pyigd 1.4

Parser and writer of IGD files for genetic data

pyigd

PyIGD is a Python-only parser the Indexable Genotype Data (IGD) format. See our short paper (or the preprint) that describes the format and some of its advantages.

For tools to manipulate IGD files (and convert VCF to IGD), use igdtools (pip install igdtools).

For a C++ library that supports creating and parsing IGD, see picovcf (which supports VCF to IGD conversion).

Installation

You can install the latest release of PyIGD from pypi, via pip install pyigd.

For development, you can clone the code and install it directly from the directory (this will automatically reflect any code changes you make):

pip install -e pyigd/

or build and install via the wheel:

cd pyigd/ && python setup.py bdist_wheel
pip install --force-reinstall dist/*.whl

Usage

The pyigd.IGDReader class reads IGD data from a buffer. See the example script that loads an IGD file, prints out some meta-data, and then iterates the genotype data for all variants. Generally the usage pattern is:

with open(filename, "rb") as f:
  igd_reader = pyigd.IGDReader(f)

There is also the pyigd.IGDWriter class to construct IGD files. Related is pyigd.IGDTransformer, which is a way to create a copy of an IGD while modifying its contents. See the IGDTransformer sample list example and bitvector example.

IGD can be highly performant for a few reasons:

1. It stores sparse data sparsely. Low-frequency variants are stored as sample lists. Medium/high frequency variants are stored as bit vectors.
2. It is indexable (you can jump directly to data for the ith variant). Since the index is stored in its own section of the file, scanning the index is extremely fast. So only looking at variants for a particular range of the genome is very fast (in this case you would use pyigd.IGDFile.get_position_and_flags() to find the first variant index within the range, and then use pyigd.IGDFile.get_samples() after that).
3. The genotype data is stored in one of two very simple binary formats. This makes parsing fast, and the compact nature of the file makes reading from disk/memory fast as well.

How do I use IGD in my project?

• Install igdtools. The easiest way is via pip install igdtools.
  • igdtools can convert from VCF to IGD, among other things (such as filtering IGD files).
• Do one of the following:
  • If your project is C++, copy picovcf.hpp into your project, #include it somewhere and then use according to the documentation
  • If your project is Python, install pyigd per the README instructions (or just pip install pyigd).