Package for converting between genome build coordinates
Project description
python liftover utility
Converts point coordinates between genome assemblies. Inspired by pyliftover, this offers a few advantages:
- ~5X faster, and lower memory requirements, as loading the chain file and converting coordinates is implemented in c++.
- dictionary style conversion, as in access converted coordinates via
converter[chrom][pos]
Installation
Install via pip: pip install liftover
Usage
from liftover import get_lifter
converter = get_lifter('hg19', 'hg38')
chrom = '1'
pos = 103786442
converter[chrom][pos]
# other synonyms for the lift call
converter.convert_coordinate(chrom, pos)
converter.query(chrom, pos)
# alternatively create a converter directly from a chainfile
from liftover import ChainFile
converter = ChainFile('/home/user/hg18ToHg38.over.chain.gz', 'hg18', 'hg38')
converter[chrom][pos]
# you can also specify an alternative website to load chain files from
converter = get_lifter('hg19', 'hg38', chain_server='https://www.example.com')
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
liftover-1.2.0.tar.gz
(215.0 kB
view hashes)
Built Distributions
Close
Hashes for liftover-1.2.0-cp312-cp312-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f0a95fbc2ce1982bd9387e59b220a336af941d0974dea04bb9a6507a91fa1da1 |
|
MD5 | d1c966ee2b6fe357d63dee5b10b296f8 |
|
BLAKE2b-256 | 3a5e81b2c9604bccc10dfa902d84c902e8ffc12ac83b3abdef82edceb2f6cfd8 |
Close
Hashes for liftover-1.2.0-cp312-cp312-win32.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8f1322c4b372d9f214e085596c4b48998f7ec69e828e8813f7e3ac14bfa0e76b |
|
MD5 | 935e5ba60bae0ce4816614e5272630ce |
|
BLAKE2b-256 | 0285d2eacc7b280933f2cf893f1a94785da945baf0fa94d482e60a61876f0322 |
Close
Hashes for liftover-1.2.0-cp312-cp312-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 843cb6983b23f6332e1f952e1c093aaf66dd184e8e7fb044a13e1133659964e7 |
|
MD5 | e325c56a6ba1c55acd2fc3cdbacd8596 |
|
BLAKE2b-256 | ace73336a220364cf6739e2b2325e2b9465c04cc2f5f8a0fa520ccef1fd7ab3e |
Close
Hashes for liftover-1.2.0-cp312-cp312-musllinux_1_1_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a70584d54dd0f7d7ba37a4dad89bc020b84db2b5dad5a3596591d1911eea6d9b |
|
MD5 | 5a10e06538e536f0c9e1b358dca1fda1 |
|
BLAKE2b-256 | 4d9e8aa7b7c3bfef02f49ffbdcb7c1843b628443a99e07e99eaa4513ec15f71b |
Close
Hashes for liftover-1.2.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | abd360a18fdd1267b36d339bd549624f8725f357522359e4620d3e45f98cbb48 |
|
MD5 | 765d292efde5abc26c419854357f3ca2 |
|
BLAKE2b-256 | 977a159d4f3409a5716872b6895a30103806e1ff73eb4e93b435687f8d17569d |
Close
Hashes for liftover-1.2.0-cp312-cp312-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 260560b66512bc26f97b8d47d0432802121326464b99d14298fdab9fa1a526e7 |
|
MD5 | cb3d37acc66efc64a2dfc62ac78b05b8 |
|
BLAKE2b-256 | bfede0bbf2a4dccf9d9305f0f229876e497eb91a9dedc029dd68d0b97fbd8bf5 |
Close
Hashes for liftover-1.2.0-cp312-cp312-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7c7c75d51e7a4abfef9df84d2b7cd6e6f0b386e48cc0afef13f5b07e8a8639f6 |
|
MD5 | b892f305502cd22fa3af177a4a7393fd |
|
BLAKE2b-256 | 4dea2e925ee815ea5ceaa812bab171d0a3b6bae8e7eddfcc02c79d27100dc631 |
Close
Hashes for liftover-1.2.0-cp311-cp311-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | a5e1fe3f27e82d9309e17e5cdf5d7ea583ba6fa1eade18e5573d507325347bd3 |
|
MD5 | 318fbe745dc0d4231c40f88aba72b4e4 |
|
BLAKE2b-256 | fc1bdb55e2dca4b5d5688710c9f0ac9e71dcfd367b7b35caa9ccf629154438ee |
Close
Hashes for liftover-1.2.0-cp311-cp311-win32.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 307b5f7f0270f96ee961f82199563eef371323ded9cbcf565bb015ddb3679bf4 |
|
MD5 | e03673579c78371ec31c4f8c6ca80e89 |
|
BLAKE2b-256 | 2e495bf51a270e9d817dce44d9646163915bb5c4276dd4f95e248c7ec6908fee |
