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import collections
import re
import csv
import gzip
import sys
import itertools
import codecs
try:
from collections import OrderedDict
except ImportError:
from ordereddict import OrderedDict
try:
import pysam
except ImportError:
pysam = None
try:
import cparse
except ImportError:
cparse = None
# Metadata parsers/constants
RESERVED_INFO = {
'AA': 'String', 'AC': 'Integer', 'AF': 'Float', 'AN': 'Integer',
'BQ': 'Float', 'CIGAR': 'String', 'DB': 'Flag', 'DP': 'Integer',
'END': 'Integer', 'H2': 'Flag', 'MQ': 'Float', 'MQ0': 'Integer',
'NS': 'Integer', 'SB': 'String', 'SOMATIC': 'Flag', 'VALIDATED': 'Flag',
# VCF 4.1 Additions
'IMPRECISE':'Flag', 'NOVEL':'Flag', 'END':'Integer', 'SVTYPE':'String',
'CIPOS':'Integer','CIEND':'Integer','HOMLEN':'Integer','HOMSEQ':'Integer',
'BKPTID':'String','MEINFO':'String','METRANS':'String','DGVID':'String',
'DBVARID':'String','MATEID':'String','PARID':'String','EVENT':'String',
'CILEN':'Integer','CN':'Integer','CNADJ':'Integer','CICN':'Integer',
'CICNADJ':'Integer'
}
RESERVED_FORMAT = {
'GT': 'String', 'DP': 'Integer', 'FT': 'String', 'GL': 'Float',
'GQ': 'Float', 'HQ': 'Float',
# VCF 4.1 Additions
'CN':'Integer','CNQ':'Float','CNL':'Float','NQ':'Integer','HAP':'Integer',
'AHAP':'Integer'
}
# Spec is a bit weak on which metadata lines are singular, like fileformat
# and which can have repeats, like contig
SINGULAR_METADATA = ['fileformat', 'fileDate', 'reference']
# Conversion between value in file and Python value
field_counts = {
'.': None, # Unknown number of values
'A': -1, # Equal to the number of alleles in a given record
'G': -2, # Equal to the number of genotypes in a given record
}
_Info = collections.namedtuple('Info', ['id', 'num', 'type', 'desc'])
_Filter = collections.namedtuple('Filter', ['id', 'desc'])
_Alt = collections.namedtuple('Alt', ['id', 'desc'])
_Format = collections.namedtuple('Format', ['id', 'num', 'type', 'desc'])
_SampleInfo = collections.namedtuple('SampleInfo', ['samples', 'gt_bases', 'gt_types', 'gt_phases'])
class _AltRecord(object):
'''An alternative allele record: either replacement string, SV placeholder, or breakend'''
def __init__(self, type):
#: String to describe the type of variant, by default "SNV" or "MNV", but can be extended to any of the types described in the ALT lines of the header (e.g. "DUP", "DEL", "INS"...)
self.type = type
def __str__(self):
assert False, "_AltRecord is an abstract class, you should be using a subclass instead"
def __eq__(self, other):
return self.type == other.type
class _Substitution(_AltRecord):
'''A basic ALT record, where a REF sequence is replaced by an ALT sequence'''
def __init__(self, nucleotides):
if len(nucleotides) == 1:
super(_Substitution, self).__init__("SNV")
else:
super(_Substitution, self).__init__("MNV")
#: Alternate sequence
self.sequence = str(nucleotides)
def __str__(self):
return self.sequence
def __repr__(self):
return str(self)
def __len__(self):
return len(self.sequence)
def __eq__(self, other):
if isinstance(other, basestring):
return self.sequence == other
else:
return super(_Substitution, self).__eq__(other) and self.sequence == other.sequence
class _Breakend(_AltRecord):
'''A breakend which is paired to a remote location on or off the genome'''
def __init__(self, chr, pos, orientation, remoteOrientation, connectingSequence, withinMainAssembly):
super(_Breakend, self).__init__("BND")
#: The chromosome of breakend's mate.
self.chr = str(chr)
#: The coordinate of breakend's mate.
self.pos = int(pos)
#: The orientation of breakend's mate. If the sequence 3' of the breakend's mate is connected, True, else if the sequence 5' of the breakend's mate is connected, False.
self.remoteOrientation = remoteOrientation
#: If the breakend mate is within the assembly, True, else False if the breakend mate is on a contig in an ancillary assembly file.
