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# Author: Lance Hepler
from __future__ import absolute_import
from __future__ import print_function
"""
I/O support for VCF4 files.
The specification for the VCF4 format is available at:
https://samtools.github.io/hts-specs
"""
from collections import OrderedDict
from functools import total_ordering
__all__ = ["Vcf4Record"]
def _int_float_or_string(s):
try:
return int(s)
except ValueError:
pass
try:
return float(s)
except ValueError:
pass
return str(s)
def _fmt(x):
if isinstance(x, float):
return "{0:.3g}".format(x)
return x
def _empty_then(xs):
if not xs:
return
yield ""
for x in xs:
yield x
@total_ordering
class Vcf4Record(object):
"""
Class for VCF record, providing uniform access to standard
VCF fields and attributes.
.. doctest::
>>> from pbcore.io import Vcf4Record
>>> rec1 = Vcf4Record("ecoliK12_pbi_March2013", \
84, ".", "TG", "T", 48, "PASS", [("DP", 53)])
>>> str(rec1)
'ecoliK12_pbi_March2013\\t84\\t.\\tTG\\tT\\t48\\tPASS\\tDP=53'
>>> rec2 = Vcf4Record.fromString(str(rec1))
>>> rec1 == rec2
True
>>> rec1.pos
84
>>> rec1.filter
'PASS'
"""
__slots__ = ("chrom", "pos", "id", "ref", "alt", "qual", "filter", "info", "fields")
def __init__(self, chrom, pos, id, ref, alt, qual, filt, info, *fields):
self.chrom = chrom
self.pos = pos
self.id = id
self.ref = ref
self.alt = alt
self.qual = qual
self.filter = filt
self.info = OrderedDict(info)
self.fields = fields
@staticmethod
def fromString(s):
try:
fields = s.strip().split('\t')
fields[1] = int(fields[1])
fields[5] = _int_float_or_string(fields[5])
fields[7] = OrderedDict((k.strip(), _int_float_or_string(v.strip()))
for k, v in (x.strip().split('=')
for x in fields[7].split(';')))
return Vcf4Record(*fields)
except TypeError:
raise ValueError("Could not interpret string as a Vcf4Record: '{0}'".format(s))
def __lt__(self, other):
return (self.chrom, self.pos) < (other.chrom, other.pos)
def __eq__(self, other):
return (self.chrom == other.chrom and self.pos == other.pos and self.id == other.id and \
self.ref == other.ref and self.alt == other.alt and self.qual == other.qual and \
self.filter == other.filter and self.info == other.info and \
self.fields == other.fields)
def __str__(self):
return "{chrom}\t{pos}\t{id}\t{ref}\t{alt}\t{qual}\t{filter}\t{info}{fields}".format(
chrom=self.chrom, pos=self.pos, id=self.id,
ref=self.ref, alt=self.alt, qual=_fmt(self.qual),
filter=self.filter,
info=";".join("{0}={1}".format(k, _fmt(v)) for k, v in self.info.iteritems()),
fields="\t".join(_empty_then(self.fields)))
def merge_vcfs_sorted(vcf_files, output_file_name):
"""
Utility function to combine N (>=1) VCF files, with records
sorted by contig then contig position. This assumes each file is already
sorted, and forms a contiguous set of records.
"""
# get the headers and the first record of each file, so we can compare
meta = OrderedDict([])
hdr = OrderedDict([])
fst_recs = []
for f in vcf_files:
with open(f) as h:
for line in h:
line = line.strip()
if not line:
continue
elif line[:2] == "##":
meta[line] = ()
elif line[:6] == "#CHROM":
hdr.update((h, ()) for h in line.lstrip("#").split("\t"))
else:
fst_recs.append((Vcf4Record.fromString(line), f))
break
sorted_files = sorted(fst_recs, key=lambda x: x[0])
nrec = 0
with open(output_file_name, "w") as oh:
for m, _ in meta.iteritems():
print(m, file=oh)
print("#{0}".format("\t".join(h for h, _ in hdr.iteritems())), file=oh)
for _, f in sorted_files:
with open(f) as h:
for line in h:
line = line.strip()
if not line or line[0] == "#":
continue
else:
print(line, file=oh)
nrec += 1
return nrec
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