def getMthaologroupResult(slugfilename):
# 芯片数据
sdata = snp.reader_dict_mtpos(slugfilename)
# 存储运算结果
result = {"0": {'matchrsid': None, 'nomathrsid': None, 'weight': 0, 'name': None,'lain':0,'mandn':0}}
#
getMthaologroup(mttree, sdata, result)
return result
def main_2m_n(filename):
#更新位置信息
#update23andmeFilePos(filename)
sdata = snp.reader_dict_mtpos(filename)
#所有命中snp的权重和
weightTree = getTotalWeightTree(sdata, weightdict, mttree)
if weightTree > 0:
getMthaologroupPath(sdata, weightTree)
else:
print('请检查文件')
return retreepath
def getFormatYhaologroupPath(treepath):
re = []
for item in treepath:
for k, v in item.items():
re.append(k)
return re
if __name__ == "__main__":
filename = filename = '/Users/similarface/Documents/user2643_file1659_yearofbirth_unknown_sex_XY.23andme.txt'
if len(sys.argv) != 1:
print("param error!", "Use: python mthaplogroup andmefile")
else:
filename = filename = '/Users/similarface/Documents/user2643_file1659_yearofbirth_unknown_sex_XY.23andme.txt'
#更新位置信息
#update23andmeFilePos(filename)
loggername = os.path.basename(
filename)[0:os.path.basename(filename).rindex('.')]
logger = logging.getLogger(loggername) # 获取名为tst的logger
logger.addHandler(handler) # 为logger添加handler
logger.setLevel(logging.DEBUG)
sdata = snp.reader_dict_mtpos(filename)
#所有命中snp的权重和
weightTree = getTotalWeightTree(sdata, weightdict, mttree)
if weightTree > 0:
getMthaologroupPath(sdata, weightTree)
else:
print('请检查文件')
weightdict = getWeightDict()
redirecttree = getDictFromFile()
for k, v in redirecttree.items():
rsids = v['pos']
if len(rsids) != 0:
for rsid in rsids:
try:
if rsid[-1] == sdata[rsid[1:-1]].genotype[0]:
weightTree = weightTree + weightdict[rsid]
except Exception, e:
pass
return weightTree
weightTree = getTotalWeightTree(
snp.reader_dict_mtpos('/Users/similarface/wocao.txt'))
def getMthaologroup(mttree, sdata, result):
'''
:param ytree: Y染色体的haplogroup树
:param ysnp: Y染色体突变字典
:param sdata: 芯片数据
:param result: 结果
:return:
'''
id = mttree['id']
pid = mttree['pid']
name = mttree['name']
children = mttree['children']
#filename='/Users/similarface/Documents/reslut1/genome_wang_mian_Full_20151021231213.txt'
filename = '/Users/similarface/wocao.txt'
#filename='/Users/similarface/Documents/user10_file3_yearofbirth_1982_sex_XY.23andme.txt'
#filename='/Users/similarface/Documents/user2099_file1272_yearofbirth_unknown_sex_unknown.23andme.txt'
#filename=sys.argv[1]
#sample 02 -->争议
#N 1785 H3 T2e1a1a
#filename = '/Users/similarface/Documents/user1785_file1041_yearofbirth_unknown_sex_unknown.23andme.txt'
#filename = '/Users/similarface/Downloads/11.23andme.176'
#sample 03 -->
#N 1875 HV9a T2e1a1a
#filename = '/Users/similarface/Documents/user1875_file1113_yearofbirth_unknown_sex_unknown.23andme.txt'
weightTree = getTotalWeightTree(snp.reader_dict_mtpos(filename))
print(weightTree)
loggername = os.path.basename(
filename)[0:os.path.basename(filename).rindex('.')]
logger = logging.getLogger(loggername) # 获取名为tst的logger
logger.addHandler(handler) # 为logger添加handler
logger.setLevel(logging.DEBUG)
# for file in ['/Users/similarface/Documents/reslut1/genome_wang_mian_Full_20151021231213.txt',
# '/Users/similarface/Documents/reslut1/genome_wang_jun_chen_Full_20151021231123.txt',
# '/Users/similarface/Downloads/I2b1.txt',
# '/Users/similarface/Downloads/H6a1b2.txt',
# '/Users/similarface/Downloads/1718.23andme.993',
# '/Users/similarface/Downloads/1718.23andme.993',
# '/Users/similarface/Downloads/4763.23andme.3353',
# '/Users/similarface/Downloads/T',