self.withinMainAssembly = withinMainAssembly
#: The orientation of breakend. If the sequence 3' of the breakend is connected, True, else if the sequence 5' of the breakend is connected, False.
self.orientation = orientation
#: The breakpoint's connecting sequence.
self.connectingSequence = connectingSequence
def __repr__(self):
return str(self)
def __str__(self):
if self.chr is None:
remoteTag = '.'
else:
if self.withinMainAssembly:
remoteChr = self.chr
else:
remoteChr = "<" + self.chr + ">"
if self.remoteOrientation:
remoteTag = "[" + remoteChr + ":" + str(self.pos) + "["
else:
remoteTag = "]" + remoteChr + ":" + str(self.pos) + "]"
if self.orientation:
return remoteTag + self.connectingSequence
else:
return self.connectingSequence + remoteTag
def __eq__(self, other):
return super(_Breakend, self).__eq__(other) \
and self.chr == other.chr \
and self.pos == other.pos \
and self.remoteOrientation == other.remoteOrientation \
and self.withinMainAssembly == other.withinMainAssembly \
and self.orientation == other.orientation \
and self.connectingSequence == other.connectingSequence
class _SingleBreakend(_Breakend):
'''A single breakend'''
def __init__(self, orientation, connectingSequence):
super(_SingleBreakend, self).__init__(None, None, orientation, None, connectingSequence, None)
class _SV(_AltRecord):
'''An SV placeholder'''
def __init__(self, type):
super(_SV, self).__init__(type)
def __str__(self):
return "<" + self.type + ">"
def __repr__(self):
return str(self)
class _vcf_metadata_parser(object):
'''Parse the metadat in the header of a VCF file.'''
def __init__(self):
super(_vcf_metadata_parser, self).__init__()
self.info_pattern = re.compile(r'''\#\#INFO=<
ID=(?P<id>[^,]+),
Number=(?P<number>-?\d+|\.|[AG]),
Type=(?P<type>Integer|Float|Flag|Character|String),
Description="(?P<desc>[^"]*)"
>''', re.VERBOSE)
self.filter_pattern = re.compile(r'''\#\#FILTER=<
ID=(?P<id>[^,]+),
Description="(?P<desc>[^"]*)"
>''', re.VERBOSE)
self.alt_pattern = re.compile(r'''\#\#ALT=<
ID=(?P<id>[^,]+),
Description="(?P<desc>[^"]*)"
>''', re.VERBOSE)
self.format_pattern = re.compile(r'''\#\#FORMAT=<
ID=(?P<id>.+),
Number=(?P<number>-?\d+|\.|[AG]),
Type=(?P<type>.+),
Description="(?P<desc>.*)"
>''', re.VERBOSE)
self.meta_pattern = re.compile(r'''##(?P<key>.+?)=(?P<val>.+)''')
def vcf_field_count(self, num_str):
"""Cast vcf header numbers to integer or None"""
if num_str not in field_counts:
# Fixed, specified number
return int(num_str)
else:
return field_counts[num_str]
def read_info(self, info_string):
'''Read a meta-information INFO line.'''
match = self.info_pattern.match(info_string)
if not match:
raise SyntaxError(
"One of the INFO lines is malformed: %s" % info_string)
num = self.vcf_field_count(match.group('number'))
info = _Info(match.group('id'), num,
match.group('type'), match.group('desc'))
return (match.group('id'), info)
def read_filter(self, filter_string):
'''Read a meta-information FILTER line.'''
match = self.filter_pattern.match(filter_string)
if not match:
raise SyntaxError(
"One of the FILTER lines is malformed: %s" % filter_string)
filt = _Filter(match.group('id'), match.group('desc'))
return (match.group('id'), filt)
def read_alt(self, alt_string):
'''Read a meta-information ALTline.'''
match = self.alt_pattern.match(alt_string)
if not match:
raise SyntaxError(
"One of the FILTER lines is malformed: %s" % alt_string)
alt = _Alt(match.group('id'), match.group('desc'))
return (match.group('id'), alt)
def read_format(self, format_string):
'''Read a meta-information FORMAT line.'''
