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How to use merge_family method in Pytest

Best Python code snippet using pytest

junitxml.py

Source:junitxml.py

...48            return u"#x%02X" % i49        else:50            return u"#x%04X" % i51    return py.xml.raw(illegal_xml_re.sub(repl, py.xml.escape(arg)))52def merge_family(left, right):53    result = {}54    for kl, vl in left.items():55        for kr, vr in right.items():56            if not isinstance(vl, list):57                raise TypeError(type(vl))58            result[kl] = vl + vr59    left.update(result)60families = {}61families["_base"] = {"testcase": ["classname", "name"]}62families["_base_legacy"] = {"testcase": ["file", "line", "url"]}63# xUnit 1.x inherits legacy attributes64families["xunit1"] = families["_base"].copy()65merge_family(families["xunit1"], families["_base_legacy"])66# xUnit 2.x uses strict base attributes67families["xunit2"] = families["_base"]68class _NodeReporter(object):69    def __init__(self, nodeid, xml):70        self.id = nodeid71        self.xml = xml72        self.add_stats = self.xml.add_stats73        self.family = self.xml.family74        self.duration = 075        self.properties = []76        self.nodes = []77        self.testcase = None78        self.attrs = {}79    def append(self, node):...

main.py

Source:main.py

1import os2import argparse3IS_HIC=False4def execute_cmd(cmd):5    print("Info: ", cmd)6    os.system(cmd)7def bgzip_and_index(vcf, bgzip, tabix):8    bgzip_cmd = "{} -f {}".format(bgzip, vcf)9    tabix_cmd = "{} -f {}".format(tabix, vcf+".gz")10    execute_cmd(bgzip_cmd)11    execute_cmd(tabix_cmd)12    return vcf+".gz"13def bgunzip(vcf):14    if "gz" in vcf:15        unzip_cmd = "gunzip {}".format(vcf)16        execute_cmd(unzip_cmd)17        return vcf.replace(".gz","")18    else:19        return vcf20def sc_file(d,df):21    # f_name = f.split("/")[-1]22    ds = os.path.join(d, df)23    # mv_cmd = "mv {} {}".format(f,ds)24    # execute_cmd(mv_cmd)25    return ds26def i_phase(spechap,extract,bgzip,tabix,bam, vcf, out_dir, name, ref):27    vcf = bgunzip(vcf)28    lst_out = os.path.join(out_dir, name+".lst")29    lst_sorted_out = os.path.join(out_dir, name+".sorted.lst")30    phased_vcf = os.path.join(out_dir, name+".phased.vcf")31    sort_cmd = "sort -n -k6 {} > {}".format(lst_out,lst_sorted_out)32    if IS_HIC:33        e_cmd = "{} --vcf {} --bam {} -o {} --ref {} --hic 1 --maxfragments 300000000".format(extract, vcf, bam, lst_out, ref)34        execute_cmd(e_cmd)35        vcf = bgzip_and_index(vcf, bgzip, tabix)36        execute_cmd(sort_cmd)37        s_cmd = "{} -f {} -v {} -o {} --hic".format(spechap, lst_sorted_out, vcf, phased_vcf)38        execute_cmd(s_cmd)39    else:40        e_cmd = "{} --vcf {} --bam {} -o {} --ref {}".format(extract, vcf, bam, lst_out, ref)41        execute_cmd(e_cmd)42        vcf = bgzip_and_index(vcf, bgzip, tabix)43        execute_cmd(sort_cmd)44        s_cmd = "{} -f {} -v {} -o {}".format(spechap, lst_sorted_out, vcf, phased_vcf)45        execute_cmd(s_cmd)46    # execute_cmd(e_cmd)47    # execute_cmd(sort_cmd)48    # execute_cmd(s_cmd)49    return phased_vcf50def e_lst(extract, bams, vcf, out_dir, name, ref):51    lst_a = ""52    lst_l = os.path.join(out_dir,name+".all.lst")53    lst_l_sorted = os.path.join(out_dir,name+".all.sorted.lst")54    for i in range(len(bams)):55        b = bams[i]56        lst = os.path.join(out_dir, name+".tmp"+str(i)+".lst")57        e_cmd = "{} --vcf {} --bam {} -o {} --ref {}".format(extract, vcf, b, lst,ref)58        if IS_HIC:59            e_cmd = "{} --vcf {} --bam {} -o {} --ref {} --hic 1 --maxfragments 