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, BGEN and VCF).

Dependencies

The tool requires a standard Python installation (3.6 or higher are supported) with the following modules:

1. numpy
2. pandas
3. pyplink
4. pybgen
5. cyvcf2
6. biopython

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

Installation

You can install or update geneparse using pip:

pip install -U geneparse

Testing

To test the module, just perform the following command:

$ python -m geneparse.tests
..sssss.........s..sssss.........ssssssss...ss.ss...s.................
.......................................................s....ss.....
----------------------------------------------------------------------
Ran 137 tests in 1.549s

OK (skipped=27)

Indexing

Some genotype data require indexing for fast access. This can be done using geneparse.

$ python -m geneparse.index --help
usage: geneparse-indexer [-h] [--impute2 IMPUTE2 [IMPUTE2 ...]]
                         [--bgen BGEN [BGEN ...]] [--legacy]

Genotype file indexer.

optional arguments:
  -h, --help            show this help message and exit

IMPUTE2 index:
  --impute2 IMPUTE2 [IMPUTE2 ...]
                        Index an IMPUTE2 genotype file format. The file can be
                        plain text or bgzipped.

BGEN index:
  --bgen BGEN [BGEN ...]
                        Index a BGEN genotype file. This requires 'bgenix' to
                        be in the PATH.
  --legacy              Index the file using the '-with-rowid' option. This
                        flag enables compatibility with SQLITE prior to
                        version 3.8.2. See
                        https://bitbucket.org/gavinband/bgen/wiki/bgenix for
                        more information.

Extraction

We provide a simple tool to extract genotypes from different format to either VCF or Binary plink files.

$ python -m geneparse.extract --help
usage: geneparse-extractor [-h] -f FORMAT [-e FILE] [-k FILE] [--maf] -o FILE
                           [--output-format FORMAT]
                           PARSER_ARGS [PARSER_ARGS ...]

Genotype file extractor. This tool will extract markers according to names or
to genomic locations.

optional arguments:
  -h, --help            show this help message and exit

Input Options:
  -f FORMAT, --format FORMAT
                        The input file format.
  PARSER_ARGS           The arguments that will be passed to the genotype
                        parsers.

Extract Options:
  -e FILE, --extract FILE
                        The list of markers to extract (one per line, no
                        header).
  -k FILE, --keep FILE  The list of samples to keep (one per line, no header).
  --maf                 Check MAF and flip the allele coding if the MAF is
                        higher than 50%.

Output Options:
  -o FILE, --output FILE
                        The output file (can be '-' for STDOUT when using VCF
                        or CSV as output format).
  --output-format FORMAT
                        The output file format. Note that the extension will
                        be added if absent. Note that CSV is a long format
                        (hence it might take more disk space).

The parser arguments (PARSER_ARGS) are the same as the one in the API. For
example, the arguments for the Plink parser is 'prefix:PREFIX' (where PREFIX
is the prefix of the BED/BIM/FAM files).