match = self.format_pattern.match(format_string)
if not match:
raise SyntaxError(
"One of the FORMAT lines is malformed: %s" % format_string)
num = self.vcf_field_count(match.group('number'))
form = _Format(match.group('id'), num,
match.group('type'), match.group('desc'))
return (match.group('id'), form)
def read_meta_hash(self, meta_string):
items = re.split("[<>]", meta_string)
# Removing initial hash marks and final equal sign
key = items[0][2:-1]
hashItems = items[1].split(',')
val = dict(item.split("=") for item in hashItems)
return key, val
def read_meta(self, meta_string):
if re.match("##.+=<", meta_string):
return self.read_meta_hash(meta_string)
else:
match = self.meta_pattern.match(meta_string)
return match.group('key'), match.group('val')
class _Call(object):
__slots__ = ['site', 'sample', 'data', 'gt_nums', 'called']
""" A genotype call, a cell entry in a VCF file"""
def __init__(self, site, sample, data):
#: The ``_Record`` for this ``_Call``
self.site = site
#: The sample name
self.sample = sample
#: Dictionary of data from the VCF file
self.data = data
self.gt_nums = self.data.get('GT')
#: True if the GT is not ./.
self.called = self.gt_nums is not None
def __repr__(self):
return "Call(sample=%s, GT=%s%s)" % (self.sample, self.gt_nums,
"".join([", %s=%s" % (X, self.data[X]) for X in self.data if X != 'GT']))
def __eq__(self, other):
""" Two _Calls are equal if their _Records are equal
and the samples and ``gt_type``s are the same
"""
return (self.site == other.site
and self.sample == other.sample
and self.gt_type == other.gt_type)
def gt_phase_char(self):
return "/" if not self.phased else "|"
@property
def gt_alleles(self):
'''The numbers of the alleles called at a given sample'''
# grab the numeric alleles of the gt string; tokenize by phasing
return self.gt_nums.split(self.gt_phase_char())
@property
def gt_bases(self):
'''The actual genotype alleles.
E.g. if VCF genotype is 0/1, return A/G
'''
# nothing to do if no genotype call
if self.called:
# lookup and return the actual DNA alleles
try:
return self.gt_phase_char().join(str(self.site.alleles[int(X)]) for X in self.gt_alleles)
except:
sys.stderr.write("Allele number not found in list of alleles\n")
else:
return None
@property
def gt_type(self):
'''The type of genotype.
hom_ref = 0
het = 1
hom_alt = 2 (we don;t track _which+ ALT)
uncalled = None
'''
# extract the numeric alleles of the gt string
if self.called:
alleles = self.gt_alleles
if all(X == alleles[0] for X in alleles[1:]):
if alleles[0] == "0": return 0
else: return 2
else: return 1
else: return None
@property
def phased(self):
'''A boolean indicating whether or not
the genotype is phased for this sample
'''
return self.gt_nums is not None and self.gt_nums.find("|") >= 0
def __getitem__(self, key):
""" Lookup value, backwards compatibility """
return self.data[key]
@property
def is_variant(self):
""" Return True if not a reference call """
if not self.called:
return None
return self.gt_type != 0
@property
def is_het(self):
""" Return True for heterozygous calls """
if not self.called:
return None
return self.gt_type == 1
class _Record(object):
""" A set of calls at a site. Equivalent to a row in a VCF file.
The standard VCF fields CHROM, POS, ID, REF, ALT, QUAL, FILTER,
INFO and FORMAT are available as properties.
The list of genotype calls is in the ``samples`` property.
