome name or sequence name\n\n\t\t@param start: start of range\n\n\t\t@param end: end of range\n\n\t\t@param label: an integer\n\n\tindex()\n\n\t\tAfter add new genomic ranges, use this method to build index\n\n\toverlap(chrom, start, end)\n\n\t\tget genomic ranges that overlapped with your given range (start, end)\n\n\t\t@param chrom: chromosome or sequence name\n\n\t\t@param start: start of range\n\n\t\t@param end: end of range\n\n\t\t@return: a list of ranges \n\n\twithin(chrom, start, end)\n\n\t\tget genomic ranges within given range (start, end)\n\n\t\t@param chrom: chromosome or sequence name\n\n\t\t@param start: start of range\n\n\t\t@param end: end of range\n\n\t\t@return: a list of ranges\n\n\tcontain(chrom, start, end)\n\n\t\tget genomic ranges that contained in given range (start, end)\n\n\t\t@param chrom: chromosome or sequence name\n\n\t\t@param start: start of range\n\n\t\t@param end: end of range\n\n\t\t@return: a list of ranges\n",
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