Close
Hashes for liftover-1.2.0-cp311-cp311-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2c7a617983fe7add0e6d7676248f7592b881af2cde89a280f4482c6befb2a337 |
|
MD5 | 8ca105c42f38ccfbce5a182e27b38ab6 |
|
BLAKE2b-256 | 837fb01701d43776e945c38fbd635623bcd21e9097716367b4c48e0150085220 |
Close
Hashes for liftover-1.2.0-cp311-cp311-musllinux_1_1_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b1c19fbb83b3a22f617bb92a45afbfb16afb286857899c66ffddfdbd1faddb2d |
|
MD5 | a8eb8a37de23f804dff0c4c839c4ee3e |
|
BLAKE2b-256 | 99edb8e117d62edf1b9de1ad65f4efbf6dcd7001e111676d75b36b1f7c7583bf |
Close
Hashes for liftover-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b36aef9352ae12ee7b3eedae8d49dece2745563565ca4a44c178dec246675ae4 |
|
MD5 | 71fad7665afc1ca6416711e635d5d2a7 |
|
BLAKE2b-256 | 2b8288c07cd0d4f0b232a8b828a0b2bab48c4742a4118457f5654b8575de4475 |
Close
Hashes for liftover-1.2.0-cp311-cp311-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 846daa1f5d35505372786ca5bb9196153a6ff6ff7f8b6087dea3d92addc2c6ac |
|
MD5 | f8d5249fc8325317cdfc688b8cbaaac7 |
|
BLAKE2b-256 | de51f9f4aad1be9383c2378234a580b01793bbe81dd39adad7b571aec3def8d5 |
Close
Hashes for liftover-1.2.0-cp311-cp311-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 83bcf5b5b99152b80c9212a2d289967a588a98248fca614d6c18a8348d26c3dc |
|
MD5 | f6cdc4375d6460ae1cc327e6a17de589 |
|
BLAKE2b-256 | f2bf9aa2d06d14f4662b818cda056737be5a4d82b05f046a6985d7d516fc51e6 |
Close
Hashes for liftover-1.2.0-cp310-cp310-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 4adc618e500f14324253246b96e77b82ef6c861a9e9e55c6f4ab33b4e30443df |
|
MD5 | 94524dad7f73a09c21de536001a7223d |
|
BLAKE2b-256 | f47b1db7122d469b685cd84d3f41f747f6351180421f7a9c0326820e5ceb3b84 |
Close
Hashes for liftover-1.2.0-cp310-cp310-win32.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 69077d4a1ce512b05fcfb77825a7c6270ca647c5bdc91d74a6b6768918d186c3 |
|
MD5 | 9d93d58fb315b5487f87ae9449395b51 |
|
BLAKE2b-256 | 1a0c3767769bd75c2f1863075eb4b8e1b96b5b0e0dc8346956a9d0d5543769d0 |
Close
Hashes for liftover-1.2.0-cp310-cp310-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | da5661f5401f857e77a9707e366fd46724ceb55a5da9c1724477359b56c8e1b0 |
|
MD5 | b9fa3743272a983c0ee72db67e253ece |
|
BLAKE2b-256 | d17f69f4d771a5a5537511e0055b168759d3ca0f4d1277ba031866cbc8caea04 |
Close
Hashes for liftover-1.2.0-cp310-cp310-musllinux_1_1_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 882bb79cc13d387d0af9d8a9f52ad1a1e4dc2a929f78b120015c487fec6d52f4 |
|
MD5 | 6cd425b53ed17840ea25532623f14a19 |
|
BLAKE2b-256 | 384d7470f7f613699a9944cba653b97510072ea09e962e9f6f72fdea48b38a89 |
Close
Hashes for liftover-1.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 30569a39e4fc83497c2d9be74f2c3876f0f1b4d60ba952754331ede2668162cb |
|
MD5 | 8968c3edc357ef488ba3719f58ca800a |
|
BLAKE2b-256 | d402408d3acf0a647780d7c5f4606e257e4b211cff6eaa5063c7113fbe45ea2b |
Close
Hashes for liftover-1.2.0-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 0a361307c546d7834474675db33bb23e8dffd43572ffb13c2d720536ecde9948 |
|
MD5 | c149c31c724991c7e2714d93cdae249a |
|
BLAKE2b-256 | 7f6c5dd701ef046bc1805888139069527f79ef099d85ddc897cb5077d5c5ee0c |
Close
Hashes for liftover-1.2.0-cp310-cp310-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 437064fada2bf032b9c44c041c1fb476ee3a3f8627b66ccdfaddb7087db40bcd |
|
MD5 | dc416e49fa37d47d8dcbde6741221413 |
|
BLAKE2b-256 | c20ad9aa8a522d8ac234e2c56327828e6ddc79d353d2d30204d05018e70e4bf5 |
Close
Hashes for liftover-1.2.0-cp39-cp39-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1e706c994cdb484252c13afbcdc058deb8bb2a6e16c67a54dd8b9d072e97b5a2 |
|
MD5 | c42e23c4e9a5e2a819d76e1cfdb7615e |
|
BLAKE2b-256 | 2413e912059c0af38c2a0a3fe2eaea45ab4c31cb626449e9e7bbb30ac4c8834b |
