rochefca / geneparse

Clean interface to parse genotype files

geneparse - Module to parse genetics data file

geneparse is a module that helps developers to parse multiple genetics file format (e.g. Plink binary files, IMPUTE2 files and VCF).

Dependencies

The tool requires a standard Python installation (3.3 or higher are supported) with the following modules:

1. numpy version 1.8.2 or latest
2. pandas version 0.14.1 or latest
3. pyplink version 1.3.4 or latest
4. pysam version 0.9.0 or latest
5. biopython version 1.68 or latest

The tool has been tested on Linux only, but should work on MacOS operating systems as well.

Installation

Using pip:

pip install geneparse

Updating

To update the module using pip:

pip install -U geneparse

Testing

To test the module, just perform the following command:

$ python -m geneparse.tests
sssssss...ss.ss..............................
----------------------------------------------------------------------
Ran 45 tests in 0.395s

OK (skipped=11)