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<key>[^<#]+?)=(?P<val>[^<#]+$)''', re.M)
self.metadata = OrderedDict(comp.findall(self.raw_header))
# Contigs
self.contigs = OrderedDict(
list(
zip(
re.compile("##contig=<ID=(.*?),").findall(self.raw_header),
list(
map(
int,
re.compile("##contig.*length=([^,>]*?)>").findall(
self.raw_header))))))
self.info_set = [x for x in self.header_iter() if x.type == "INFO"]
self.filter_set = [x for x in self.header_iter() if x.type == "FILTER"]
self.format_set = [x for x in self.header_iter() if x.type == "FORMAT"]
self.header = copy(self.raw_header)
def __init__(self, filename, reference=None):
if not os.path.isfile(filename) and filename != "-":
exit(message("Error: " + filename + " does not exist"))
self.filename = filename
if reference:
self.reference = reference
self.reference_file = resolve_reference_genome(reference)
cyvcf2.__init__(self, self.filename)
# Check if file exists
self.n = len(self.samples) # Number of Samples
# Meta Data
comp = re.compile(r'''^##(?P<key>[^<#]+?)=(?P<val>[^<#]+$)''', re.M)
self.metadata = OrderedDict(comp.findall(self.raw_header))
# Contigs
self.contigs = OrderedDict(zip(
re.compile("##contig=<ID=(.*?),").findall(self.raw_header),
map(int, re.compile("##contig.*length=([^,>]*?)>").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"]
self.header = copy(self.raw_header)
def __init__(self,
filename,
reference=None,
use_template="ALT",
polymorphic=True):
if not filename.startswith("http") and not os.path.isfile(
filename) and filename != "-":
exit(message(f"Error: {filename} does not exist", color='red'))
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<key>[^<#]+?)=(?P<val>[^<#]+$)''', re.M)
self.metadata = OrderedDict(comp.findall(self.raw_header))
# Contigs
self.contigs = OrderedDict(
list(
zip(
re.compile("##contig=<ID=(.*?),").findall(self.raw_header),
list(
map(
int,
re.compile("##contig.*length=(.*?)>").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"]
self.header = copy(self.raw_header)
# Make sure index exists for this VCF.
if not self.filename.startswith("http") and not os.path.isfile(
self.filename + ".csi"):
message("VCF is not indexed; Indexing.")
comm = "bcftools index {f}".format(f=self.filename)
out = check_output(comm, shell=True)
message(out.decode("utf-8"))
# Setup use_template
if self.use_template not in self.samples + ["REF", "ALT"]:
exit(message(self.use_template + " use_template not found."))
def __init__(self, *args, **kwargs):
from cyvcf2 import VCF
VCF.__init__(self, *args, **kwargs, strict_gt=True)
self.sample_mapping = dict(zip(self.samples, range(len(self.samples))))