Close
Hashes for liftover-1.2.0-cp39-cp39-win32.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 6a20ab2b486ffd7e30faeedf3cec3a6632e7dbd542a5596ef16ff3cb0ac7d422 |
|
MD5 | ce5dd76c074918d34d8f3688ff376cf8 |
|
BLAKE2b-256 | 5d5a0a660d6007db732f4a58dc77c2545e34ceae5510c7988dbb868a8d1b1cba |
Close
Hashes for liftover-1.2.0-cp39-cp39-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8c4878d8fd5860e690ee75510174e612a4d0cbc0aac1ea5d0f4d27e057b00e2e |
|
MD5 | a73dabc7afa3fad22bfccec4197ac578 |
|
BLAKE2b-256 | 81c0d3c34037a9efd4563593758509e41534eac4963dbcc040d41937c3f1a8b9 |
Close
Hashes for liftover-1.2.0-cp39-cp39-musllinux_1_1_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1a1c8bca7fd05ca1a0db3fde22d3302ca8071696a3da039ec1987cc92ebff689 |
|
MD5 | 1bc498434e8bc5c0b15daac056eb7ce4 |
|
BLAKE2b-256 | 324a9ae39c4a6ee6710462b69b8aa3d8f2b576c8812228650fd7311646a1953a |
Close
Hashes for liftover-1.2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | e2f30989e4c3a53f11eeadec1227640bed990629a4b82b0e043b8a9873dd5af0 |
|
MD5 | b23f473b4929124f8cf7f223180ab73a |
|
BLAKE2b-256 | d73cf642c46ea3afc6a8684aa7896c8b6eaf4421d25ebd22d91cdf431bbdb12f |
Close
Hashes for liftover-1.2.0-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8d5b4f1706fe153aea79aaff51f67fb625e321daf621ab751d8575db7d73149a |
|
MD5 | 90444757b6532c9cf6a648746e340fce |
|
BLAKE2b-256 | fe1121ce0949768cbaf6c20e44da74eb0b76f47f9095a50523dea6c7ed879a17 |
Close
Hashes for liftover-1.2.0-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | fd6e6cc2b90e6926049c3ca792cb61ba3d5e8a01aac9dad387f46a98550ca31d |
|
MD5 | dbc90374dac20bc7c40e66ab9e3c0b3e |
|
BLAKE2b-256 | 3fc08ef19bb501f6c4420f5a0d9158eec4174c5ad61549a89abb4789d90d6001 |
Close
Hashes for liftover-1.2.0-cp38-cp38-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 86d0a7c05584579245cd9e3427180309589bcb1947f749e05c8f90b16872a568 |
|
MD5 | 152ff4ad39fa054015454e44f5233bc9 |
|
BLAKE2b-256 | 1b75d4c93c8ba1618d8dd899545aaa39e779ae4f5d5e8f9700f2dc31552c9627 |
Close
Hashes for liftover-1.2.0-cp38-cp38-win32.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 10c808c9db53d8715e84b26600efcaf03de750e434540dcf79798c0eae020bb3 |
|
MD5 | b7c4455311903046f6cc0375e4fad2b9 |
|
BLAKE2b-256 | d06fdf695c0ddfa3063fe33a5381a9510cda5114a12b8918326ed903f60ed3c0 |
Close
Hashes for liftover-1.2.0-cp38-cp38-musllinux_1_1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8f7a8443367fde83f9da98ea1ad8c51365c74dd9b8445bb5b2102daa052e4a83 |
|
MD5 | 7783be61f02074b3dc75d1cc4c044c6d |
|
BLAKE2b-256 | ffdf875d778a36a392ed2aef0e3fc702995fec8f5a55beadcdc5cb0a164d6f54 |
Close
Hashes for liftover-1.2.0-cp38-cp38-musllinux_1_1_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | cb3f344b2887b91eec52d0ed258c69ecc23f81ccd00503e6f2bb648aa41dc3fc |
|
MD5 | db191c461cc4a126d3b0a0a77373da2d |
|
BLAKE2b-256 | b71b667a3462ab4c3bff440893a38824a4576c8884861752da44ebfa07accf17 |
Close
Hashes for liftover-1.2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | f6ea85a820c4b734812f52c04d690e5fdc4309806f91b50da2ab3e8ca7adcb74 |
|
MD5 | 359fe9de6243c85d5d86d92858712d93 |
|
BLAKE2b-256 | 3188e2b53f1fa861bef57695b24a551e373b7ac5684be9b00499dc5aba0607a5 |
Close
Hashes for liftover-1.2.0-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d895dbb66f71476cef23299d79fdee1b58c70852da7cdb6f6bcb8f316e4c9064 |
|
MD5 | b3bf0ad47072128acc052902ac981765 |
|
BLAKE2b-256 | 9e2b0a261912dfde6cd1cac58c5ffe85ed4f2f8f3b13bdf578595524d3826e79 |
Close
Hashes for liftover-1.2.0-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | fef6e6bf542476448b0fbc62818951f4d1a63597c5115f0fcd87189e68363345 |
|
MD5 | 088cc23d9f9bed7f816f8b50ae05409b |
|
BLAKE2b-256 | d2223d1d7278186d01396e184746c9926762a5e53dafe8c0b6f9367bc2aee53b |