genomicassertions

genomicassertions

genomicassertions is a python package which adds methods to test commonly generated files in the genomics field.

Installation

pip install genomicassertions

Examples

Use the VariantAssertions or ReadAssertions mixin in your test class to get access to the methods.

VCF files

For VCF files, the following methods exist:

• assertVcfHasVariantAt(vcf, chrom, pos)
• assertVcfHasSample(vcf, sample)
• assertVcfHasVariantWithChromPosRefAlt(vcf, chrom, pos, ref, alt)
• assertVcfHasVariantWithChromPosId(vcf, chrom, pos, variant_id)
• assertVcfHasVariantWithCall(vcf, chrom, pos, sample, call)

BAM files

• assertBamHasCoverageAt(self, bam, coverage, chrom, pos)
• assertBamHasHeaderElement(self, bam, header_element)
• assertBamHeaderElementEquals(self, bam, header_element_name, header_element_value)

Examples

VCF files

from genomicassertions.variantassertions import VariantAssertions

class TestVariants(unittest.TestCase, VariantAssertions):
    vcf = "tests/variants.vcf.gz"
    vcf_with_genotypes = "tests/variants-with-genotypes.vcf.gz"

    def test_variant_at(self):
        self.assertVcfHasVariantAt(self.vcf, 3, 178936091)

    def test_variant_with_chrom_pos_ref_alt(self):
        self.assertVcfHasVariantWithChromPosRefAlt(self.vcf_with_genotypes, 1, 3062915, 'G', 'C')
        self.assertVcfHasVariantWithChromPosRefAlt(self.vcf_with_genotypes, 1, 3062915, 'G', 'T')

    def test_variant_with_id(self):
        self.assertVcfHasVariantWithChromPosId(self.vcf_with_genotypes, 1, 3062915, 'id3D')

assertVcfHasVariantWithCall() asserts that individual items in a sample call are set. The parameter call is a dict with the items to test. The dict does not have to be complete, i.e. not all fields in the call have to be tested.

    def test_vcf_has_variant_with_call(self):
        self.assertVcfHasVariantWithCall(self.vcf_with_genotypes, 1, 3184885, 'B',
                                         call={'GT': '1/2', 'DP': 10})

BAM files

from genomicassertions.readassertions import ReadAssertions

class TestReads(unittest.TestCase, ReadAssertions):
    bam = "tests/3_178936091.bam"

    # assert coverage as chrom:pos
    def test_has_coverage_as_pos(self):
        self.assertBamHasCoverageAt(self.bam, coverage=324, chrom=3, pos=178936091)

    def test_bam_has_header_element(self):
        self.assertBamHasHeaderElement(self.bam, header_element="HD")

    def test_header_element_equals(self):
        self.assertBamHeaderElementEquals(self.bam,
                                          header_element_name='HD',
                                          header_element_value={'SO': 'coordinate',
                                                                'VN': '1.3'}
                                          )

File requirements

genomicassertions requires the vcf files to be compressed with bgzip and indexed with tabix in order to work. This is required for the random access to variants provided by the index, which gives a significant performance increase over using non-indexed vcf files. Bam files have to be indexed.