<filename>tests/test_parser_parse_header.py<gh_stars>0
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
# Created by <NAME>
"""Test parsing of full VCF header
"""

import io
import sys

import pytest

from vcfpy2 import parser

__author__ = "<NAME> <<EMAIL>>"

MEDIUM_HEADER = """
##fileformat=VCFv4.3
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003
""".lstrip()


@pytest.fixture(scope="function")
def medium_header():
    return io.StringIO(MEDIUM_HEADER)


def test_parse_header(medium_header):
    p = parser.Parser(stream=medium_header, path="<builtin>")
    header = p.parse_header()
    assert header.lines
    assert len(header.lines) == 18
    EXPECTED = "HeaderLine('fileformat', 'VCFv4.3')"
    assert str(header.lines[0]) == EXPECTED
    if sys.version_info < (3, 6):
        EXPECTED = (
            "FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,"
            "Description=\"Haplotype Quality\">', OrderedDict([('ID', 'HQ'), "
            "('Number', 2), ('Type', 'Integer'), ('Description', "
            "'Haplotype Quality')]))"
        )
    else:
        EXPECTED = (
            "FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,Description=\"Haplotype Quality\">', "
            "{'ID': 'HQ', 'Number': 2, 'Type': 'Integer', 'Description': 'Haplotype Quality'})"
        )
    assert str(header.lines[-1]) == EXPECTED
    assert header.samples.names == ["NA00001", "NA00002", "NA00003"]

<filename>tests/test_parser_parse_header.py<gh_stars>0
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
# Created by <NAME>
"""Test parsing of full VCF header
"""

import io
import sys

import pytest

from vcfpy2 import parser

__author__ = "<NAME> <<EMAIL>>"

MEDIUM_HEADER = """
##fileformat=VCFv4.3
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003
""".lstrip()


@pytest.fixture(scope="function")
def medium_header():
    return io.StringIO(MEDIUM_HEADER)


def test_parse_header(medium_header):
    p = parser.Parser(stream=medium_header, path="<builtin>")
    header = p.parse_header()
    assert header.lines
    assert len(header.lines) == 18
    EXPECTED = "HeaderLine('fileformat', 'VCFv4.3')"
    assert str(header.lines[0]) == EXPECTED
    if sys.version_info < (3, 6):
        EXPECTED = (
            "FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,"
            "Description=\"Haplotype Quality\">', OrderedDict([('ID', 'HQ'), "
            "('Number', 2), ('Type', 'Integer'), ('Description', "
            "'Haplotype Quality')]))"
        )
    else:
        EXPECTED = (
            "FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,Description=\"Haplotype Quality\">', "
            "{'ID': 'HQ', 'Number': 2, 'Type': 'Integer', 'Description': 'Haplotype Quality'})"
        )
    assert str(header.lines[-1]) == EXPECTED
    assert header.samples.names == ["NA00001", "NA00002", "NA00003"]

#!/usr/bin/env python # -*- coding: UTF-8 -*- # Created by <NAME> Test parsing of full VCF header ##fileformat=VCFv4.3 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta ##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x> ##phasing=partial ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> ##FILTER=<ID=q10,Description="Quality below 10"> ##FILTER=<ID=s50,Description="Less than 50% of samples have data"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003