How to use the cyvcf2.VCF.__init__ function in cyvcf2
To help you get started, we’ve selected a few cyvcf2 examples, based on popular ways it is used in public projects.
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AndersenLab / VCF-kit / vcfkit / utils / vcf.py View on Github 
def __init__(self, filename, reference=None):
if not os.path.isfile(filename) and filename != "-":
exit(message("Error: " + filename + " does not exist"))
self.filename = filename
if reference:
self.reference = reference
self.reference_file = resolve_reference_genome(reference)
cyvcf2.__init__(self, self.filename)
# Check if file exists
self.n = len(self.samples) # Number of Samples
# Meta Data
comp = re.compile(r'''^##(?P[^<#]+?)=(?P[^<#]+$)''', re.M)
self.metadata = OrderedDict(comp.findall(self.raw_header))
# Contigs
self.contigs = OrderedDict(zip(
re.compile("##contig=]*?)>").findall(self.raw_header))
))
self.info_set = [x for x in self.header_iter() if x.type == "INFO"]
self.filter_set = [x for x in self.header_iter() if x.type == "FILTER"]
self.format_set = [x for x in self.header_iter() if x.type == "FORMAT"]def __init__(self, filename, reference=None, use_template="ALT", polymorphic=True):
if not os.path.isfile(filename) and filename != "-":
exit(message("Error: " + filename + " does not exist"))
self.filename = filename
self.use_template = use_template
self.use_polymorphic = polymorphic
if reference:
self.reference = reference
self.reference_file = resolve_reference_genome(reference)
cyvcf2.__init__(self, self.filename)
# Check if file exists
self.n = len(self.samples) # Number of Samples
# Meta Data
comp = re.compile(r'''^##(?P[^<#]+?)=(?P[^<#]+$)''', re.M)
self.metadata = OrderedDict(comp.findall(self.raw_header))
# Contigs
self.contigs = OrderedDict(zip(
re.compile("##contig=").findall(self.raw_header))
))
self.info_set = [x for x in self.header_iter() if x.type == "INFO"]
self.filter_set = [x for x in self.header_iter() if x.type == "FILTER"]
self.format_set = [x for x in self.header_iter() if x.type == "FORMAT"]def __init__(self, filename, reference=None):
if not os.path.isfile(filename) and filename != "-":
with indent(4):
exit(puts(colored.red("\nError: " + filename + " does not exist\n")))
self.filename = filename
if reference:
self.reference = reference
cyvcf2.__init__(self, self.filename)
# Check if file exists
self.n = len(self.samples) # Number of Samples
# Meta Data
comp = re.compile(r'''^##(?P[^<#]+?)=(?P[^<#]+$)''', re.M)
self.metadata = OrderedDict(comp.findall(self.raw_header))
# Contigs
self.contigs = OrderedDict(zip(
re.compile("##contig=").findall(self.raw_header))
))
# Info
r = re.compile(r'''\#\#INFO=<
ID=(?P[^,]+),
Number=(?P-?\d+|\.|[AG]),def __init__(self, filename, reference=None):
if not os.path.isfile(filename) and filename != "-":
with indent(4):
exit(puts(colored.red("\nError: " + filename + " does not exist\n")))
self.filename = filename
if reference:
self.reference = reference
self.reference_file = resolve_reference_genome(reference)
cyvcf2.__init__(self, self.filename)
# Check if file exists
self.n = len(self.samples) # Number of Samples
# Meta Data
comp = re.compile(r'''^##(?P[^<#]+?)=(?P[^<#]+$)''', re.M)
self.metadata = OrderedDict(comp.findall(self.raw_header))
# Contigs
self.contigs = OrderedDict(zip(
re.compile("##contig=").findall(self.raw_header))
))
self.info_set = [x for x in self.header_iter() if x.type == "INFO"]
self.filter_set = [x for x in self.header_iter() if x.type == "FILTER"]
self.format_set = [x for x in self.header_iter() if x.type == "FORMAT"]