300000000".format(extract, vcf, b, lst,ref)60        lst_a = lst_a+" "+lst61        execute_cmd(e_cmd)62    cat_cmd = "cat {} > {}".format(lst_a, lst_l)63    sort_cmd = "sort -n -k6 {} > {}".format(lst_l,lst_l_sorted)64    execute_cmd(cat_cmd)65    execute_cmd(sort_cmd)66    return lst_l_sorted67def phase_with_lst(spechap, lst, vcf, out_file, bgzip, tabix):68    vcf = bgzip_and_index(vcf,bgzip,tabix)69    s_cmd = "{} -f {} -v {} -o {} --keep_phasing_info".format(spechap, lst, vcf, out_file)70    if IS_HIC:71        s_cmd = "{} -f {} -v {} -o {} --keep_phasing_info --hic".format(spechap, lst, vcf, out_file)72    execute_cmd(s_cmd)73    bgzip_and_index(out_file,bgzip,tabix)74    return out_file+".gz"75def extract_hete(vcf,out, bcftools):76    out_vcf = os.path.join(out,vcf.split("/")[-1].replace(".vcf",".hete.vcf").replace(".bcf",".hete.vcf").replace(".gz",""))77    cmd = "{} view -g het {} > {}".format(bcftools,vcf,out_vcf)78    execute_cmd(cmd)79    return out_vcf80def main():81    parser = argparse.ArgumentParser("trio phase")82    parser.add_argument(83        '--father_v', help='Father VCF file not in gz format', required=False)84    parser.add_argument(85        '--mother_v', help='Mother VCF file not in gz format', required=False)86    parser.add_argument(87        '--child_v', help='Child VCF file not in gz format', required=True)88    parser.add_argument(89        '--father_b', help='Father bam file indexed', required=False)90    parser.add_argument(91        '--mother_b', help='Mother bam file indexed', required=False)92    parser.add_argument(93        '--child_b', help='Child bam file indexed', required=True)94    parser.add_argument(95        '--spechap', help='spechap path', required=True)96    parser.add_argument(97        '--extractHairs', help='extractHairs path', required=True)98    parser.add_argument(99        '--bgzip', help='bgzip path', required=True)100    parser.add_argument(101        '--tabix', help='tabix path', required=True)102    parser.add_argument(103        '--bcftools', help='bcftools path', required=True)104    parser.add_argument('-o', '--out_dir', help='Out dir', required=True)105    parser.add_argument('--ref', help='reference', required=True)106    parser.add_argument('--data_type', help='Data type: hic, ngs, ', required=False, default="ngs")107    parser.add_argument(108        '--step', help='which step', required=False)109    parser.add_argument(110        '--hic', help='Is hic data',action='store_true', required=False, default=False)111    parser.add_argument(112        '--script_root', help='script root', required=True)113    args = parser.parse_args()114    IS_HIC = args.hic115    if not os.path.exists(args.out_dir):116        os.mkdir(args.out_dir)117    if args.step == "2":118        print("skip individual phase")119        m_phased_v1= bgunzip(args.mother_v)120        f_phased_v1= bgunzip(args.father_v)121        c_phased_v1= bgunzip(args.child_v)122        c_phased_v2 = sc_file(args.out_dir,"child.vcf")123        m_phased_v2 = sc_file(args.out_dir,"mother.vcf")124        f_phased_v2 = sc_file(args.out_dir,"father.vcf")125    else:126        print("extract hete..")127        if args.mother_v:128            m_hete = extract_hete(args.mother_v,args.out_dir,args.bcftools)129        if args.father_v:130            f_hete = extract_hete(args.father_v,args.out_dir,args.bcftools)131        if args.child_v:132            c_hete = extract_hete(args.child_v,args.out_dir,args.bcftools)133        print("individual phase..")134        m_phased_v1=""135        f_phased_v1=""136        c_phased_v1 = i_phase(args.spechap, args.extractHairs, args.bgzip, args.tabix, args.child_b, c_hete, args.out_dir, "child", args.ref)137        