A python package for finding genomic range overlaps
Project description
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
Hashes for pygros-0.1.2-cp312-cp312-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 28eb036f839a4b5076d644a50aa965308311fc2396514c467b723630962fc9e5 |
|
MD5 | e26a00520d2efcf070da71aca48bd8bc |
|
BLAKE2b-256 | ce7baa41dec296030661aaf25fa0088fff874c10c15ff23e2a6768214abf4f74 |
Hashes for pygros-0.1.2-cp312-cp312-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4a6768dc38b172c98b4fc6a039e0b59ca6fb0f0106f632c98a395699bcb086ae |
|
MD5 | 6bccffffbfd7fa88ce038d275c7bba23 |
|
BLAKE2b-256 | f1a1ecbb1a9ef61bce5158749d47deda11d1292ec348f2e06e3af039258c11cd |
Hashes for pygros-0.1.2-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | af69b2a6b08db52de2fb418adc45ee005ea1e1d80b55d3815831c9ad65907dd0 |
|
MD5 | d61cbda5d72252977044783cd480d96e |
|
BLAKE2b-256 | 082edbf5dda41a7be887d33dc9d64700d2570d82cd24d7a92d40e30268130f81 |
Hashes for pygros-0.1.2-cp312-cp312-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c7a0b1ed2d5d96e0985a4f920f1b0a21308153885af99e7b3410ed529ce92b21 |
|
MD5 | b8664de1f06fa34738d1b7011a23d2cc |
|
BLAKE2b-256 | f1b7689655260dee0795a9d309f275a8e45024cec16f5c331bb5ce6438096b55 |
Hashes for pygros-0.1.2-cp311-cp311-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a836b44fcacf4535e47fbe4f026bd21b3e520c4f13907da3e95c24d076c4fba5 |
|
MD5 | 13cdb57deba4f94abdc840c5bb5f1504 |
|
BLAKE2b-256 | 00a180e0b9dfd135e7ca29dd469a983499683ce7b0c00912db0792c05ecfb8e3 |
Hashes for pygros-0.1.2-cp311-cp311-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 43b3b8e65da101ccb0ab274a85cb32da2c7cbf8a7b9709cae892dbb948fedb78 |
|
MD5 | f4ff7873245724d56ece688e54d28a9b |
|
BLAKE2b-256 | c7dd25836936da6f7fd2713c7422eb9e66036bf06bab728f8b4374c9a9a77f4a |
Hashes for pygros-0.1.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | aa99e0e90fd97d1c40564b4e6d56c83eaee25b586442aa14ba123ce79b9ae962 |
|
MD5 | 15cf050706b487f0b193c657d2a5552c |
|
BLAKE2b-256 | 67ce0b6c79ac4c4ae06a3fabdc3cee2ee07aa16adea1adf1072c200492abb6ef |
Hashes for pygros-0.1.2-cp311-cp311-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 41237a70fb3e4fc0ee2fc524c4fe7cf14d40fbf5beee0c4759846bccb02fa803 |
|
MD5 | 114487740ba6c52332dd161681759553 |
|
BLAKE2b-256 | 7de37469a78547e122b9c21f5c5a9e90519a637584d3461ab4c01b2e92f76822 |
Hashes for pygros-0.1.2-cp310-cp310-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8be84d38c9ec08215078629fa75ca74c510ca29abaf501c15e44a05a9f6e777a |
|
MD5 | 41349483469cb29ee4b6b4d07ab13b89 |
|
BLAKE2b-256 | d0baa35270ecafe69998bc4cabcb357e665b9ccad58beb06cad01c3eabbea73c |
Hashes for pygros-0.1.2-cp310-cp310-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8da9ff9fca1b70f6981bdc1333a7a91b8d82d71760ddbf40d53a1923fdce1264 |
|
MD5 | 1dcef2618f4e3e1a59ed97ecdfd6bbc5 |
|
BLAKE2b-256 | 838db88c252d24a7e04043ff70db7c796d2cb16b91573c6acdc31830f3520c83 |
Hashes for pygros-0.1.2-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8f8341eab42d260c96f987cad2083ee3daf91a488f21b2065d320b8b960f9e6c |
|
MD5 | d35f4735cded4bb259eceff45c3d96c2 |
|
BLAKE2b-256 | a0c92edc7fd323196bde7c1f0518ae3bc877830203ba6b28d0743519629505fb |
Hashes for pygros-0.1.2-cp310-cp310-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b0204406da8f137b8f5f765f28e584f488b2314f7e2695c4c2cf8548eb775272 |
|
MD5 | fd90a9049feb9ebe610a558a0f40fa6d |
|
