Metadata-Version: 2.4
Name: liftover
Version: 1.3.3
Summary: Package for converting between genome build coordinates
Home-page: https://github.com/jeremymcrae/liftover
Author: Jeremy McRae
Author-email: jmcrae@illumina.com
License: MIT
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: urllib3
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license
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![liftover](https://github.com/jeremymcrae/liftover/workflows/liftover/badge.svg)

### python liftover utility

Converts point coordinates between genome assemblies.
Inspired by [pyliftover](https://github.com/konstantint/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

```python
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')
```

