pgxcentre/ref_finder

Finds the reference (and alternative) allele in the reference genome

ref_finder - Script to find and check the reference allele.

Version 0.2

ref_finder is a Python script created to find the reference (and alternative) allele using a BIM file (from Plink) and a reference genome (in Fasta format).

Dependencies

The tool requires a standard Python installation (2.7 or 3) with the following module:

1. pyfaidx version 0.3.0 or latest
2. pandas version 0.15.2 or latest

The tool has been tested on Linux, but should work on Windows and MacOS operating system as well.

Usage

$ ref_finder.py --help
usage: ref_finder.py [-h] [-v] [--debug] [--log LOGFILE] -i FILE -r FASTA
                     [-o FILE]

Finds the human reference allele (version 0.2).

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  --debug               Set the logging to debug
  --log LOGFILE         The log file [ref_finder.log]

Input Files:
  -i FILE, --input FILE
                        The input file (BIM format).
  -r FASTA, --reference FASTA
                        The human reference genome in FASTA format.

Result File:
  -o FILE, --output-prefix FILE
                        The name of the output file [ref_alleles.vcf]

Testing

Basic testing is available.

$ python -m unittest -q ref_finder