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-- coding: utf-8 --()					 -- 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 aim-
       ing 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	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',  `ACCCC-
       CACC', `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

	      >> 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 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 in-
       cluded yet.  See	vcflib's pythonffi.cpp for the existing	 bindings  and
       Variant.h for the classes and accessors.

							 -- coding: utf-8 --()

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