"""
def __init__(self, CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT,
sample_indexes, samples=None):
self.CHROM = CHROM
self.POS = POS
self.ID = ID
self.REF = REF
self.ALT = ALT
self.QUAL = QUAL
self.FILTER = FILTER
self.INFO = INFO
self.FORMAT = FORMAT
#: 0-based start coordinate
self.start = self.POS - 1
#: 1-based end coordinate
self.end = self.start + len(self.REF)
#: list of alleles. [0] = REF, [1:] = ALTS
self.alleles = [self.REF]
self.alleles.extend(self.ALT)
#: list of ``_Calls`` for each sample ordered as in source VCF
self.samples = samples
self._sample_indexes = sample_indexes
def __eq__(self, other):
""" _Records are equal if they describe the same variant (same position, alleles) """
return (self.CHROM == other.CHROM and
self.POS == other.POS and
self.REF == other.REF and
self.ALT == other.ALT)
def __iter__(self):
return iter(self.samples)
def __str__(self):
return "Record(CHROM=%(CHROM)s, POS=%(POS)s, REF=%(REF)s, ALT=%(ALT)s)" % self.__dict__
def __cmp__(self, other):
return cmp( (self.CHROM, self.POS), (other.CHROM, other.POS))
def add_format(self, fmt):
self.FORMAT = self.FORMAT + ':' + fmt
def add_filter(self, flt):
if self.FILTER is None \
or self.FILTER == 'PASS'\
or self.FILTER == '.':
self.FILTER = ''
else:
self.FILTER = self.FILTER + ';'
self.FILTER = self.FILTER + flt
def add_info(self, info, value=True):
self.INFO[info] = value
def genotype(self, name):
""" Lookup a ``_Call`` for the sample given in ``name`` """
return self.samples[self._sample_indexes[name]]
@property
def num_called(self):
""" The number of called samples"""
return sum(s.called for s in self.samples)
@property
def call_rate(self):
""" The fraction of genotypes that were actually called. """
return float(self.num_called) / float(len(self.samples))
@property
def num_hom_ref(self):
""" The number of homozygous for ref allele genotypes"""
return len([s for s in self.samples if s.gt_type == 0])
@property
def num_hom_alt(self):
""" The number of homozygous for alt allele genotypes"""
return len([s for s in self.samples if s.gt_type == 2])
@property
def num_het(self):
""" The number of heterozygous genotypes"""
return len([s for s in self.samples if s.gt_type == 1])
@property
def num_unknown(self):
""" The number of unknown genotypes"""
return len([s for s in self.samples if s.gt_type is None])
@property
def aaf(self):
""" The allele frequency of the alternate allele.
NOTE 1: Punt if more than one alternate allele.
NOTE 2: Denominator calc'ed from _called_ genotypes.
"""
# skip if more than one alternate allele. assumes bi-allelic
if len(self.ALT) > 1:
return None
hom_ref = self.num_hom_ref
het = self.num_het
hom_alt = self.num_hom_alt
num_chroms = float(2.0 * self.num_called)
return float(het + 2 * hom_alt) / float(num_chroms)
@property
def nucl_diversity(self):
"""
pi_hat (estimation of nucleotide diversity) for the site.
This metric can be summed across multiple sites to compute regional
nucleotide diversity estimates. For example, pi_hat for all variants
in a given gene.
Derived from:
\"Population Genetics: A Concise Guide, 2nd ed., p.45\"
John Gillespie.
"""
# skip if more than one alternate allele. assumes bi-allelic
if len(self.ALT) > 1:
return None
p = self.aaf
q = 1.0 - p
num_chroms = float(2.0 * self.num_called)
return float(num_chroms / (num_chroms - 1.0)) * (2.0 * p * q)
def get_hom_refs(self):
""" The list of hom ref genotypes"""
return [s for s in self.samples if s.gt_type == 0]
def get_hom_alts(self):
""" The list of hom alt genotypes"""
return [s for s in self.samples if s.gt_type == 2]
def get_hets(self):
""" The list of het genotypes"""
return [s for s in self.samples if s.gt_type == 1]
def get_unknowns(self):
""" The list of unknown genotypes"""
return [s for s in self.samples if s.gt_type is None]
@property
def is_snp(self):
""" Return whether or not the variant is a SNP """
if len(self.REF) > 1: return False
for alt in self.ALT:
if alt is None or alt.type != "SNV":
return False
if alt not in ['A', 'C', 'G', 'T']:
return False
return True
@property
def is_indel(self):
""" Return whether or not the variant is an INDEL """
is_sv = self.is_sv
if len(self.REF) > 1 and not is_sv: return True
for alt in self.ALT:
if alt is None:
return True
if alt.type != "SNV" and alt.type != "MNV":
return False
elif len(alt) != len(self.REF):
