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% -*- coding: utf-8 -*-
# VCFLib Python FFI
We are 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. See below for adding new bindings.
## Setting it up and example
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'
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](../../samples/10158243.vcf) that has only one record:
```python
>>> 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!
## 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
```python
>> 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.
## Another example
See [realign.py](../tests/realign.py) for examples of using the FFI in the form of a python unit test. We used that to develop the vcfwave module.
## Additional bindings
It may be the case you want additional bindings that we have not included yet. See vcflib's [pythonffi.cpp](../../src/pythonffi.cpp) for the existing bindings and [Variant.h](../../src/Variant.h) for the classes and accessors.
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