PYVCFLIB(1)

👑 PYVCFLIB(1) — VCFLib Python FFI 💖

okay bestie, so this is the manual for PYVCFLIB(1), aka the VCFLib Python FFI. Like, we're building up a Python FFI for vcflib using the brilliant Python pybind11 module ✨. Mostly for (our) testing purposes, so we are not aiming for complete coverage — it's giving "good enough, bestie". See below for adding new bindings 🫶.

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🌸 DESCRIPTION — Setting it up and example 🌸

First things first: import the module 💅. It may require setting the PYTHONPATH to the shared library pyvcflib.cpython-39-x86_64-linux-gnu.so.

env PYTHONPATH=./build python3 -c 'import pyvcflib'

and in a GNU Guix shell you may prepend LD_LIBRARY_PATH to find GLIBC etc. 🧚

LD_LIBRARY_PATH=$LIBRARY_PATH

Now you should be able to use the pyvcflib module. Let's try with a VCF samples/10158243.vcf that has only one record:

>>> from pyvcflib import *

>>> vcf = VariantCallFile()
>>> vcf.openFile("../samples/10158243.vcf")
True

# ...    list(rec.name,rec.pos,rec.ref,rec.alt)

>>> rec = Variant(vcf)
>>> while (vcf.getNextVariant(rec)):
...    [rec.name,rec.pos,rec.ref]
['grch38#chr4', 10158243, 'ACCCCCACCCCCACC']

>>> rec.alt[0]
'ACC'

>>> rec.alleles
['ACCCCCACCCCCACC', 'ACC', 'AC', 'ACCCCCACCCCCAC', 'ACCCCCACC', 'ACA']

So the one input record shows it has a ref of ACCCCCACCCCCACC and six alt alleles [ACCCCCACCCCCACC, ACC, AC, ACCCCCACCCCCAC, ACCCCCACC, ACA] 🔥

This works fine! No cap 🎀

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💜 Masking genotypes 💜

With vcfwave's allelic primitives, when two VCF records get combined, we need to combine the genotypes. This happens, for example, with vcfwave deletions 👀.

When a deletion spans any SNPs from realignment we want to make sure the SNPs are masked for those deletions. I.e. 🌈

6/28/2022, 4:21:44 PM - erikg: if you have a deletion in hap 1 .|0 or .|1 in hap 2 0|. or 1|. etc.

So, if we have input two variants at the same position with the first a DEL and the second a SNP the SNP genotypes need to be masked as

>> deletion_mask_genotypes(['1|0', '0|0', '0|1', '1|1', '1|0', '1|0', '1|1'],
...                         ['0|0', '1|1', '1|0', '0|0', '1|0', '1|1', '1|1'])
                            ['0|0', '1|1', '1|0', '0|0', '.|0', '.|1', '.|.']

In the 5-7th column the deletion has the same genotype and gets masked 💅✨

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🦋 Another example 🦋

See realign.py for examples of using the FFI in the form of a python unit test 🧪. We used that to develop the vcfwave module. Iconic behaviour, honestly 👑

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🎀 Additional bindings 🎀

It may be the case you want additional bindings that we have not included yet 🙈. See vcflib's pythonffi.cpp for the existing bindings and Variant.h for the classes and accessors 💖.

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💖 that's the whole page, bestie 💖 — this one's signed off from the <rainbow>-- coding: utf-8 --()</rainbow> era, brought to you by the VCFLib Python FFI, and you *know* it's giving -- coding: utf-8 --()` energy fr fr 🌸✨🫶