# the diff. b/w INDELs and SVs can be murky.
if not is_sv:
# 1 2827693 . CCCCTCGCA C . PASS AC=10;
return True
else:
# 1 2827693 . CCCCTCGCA C . PASS SVTYPE=DEL;
return False
return False
@property
def is_sv(self):
""" Return whether or not the variant is a structural variant """
if self.INFO.get('SVTYPE') is None:
return False
return True
@property
def is_transition(self):
""" Return whether or not the SNP is a transition """
# if multiple alts, it is unclear if we have a transition
if len(self.ALT) > 1: return False
if self.is_snp:
# just one alt allele
alt_allele = self.ALT[0]
if ((self.REF == "A" and alt_allele == "G") or
(self.REF == "G" and alt_allele == "A") or
(self.REF == "C" and alt_allele == "T") or
(self.REF == "T" and alt_allele == "C")):
return True
else: return False
else: return False
@property
def is_deletion(self):
""" Return whether or not the INDEL is a deletion """
# if multiple alts, it is unclear if we have a transition
if len(self.ALT) > 1: return False
if self.is_indel:
# just one alt allele
alt_allele = self.ALT[0]
if alt_allele is None:
return True
if len(self.REF) > len(alt_allele):
return True
else: return False
else: return False
@property
def var_type(self):
"""
Return the type of variant [snp, indel, unknown]
TO DO: support SVs
"""
if self.is_snp:
return "snp"
elif self.is_indel:
return "indel"
elif self.is_sv:
return "sv"
else:
return "unknown"
@property
def var_subtype(self):
"""
Return the subtype of variant.
- For SNPs and INDELs, yeild one of: [ts, tv, ins, del]
- For SVs yield either "complex" or the SV type defined
in the ALT fields (removing the brackets).
E.g.:
<DEL> -> DEL
<INS:ME:L1> -> INS:ME:L1
<DUP> -> DUP
The logic is meant to follow the rules outlined in the following
paragraph at:
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
"For precisely known variants, the REF and ALT fields should contain
the full sequences for the alleles, following the usual VCF conventions.
For imprecise variants, the REF field may contain a single base and the
ALT fields should contain symbolic alleles (e.g. <ID>), described in more
detail below. Imprecise variants should also be marked by the presence
of an IMPRECISE flag in the INFO field."
"""
if self.is_snp:
if self.is_transition:
return "ts"
elif len(self.ALT) == 1:
return "tv"
else: # multiple ALT alleles. unclear
return "unknown"
elif self.is_indel:
if self.is_deletion:
return "del"
elif len(self.ALT) == 1:
return "ins"
else: # multiple ALT alleles. unclear
return "unknown"
elif self.is_sv:
if self.INFO['SVTYPE'] == "BND":
return "complex"
elif self.is_sv_precise:
return self.INFO['SVTYPE']
else:
return self.ALT[0].type
else:
return "unknown"
@property
def sv_end(self):
""" Return the end position for the SV """
if self.is_sv:
return self.INFO['END']
return None
@property
def is_sv_precise(self):
""" Return whether the SV cordinates are mapped
to 1 b.p. resolution.
"""
if self.INFO.get('IMPRECISE') is None and not self.is_sv:
return False
elif self.INFO.get('IMPRECISE') is not None and self.is_sv:
return False
elif self.INFO.get('IMPRECISE') is None and self.is_sv:
return True
@property
def is_monomorphic(self):
""" Return True for reference calls """
return len(self.ALT) == 1 and self.ALT[0] is None
class Reader(object):
""" Reader for a VCF v 4.0 file, an iterator returning ``_Record objects`` """
def __init__(self, fsock=None, filename=None, compressed=False, prepend_chr=False):
""" Create a new Reader for a VCF file.
You must specify either fsock (stream) or filename. Gzipped streams
or files are attempted to be recogized by the file extension, or gzipped
can be forced with ``compressed=True``
"""
super(VCFReader, self).__init__()
if not (fsock or filename):
raise Exception('You must provide at least fsock or filename')
if fsock:
self.reader = fsock
if filename is None and hasattr(fsock, 'name'):
filename = fsock.name
compressed = compressed or filename.endswith('.gz')
elif filename:
compressed = compressed or filename.endswith('.gz')
self.reader = open(filename, 'rb' if compressed else 'rt')
self.filename = filename
if compressed:
self.reader = gzip.GzipFile(fileobj=self.reader)
if sys.version > '3':
self.reader = codecs.getreader('ascii')(self.reader)
#: metadata fields from header (string or hash, depending)
self.metadata = None
#: INFO fields from header
self.infos = None
#: FILTER fields from header
self.filters = None
#: ALT fields from header
self.alts = None
#: FORMAT fields from header
self.formats = None
self.samples = None
self._sample_indexes = None
self._header_lines = []
self._tabix = None
self._prepend_chr = prepend_chr
self._parse_metainfo()
self._format_cache = {}
def __iter__(self):
return self
def _parse_metainfo(self):
'''Parse the information stored in the metainfo of the VCF.