if args.mother_v and args.mother_b:138            m_phased_v1 = i_phase(args.spechap, args.extractHairs,args.bgzip, args.tabix, args.mother_b, m_hete, args.out_dir, "mother", args.ref)139        if args.father_v and args.father_b:140            f_phased_v1 = i_phase(args.spechap, args.extractHairs,args.bgzip, args.tabix, args.father_b, f_hete, args.out_dir, "father", args.ref)141        c_phased_v2 = c_phased_v1+".trio.vcf"142        m_phased_v2 = m_phased_v1+".trio.vcf"143        f_phased_v2 = f_phased_v1+".trio.vcf"144    # print("Raw phase with only vcf")145    # raw_cmd = ""146    # if not args.mother_v:147    #     raw_cmd = "python merge_family.py -f {} -c {} -o {}".format(f_phased_v1, c_phased_v1, args.out_dir)148    # if not args.father_v:149    #     raw_cmd = "python merge_family.py -m {} -c {} -o {}".format(m_phased_v1, c_phased_v1, args.out_dir)150    # else:151    #     raw_cmd = "python merge_family.py -m {} -f {} -c {} -o {}".format(m_phased_v1, f_phased_v1, c_phased_v1, args.out_dir)152    # if execute_cmd(raw_cmd):153    #     print(raw_cmd,"running error")154    #     exit155    print("phasing child ...")156    bams = []157    if args.mother_b:158        bams.append(args.mother_b)159    if args.father_b:160        bams.append(args.father_b)161    c_lst = e_lst(args.extractHairs, bams, c_phased_v1, args.out_dir, "child", args.ref)162    c_out = phase_with_lst(args.spechap, c_lst, c_phased_v1, c_phased_v2, args.bgzip, args.tabix)163    print("phasing parent...")164    if args.mother_b and args.mother_v:165        bams = [args.child_b]166        m_lst = e_lst(args.extractHairs, bams, m_phased_v1, args.out_dir, "mother", args.ref)167        m_out = phase_with_lst(args.spechap, m_lst, m_phased_v1, m_phased_v2, args.bgzip, args.tabix)168    if args.father_b and args.father_v:169        bams = [args.child_b]170        f_lst = e_lst(args.extractHairs, bams, f_phased_v1, args.out_dir, "father", args.ref)171        f_out = phase_with_lst(args.spechap, f_lst, f_phased_v1, f_phased_v2, args.bgzip, args.tabix)172    print("Reflect...")173    m_re = os.path.join(args.out_dir,'mother.reflect.vcf')174    f_re = os.path.join(args.out_dir,'father.reflect.vcf')175    c_re = os.path.join(args.out_dir,'child.reflect.vcf')176    if args.mother_v:177        re_cmd = "python {}/reflect_back.py --hete {} --orig {} --out {}".format(args.script_root,m_phased_v2+".gz",args.mother_v, m_re)178        execute_cmd(re_cmd)179    if args.father_v:180        re_cmd = "python {}/reflect_back.py --hete {} --orig {} --out {}".format(args.script_root,f_phased_v2+".gz",args.father_v, f_re)181        execute_cmd(re_cmd)182    if args.child_v:183        re_cmd = "python {}/reflect_back.py --hete {} --orig {} --out {}".format(args.script_root,c_phased_v2+".gz",args.child_v, c_re)184        execute_cmd(re_cmd)185    print("Phase with only vcf")186    m_re_gz = bgzip_and_index(m_re, args.bgzip, args.tabix)187    f_re_gz = bgzip_and_index(f_re, args.bgzip, args.tabix)188    c_re_gz = bgzip_and_index(c_re, args.bgzip, args.tabix)189    if not args.mother_v:190        raw_cmd = "python {}/merge_family.py -f {} -c {} -o {}".format(args.script_root,f_re_gz, c_re_gz, args.out_dir)191    if not args.father_v:192        raw_cmd = "python {}/merge_family.py -m {} -c {} -o {}".format(args.script_root,m_re_gz, c_re_gz, args.out_dir)193    else:194        raw_cmd = "python {}/merge_family.py -m {} -f {} -c {} -o {}".format(args.script_root,m_re_gz, f_re_gz, c_re_gz, args.out_dir)195    if execute_cmd(raw_cmd):196        print(raw_cmd,"running error")197        exit198if __name__ == "__main__":...

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