本文整理匯總了Python中svtools.vcf.file.Vcf.add_format方法的典型用法代碼示例。如果您正苦於以下問題：Python Vcf.add_format方法的具體用法？Python Vcf.add_format怎麽用？Python Vcf.add_format使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類svtools.vcf.file.Vcf的用法示例。
在下文中一共展示了Vcf.add_format方法的2個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: write_copynumber
# 需要導入模塊: from svtools.vcf.file import Vcf [as 別名]
# 或者: from svtools.vcf.file.Vcf import add_format [as 別名]
def write_copynumber(vcf_file, sample, vcf_out, cn_list):
#go through the VCF and add the read depth annotations
in_header = True
header = []
vcf = Vcf()
i = 0
s_index = -1
for line in vcf_file:
if in_header:
if line[0] == '#' and line[1] == '#':
header.append(line)
continue
if line[0] == '#' and line[1] != '#':
try:
s_index = line.rstrip().split('\t').index(sample)
except ValueError:
sys.stderr.write("Please input valid VCF, format field for " + sample + " not found in VCF")
sys.exit(1)
line = '\t'.join(map(str, line.rstrip().split('\t')[:9] + [sample]))
header.append(line)
continue
else:
in_header = False
vcf.add_header(header)
vcf.add_format('CN', 1, 'Float', 'Copy number of structural variant segment.')
vcf_out.write(vcf.get_header() + '\n')
v = line.rstrip().split('\t')
# XXX Is this second check necessary? Wouldn't this be handled above? Missing header would hit this?
if s_index == -1:
sys.stderr.write("Input a valid sample name: " + sample + " not found in a provided VCF")
sys.exit(1)
v = v[:9] + [v[s_index]]
if not any("SVTYPE=BND" in s for s in v):
if "CN" not in v[8]:
v[8] = v[8] + ":CN"
v[9] = v[9] + ":" + str(cn_list[i])
else:
cn_index = v[8].rstrip().split(":").index("CN")
gts = v[9].rstrip().split(":")
gts[cn_index] = str(cn_list[i])
v[9] = ":".join(gts)
i += 1
# write the VCF
vcf_out.write('\t'.join(v) + '\n')
vcf_out.close()
return示例2: run_gt_refine
# 需要導入模塊: from svtools.vcf.file import Vcf [as 別名]
# 或者: from svtools.vcf.file.Vcf import add_format [as 別名]
def run_gt_refine(vcf_in, vcf_out, diag_outfile, gender_file, exclude_file):
vcf = Vcf()
header = []
in_header = True
sex={}
for line in gender_file:
v = line.rstrip().split('\t')
sex[v[0]] = int(v[1])
exclude = []
if exclude_file is not None:
for line in exclude_file:
exclude.append(line.rstrip())
outf=open(diag_outfile, 'w', 4096)
ct=1
for line in vcf_in:
if in_header:
if line[0] == "#":
header.append(line)
continue
else:
in_header = False
vcf.add_header(header)
vcf.add_info('MEDGQR', '1', 'Float', 'Median quality for refined GT')
vcf.add_info('Q10GQR', '1', 'Float', 'Q10 quality for refined GT')
vcf.add_format('GQR', 1, 'Float', 'Quality of refined genotype.')
vcf.add_format('GTR', 1, 'String', 'Refined genotype.')
vcf_out.write(vcf.get_header() + '\n')
v = line.rstrip().split('\t')
info = v[7].split(';')
svtype = None
for x in info:
if x.startswith('SVTYPE='):
svtype = x.split('=')[1]
break
# bail if not DEL or DUP prior to reclassification
if svtype not in ['DEL']:
vcf_out.write(line)
continue
var = Variant(v, vcf)
sys.stderr.write("%s\n" % var.var_id)
sys.stderr.write("%f\n" % float(var.get_info('AF')))
if float(var.get_info('AF'))<0.01:
vcf_out.write(line)
else:
df=load_df(var, exclude, sex)
recdf=recluster(df)
if ct==1:
recdf.to_csv(outf, header=True)
ct += 1
else:
recdf.to_csv(outf, header=False)
var.set_info("MEDGQR", '{:.2f}'.format(recdf.iloc[0,:].loc['med_gq_re']))
var.set_info("Q10GQR", '{:.2f}'.format(recdf.iloc[0,:].loc['q10_gq_re']))
recdf.set_index('sample', inplace=True)
for s in var.sample_list:
if s in recdf.index:
var.genotype(s).set_format("GTR", recdf.loc[s,'GTR'])
var.genotype(s).set_format("GQR", '{:.2f}'.format(recdf.loc[s,'gq_re']))
else:
var.genotype(s).set_format("GTR", "./.")
var.genotype(s).set_format("GQR", 0)
vcf_out.write(var.get_var_string(use_cached_gt_string=False) + '\n')
vcf_out.close()
vcf_in.close()
gender_file.close()
outf.close()
if exclude_file is not None:
exclude_file.close()
return