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        "author": "Daniel Klevebring",
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        "description": "# genomicassertions\n\n[![Build Status](https://travis-ci.org/dakl/genomicassertions.svg?branch=master)](https://travis-ci.org/dakl/genomicassertions)\n[![Coverage Status](https://coveralls.io/repos/github/dakl/genomicassertions/badge.svg?branch=master)](https://coveralls.io/github/dakl/genomicassertions?branch=master)\n[![PyPI version](https://badge.fury.io/py/genomicassertions.svg)](https://badge.fury.io/py/genomicassertions)\n\n`genomicassertions` is a python package which adds methods to test commonly generated files in the genomics field.\n\n# Installation\n\n`pip install genomicassertions`\n\n# Examples\n\nUse the `VariantAssertions` or `ReadAssertions` mixin in your test class to get access to the methods.\n\n## VCF files\n\nFor VCF files, the following methods exist:\n\n* `assertVcfHasVariantAt(vcf, chrom, pos)`\n* `assertVcfHasSample(vcf, sample)`\n* `assertVcfHasVariantWithChromPosRefAlt(vcf, chrom, pos, ref, alt)`\n* `assertVcfHasVariantWithChromPosId(vcf, chrom, pos, variant_id)`\n* `assertVcfHasVariantWithCall(vcf, chrom, pos, sample, call)`\n\n## BAM files\n\n* `assertBamHasCoverageAt(self, bam, coverage, chrom, pos)`\n* `assertBamHasHeaderElement(self, bam, header_element)`\n* `assertBamHeaderElementEquals(self, bam, header_element_name, header_element_value)`\n\n### Examples\n\n#### VCF files\n~~~python\nfrom genomicassertions.variantassertions import VariantAssertions\n\nclass TestVariants(unittest.TestCase, VariantAssertions):\n    vcf = \"tests/variants.vcf.gz\"\n    vcf_with_genotypes = \"tests/variants-with-genotypes.vcf.gz\"\n\n    def test_variant_at(self):\n        self.assertVcfHasVariantAt(self.vcf, 3, 178936091)\n\n    def test_variant_with_chrom_pos_ref_alt(self):\n        self.assertVcfHasVariantWithChromPosRefAlt(self.vcf_with_genotypes, 1, 3062915, 'G', 'C')\n        self.assertVcfHasVariantWithChromPosRefAlt(self.vcf_with_genotypes, 1, 3062915, 'G', 'T')\n\n    def test_variant_with_id(self):\n        self.assertVcfHasVariantWithChromPosId(self.vcf_with_genotypes, 1, 3062915, 'id3D')\n\n~~~\n\n`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.\n\n~~~python    \n    def test_vcf_has_variant_with_call(self):\n        self.assertVcfHasVariantWithCall(self.vcf_with_genotypes, 1, 3184885, 'B',\n                                         call={'GT': '1/2', 'DP': 10})\n~~~\n\n#### BAM files\n\n~~~python\nfrom genomicassertions.readassertions import ReadAssertions\n\nclass TestReads(unittest.TestCase, ReadAssertions):\n    bam = \"tests/3_178936091.bam\"\n\n    # assert coverage as chrom:pos\n    def test_has_coverage_as_pos(self):\n        self.assertBamHasCoverageAt(self.bam, coverage=324, chrom=3, pos=178936091)\n\n    def test_bam_has_header_element(self):\n        self.assertBamHasHeaderElement(self.bam, header_element=\"HD\")\n\n    def test_header_element_equals(self):\n        self.assertBamHeaderElementEquals(self.bam,\n                                          header_element_name='HD',\n                                          header_element_value={'SO': 'coordinate',\n                                                                'VN': '1.3'}\n                                          )\n~~~\n\n\n# File requirements\n\n`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.\n",
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