BLAKE2b-256 | 73ca999fa12e331b956627da3a6600b90c9c3ffe299c8122e02ca8960fdeab88 |
Hashes for pygros-0.1.2-cp39-cp39-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f6c7e0c816258d25c5ce03096e6f842a06b3fd465cfc9f08ec1ffca07d95ec40 |
|
MD5 | 8b292836936bccd1773236199b8cb82c |
|
BLAKE2b-256 | 5bee287a5dd926d182e0e4aafa5981c639c9d1b7c8f0e45de0f8b557f4a02ac9 |
Hashes for pygros-0.1.2-cp39-cp39-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 5cedc9eff21d1513f5b9cf7123ec29adaa369c4175db31b9bae49bc5cdde9457 |
|
MD5 | 56b54f41617976f6b9991d8c3588abdb |
|
BLAKE2b-256 | e5b7bd60b38ce05512ea15210ab101a07e7d9d2b3643af45c5009eadf3425121 |
Hashes for pygros-0.1.2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a49778b7fec4434f3d279df7ceff6dbd0b948e455079dd8399de880e0efc1cf8 |
|
MD5 | 2569b5d14ba92377610b0385ab02092f |
|
BLAKE2b-256 | 55b50f287ff2931a2236afeb7583ad642789ec87a37e0956c5b029fe4b9b6e31 |
Hashes for pygros-0.1.2-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 85f5df4e2997ad5c5ef33a07a20b8b590da82097c6d0ecd43226d6c6c55172ef |
|
MD5 | 7960a3c87cdd99e68b7f14d93429a9b1 |
|
BLAKE2b-256 | f31090c1e410c4b6cefbbfcdc4542a83e12c9ca9109d0181d9ba3f2042d68f93 |
Hashes for pygros-0.1.2-cp38-cp38-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | facfb9eb6f8601bc91e37446febfd7ae665c7e16947e168b10cb1d9b95ab6a85 |
|
MD5 | 7350f9f1fe7c895cb4eb0ce0673c3334 |
|
BLAKE2b-256 | 511f668b28bf19aaf01adb2310188ff0586c4a04954658021940df6009d81b8c |
Hashes for pygros-0.1.2-cp38-cp38-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 71e3c8be105633cbdaa2b85dd1b1e9740be6153492b78328117051d5fa1cba6a |
|
MD5 | 6a8d72d6a8717ab5e893f292599f5b91 |
|
BLAKE2b-256 | 3a426d2cc116b1cf255748b1f1e17261728b02fbc3ccd3564aa6866c72fb3c66 |
Hashes for pygros-0.1.2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a8d40cbbfd8d1cf8616a7235f4eb435bcd086c41c8e5d0e60a43d119c12266f0 |
|
MD5 | 7881663c8ac65f5ae6e1d56d8ebae3e0 |
|
BLAKE2b-256 | 2152adf26501789b4674767c97c80c3ef9e4f1fc7bc6cee90758d058427a791f |
Hashes for pygros-0.1.2-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 3c3cbdce0dfbb19366edc0e003aa7485fc03d52ef46b2ae6249bfaddffb2aabf |
|
MD5 | 24227ecbf6683f532f101a8bef7573ea |
|
BLAKE2b-256 | 9286bf9555bb36ee7b4d5f3660c1356d1d7e0764f4113c236b3a3b6c3c442b3c |
Hashes for pygros-0.1.2-cp37-cp37m-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 11b3cb0a2cfe8bfe85e3502464ca9aeb09d7cff6ae856f6930efb9b90922737a |
|
MD5 | 0cb2daaf269452bcc076636fbd127e1c |
|
BLAKE2b-256 | 0f929ed9d386c92c4a4bbb68bdd8d81432a188d764279eb42eb9e11286041cdb |
Hashes for pygros-0.1.2-cp37-cp37m-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8a00c2e6aa92ff342fee4feae162e0219b2cfd0feb0549a2a93c948a9050cfed |
|
MD5 | ad599de4e528dff09bf1948239965a9b |
|
BLAKE2b-256 | a6cd6f642d564d07d0edf23b708e9d294bffb9497e808bffcce4d6d538c2ecae |
Hashes for pygros-0.1.2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 336efbc380ea4e18a44f430c169c168d4bc179ea898bbccf0c90a07a168e978a |
|
MD5 | 80d7b6d5d7e384629e6d8aac5580d255 |
|
BLAKE2b-256 | 625de9beacb8010e7dae9860964954717e6cc7ca03cc03f857cb72f6d5a1d759 |
Hashes for pygros-0.1.2-cp37-cp37m-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ef5f84e7ec0b69a53f1243e3d18f3b1648e40e7e429a9bfa5e3a1a07711c5b04 |
|
MD5 | 601865586b2a3e2ddfb8b85fad9986e4 |
|
BLAKE2b-256 | 381bab2aec1095b1ac240e0efd3deed0a646c886b84325c04dca35e07c6b67b1 |