hypothesis-vcf 0.1.0

Hypothesis strategy for generating VCF

hypothesis-vcf

A Hypothesis strategy for generating VCF (Variant Call Format) files.

Description

hypothesis-vcf is designed to generate VCF files that conform to the VCF specification (version 4.3). It generates VCFs that are syntactically valid, but which don't have meaningful semantics.

For that reason, the main use case is for testing software that parses VCF or converts VCF to another format, since Hypothesis will generate examples that exercise many edge cases of the VCF spec.

In general, the generated VCFs do not have well-known INFO or FORMAT fields, such as DP or AD. There is one exception to this: GT (genotype) fields are generated, since they are found in most VCF files. The ability to generate more well-known fields may be added in the future.

API

The public API consists of just one function: hypothesis_vcf.vcf.

Usage

Generate an example interactively:

>>> from hypothesis_vcf import vcf
>>> print(vcf().example())
##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##source=hypothesis-vcf-0.1.dev2+g32cb4a6
##contig=<ID=C>
##INFO=<ID=Jw,Type=Float,Number=1,Description="INFO,Type=Float,Number=1">
##FORMAT=<ID=zS,Type=Integer,Number=3,Description="FORMAT,Type=Integer,Number=3">
##FORMAT=<ID=ky,Type=String,Number=A,Description="FORMAT,Type=String,Number=A">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
C	87	.	NCNN	CCCTTTCTCNCAGGNA,ACGCCAGTAATCGCGCNNAAAATAAGT,GNTAT	.	.	.
C	251	vRIinp	GGAATGGNTNTNNTCCA	AA,CCGTNATNAA,GAG	.	.	Jw=0.0

Generate examples in unit tests:

from hypothesis import given
from hypothesis_vcf import vcf

@given(vcf_string=vcf())
def test_vcf(vcf_string):
    assert vcf_string.startswith("##fileformat=VCF")