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How to use get_test_variants method in avocado

Best Python code snippet using avocado_python

local_test.py

Source:local_test.py

...26    args = parser.parse_args()27    test_names = args.systemtest28    tests = []29    for test_name in test_names:30        tests += get_test_variants(test_name)31    tests = filter_tests(tests, args.dockerfile)32    # Checking for older docker containers33    lst2 = docker.get_containers()34    print (lst2)35    if lst2:36        print("Deleting following docker containers:", lst2)37        answer = input("\nOk? (yes/no)\n")38        if answer in ["yes", "y"]:39            for x in lst2:40                ccall("docker container rm -f " + x)41        else:42            print("BE CAREFUL!: Not deleting previous containers can later lead to problems.")43    # Building preCICE44    print("\n\nBuilding preCICE docker image with choosen branch\n\n")...

verify_variants.py

Source:verify_variants.py

...11parser.add_argument("-v", "--vcf", help="The vcf file")12args = parser.parse_args()13test_file = args.truth14vcf_file = args.vcf15def get_test_variants():16    """17    This function returns a tuple of a set of tuples of the test variants and the chromosome.18    :return: Set of tuples of (chrom, pos, ref alt, filter) and the chromosome19    :rtype: tuple of set and str20    """21    test_variant_set = set()22    chromosome = ''23    with open(test_file, 'r') as test_obj:24        for line in test_obj:25            if not re.search('^#', line):26                line_items = line.strip().split('\t')27                chrom = line_items[0]28                pos = line_items[1]29                ref = line_items[2]30                alt = line_items[3]31                vcf_filter = line_items[4]32                chromosome = chrom + '\t'33                var = (chrom, pos, ref, alt, vcf_filter)34                test_variant_set.add(var)35            else:36                continue37    return test_variant_set, chromosome38def get_vcf_variants(chromosome):39    """40    This function returns a set of variants with the specified chromosome from the VCF file.41    :param chromosome: The variants' chromosome42    :type chromosome: str43    :return: Set of tuples of (chrom, pos, ref alt, filter)44    :rtype: set45    """46    vcf_variant_set = set()47    with open(vcf_file, 'r') as vcf_obj:48        for line in vcf_obj:49            if re.search('^' + chromosome, line) and not re.search('^#', line):50                line_items = line.strip().split('\t')51                vcf_filter = line_items[6]52                if vcf_filter == 'PASS':53                    chrom = line_items[0]54                    pos = line_items[1]55                    ref = line_items[3]56                    alt = line_items[4]57                    var = (chrom, pos, ref, alt, vcf_filter)58                    vcf_variant_set.add(var)59                else:60                    continue61            else:62                continue63    return vcf_variant_set64########################################################################################################################65#66#   MAIN67#68########################################################################################################################69def main():70    """71    This is the main function.  It prints 'Pass' to the screen if the test variants are found in the VCF variants;72    otherwise, it prints 'Fail'.73    :rtype: void74    """75    test_variant_set, chromosome = get_test_variants()76    vcf_variant_set = get_vcf_variants(chromosome)77    print 'VCF File:', vcf_file.split('/')[-1]78    print 'Truth File:', test_file.split('/')[-1]79    if test_variant_set.issubset(vcf_variant_set):80        print 'Truth Set: ', test_variant_set81        print 'Intersect:', test_variant_set.intersection(vcf_variant_set)82        print 'Pass\n'83    else:84        print 'Truth Set: ', test_variant_set85        print 'Intersect:', test_variant_set.intersection(vcf_variant_set)86        print 'Fail\n'...

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