liftover

Package for converting between genome build coordinates

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Project description

liftover

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', one_based=True)
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', one_based=True)
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

These details have not been verified by PyPI

Project links

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GitHub Statistics

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Release history Release notifications | RSS feed

This version

1.2.2

Mar 11, 2024

1.2.1

Mar 8, 2024

1.2.0

Mar 8, 2024

1.1.18

Feb 9, 2024

1.1.17

Nov 2, 2023

1.1.16

Nov 16, 2022

1.1.15

Oct 31, 2022

1.1.14

Aug 10, 2022

1.1.13

Feb 16, 2022

1.1.11

Aug 17, 2021

1.1.10

Mar 8, 2021

1.1.9

Mar 8, 2021

1.1.8

Feb 16, 2021

1.1.7 yanked

Feb 16, 2021

Reason this release was yanked:

missing interbaltree and gztream files

1.1.6

Nov 10, 2020

1.1.5

Oct 26, 2020

1.1.4

Jun 15, 2020

1.1.3

Jan 10, 2020

1.1.2

Jan 9, 2020

1.0.2

Apr 22, 2019

1.0.1

Feb 15, 2019

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Hashes for liftover-1.2.2-cp39-cp39-musllinux_1_1_x86_64.whl
Algorithm	Hash digest
SHA256	`5112498248821879024ab6517ed0259ef5cfa8061c6ae449b515199eba2ef808`
MD5	`fdd94ddf5d64157e132d527f41c82e39`
BLAKE2b-256	`e1c3ac7d0a018e0c3ce09ddee5c9af42bf4e8d60c736f360bd5b7f475f0a1cd4`

Hashes for liftover-1.2.2-cp39-cp39-musllinux_1_1_i686.whl

Hashes for liftover-1.2.2-cp39-cp39-musllinux_1_1_i686.whl
Algorithm	Hash digest
SHA256	`965e7002e5fd6e60d374fe0005f9f9e79a67cd68def1bd50efa115885e5eb29d`
MD5	`3db843edc8c7da1867c295137dc6053a`
BLAKE2b-256	`2dc983362f89e896e89e73cc20b1a41a7df0e467efaeec3f8c6dea6bdf26f507`

Hashes for liftover-1.2.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for liftover-1.2.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`19535a9b358c010e6d52ff24fa488395bb84138c204775437775b3589b52805f`
MD5	`0b814908611d5e4de8ccb90d8de6e292`
BLAKE2b-256	`749ab743421cc080154f2525fe853e16f1716d32f66090f397e86387eeafd884`

Hashes for liftover-1.2.2-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl

Hashes for liftover-1.2.2-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm	Hash digest
SHA256	`0b3d317c80d88c9d9cd354065802aa84be72cdab780100bad3021020fef8bf09`
MD5	`450fef7b2cd130073ea1cabffcd57d7c`
BLAKE2b-256	`51de4727389740cd8dbb81e155b576fe09942801c641acf56ad3475a1ba29191`

Hashes for liftover-1.2.2-cp39-cp39-macosx_10_9_x86_64.whl

Hashes for liftover-1.2.2-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`e3fa2f6b49b3d3485d2f3d4aa29fad3b5f8ea7116a63700d44df91e3f6130406`
MD5	`8ea2bdf62ca54b57d7f97935c6a6d6c7`
BLAKE2b-256	`8e05fc804eb5cb7f9fde6d3454944a77aecf9466df54eb40d1f0743268908608`

Hashes for liftover-1.2.2-cp38-cp38-win_amd64.whl

Hashes for liftover-1.2.2-cp38-cp38-win_amd64.whl
Algorithm	Hash digest
SHA256	`3b54a688ae436e5a59d23fa1f90f15cca34ae627ddc6110846ef2578fbe75c3a`
MD5	`600e81002def0e4997703b90dde18112`
BLAKE2b-256	`af7d5ced6ab2b343d6219547622716b3eec84d40be19fa75b5ddc01e410bdddc`

Hashes for liftover-1.2.2-cp38-cp38-win32.whl

Hashes for liftover-1.2.2-cp38-cp38-win32.whl
Algorithm	Hash digest
SHA256	`7c04760888081f980d47214e6d4e133137cbcaa4c92254d4aac6a5ec503758aa`
MD5	`af1d57bbbbaa6fb33d3b489f2283d4ca`
BLAKE2b-256	`159c15e6c5c6949b4d6ccd10056442941bede1a18904f96cfee10d6c753c9887`

Hashes for liftover-1.2.2-cp38-cp38-musllinux_1_1_x86_64.whl

Hashes for liftover-1.2.2-cp38-cp38-musllinux_1_1_x86_64.whl
Algorithm	Hash digest
SHA256	`26b65bf359df2d4af25764899097089cd5138be673ca5c78d2565dc1b2a882a5`
MD5	`ed891ead9d536ef2b73c4618871023c4`
BLAKE2b-256	`6ee0daec21f39f3842fcfbed8e1c56c8906096dd0f8ee7c5c302c575636a7ba5`

Hashes for liftover-1.2.2-cp38-cp38-musllinux_1_1_i686.whl

Hashes for liftover-1.2.2-cp38-cp38-musllinux_1_1_i686.whl
Algorithm	Hash digest
SHA256	`67fadae30cbb907c1d99b5356c444ae01470d4c31ec9370adc8e14cbb5f830ad`
MD5	`6aafa1f5343a5dcc8fc57afeadbcce9b`
BLAKE2b-256	`c94c8552d6cdaab9e25e8d6632fd29c014937699bace66e524e41a7d2ffa43a3`

Hashes for liftover-1.2.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for liftover-1.2.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`8116c150c3fa706a0090415b4c9973298fe3ba716d8681c5d9e065f1886d3ef8`
MD5	`c27ce105cd800c0c80546beed5f3e62c`
BLAKE2b-256	`5826797a8817117fd6533989fb81ab8fe2b9cb52511d3f633c22e181d929d085`

Hashes for liftover-1.2.2-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl

Hashes for liftover-1.2.2-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl
Algorithm	Hash digest
SHA256	`ce6409b3a3f71ea36782a5d412d3f1770a838a437a530004d7333cd4297760c1`
MD5	`aac36ab82e87d08c6f9e500ed4d6d536`
BLAKE2b-256	`4d98fc091c4cc7793860495c7f8126965e0395d214defd531096fc7038305f30`

Hashes for liftover-1.2.2-cp38-cp38-macosx_10_9_x86_64.whl

Hashes for liftover-1.2.2-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`714aa3dcde330d4690ea8d94392f07f80a38565ede500761ca08eb6d48da61c3`
MD5	`6703666242fe4599d6ef8f4b30405302`
BLAKE2b-256	`b1c52f3e1ef829ff6bfcb6292f39194b17395536b74fbfdc09141ee2c5e81597`