The end user shouldn't have to use this. She can access the metainfo
directly with ``self.metadata``.'''
for attr in ('metadata', 'infos', 'filters', 'alts', 'formats'):
setattr(self, attr, OrderedDict())
parser = _vcf_metadata_parser()
line = self.reader.next()
while line.startswith('##'):
self._header_lines.append(line)
line = line.strip()
if line.startswith('##INFO'):
key, val = parser.read_info(line)
self.infos[key] = val
elif line.startswith('##FILTER'):
key, val = parser.read_filter(line)
self.filters[key] = val
elif line.startswith('##ALT'):
key, val = parser.read_alt(line)
self.alts[key] = val
elif line.startswith('##FORMAT'):
key, val = parser.read_format(line)
self.formats[key] = val
else:
key, val = parser.read_meta(line.strip())
if key in SINGULAR_METADATA:
self.metadata[key] = val
else:
if key not in self.metadata:
self.metadata[key] = []
self.metadata[key].append(val)
line = self.reader.next()
fields = re.split('\t| +', line.rstrip())
self.samples = fields[9:]
self._sample_indexes = dict([(x,i) for (i,x) in enumerate(self.samples)])
def _map(self, func, iterable, bad='.'):
'''``map``, but make bad values None.'''
return [func(x) if x != bad else None
for x in iterable]
def _parse_info(self, info_str):
'''Parse the INFO field of a VCF entry into a dictionary of Python
types.
'''
if info_str == '.':
return {}
entries = info_str.split(';')
retdict = OrderedDict()
for entry in entries:
entry = entry.split('=')
ID = entry[0]
try:
entry_type = self.infos[ID].type
except KeyError:
try:
entry_type = RESERVED_INFO[ID]
except KeyError:
if entry[1:]:
entry_type = 'String'
else:
entry_type = 'Flag'
if entry_type == 'Integer':
vals = entry[1].split(',')
val = self._map(int, vals)
elif entry_type == 'Float':
vals = entry[1].split(',')
val = self._map(float, vals)
elif entry_type == 'Flag':
val = True
elif entry_type == 'String':
try:
val = entry[1]
except IndexError:
val = True
try:
if self.infos[ID].num == 1 and entry_type != 'String':
val = val[0]
except KeyError:
pass
retdict[ID] = val
return retdict
def _parse_sample_format(self, samp_fmt):
""" Parse the format of the calls in this _Record """
samp_fmt = samp_fmt.split(':')
samp_fmt_types = []
samp_fmt_nums = []
for fmt in samp_fmt:
try:
entry_type = self.formats[fmt].type
entry_num = self.formats[fmt].num
except KeyError:
entry_num = None
try:
entry_type = RESERVED_FORMAT[fmt]
except KeyError:
entry_type = 'String'
samp_fmt_types.append(entry_type)
samp_fmt_nums.append(entry_num)
return samp_fmt, samp_fmt_types, samp_fmt_nums
def _parse_samples(self, samples, samp_fmt, site):
'''Parse a sample entry according to the format specified in the FORMAT
column.
NOTE: this method has a cython equivalent and care must be taken
to keep the two methods equivalent
'''
# check whether we already know how to parse this format
if samp_fmt in self._format_cache:
samp_fmt, samp_fmt_types, samp_fmt_nums = \
self._format_cache[samp_fmt]
else:
sf, samp_fmt_types, samp_fmt_nums = self._parse_sample_format(samp_fmt)
self._format_cache[samp_fmt] = (sf, samp_fmt_types, samp_fmt_nums)
samp_fmt = sf
if cparse:
return cparse.parse_samples(
self.samples, samples, samp_fmt, samp_fmt_types, samp_fmt_nums, site)
samp_data = []
_map = self._map
for name, sample in itertools.izip(self.samples, samples):
# parse the data for this sample
sampdict = dict([(x, None) for x in samp_fmt])
for fmt, entry_type, entry_num, vals in itertools.izip(
samp_fmt, samp_fmt_types, samp_fmt_nums, sample.split(':')):
# short circuit the most common
if vals == '.' or vals == './.':
sampdict[fmt] = None
continue
# we don't need to split single entries
if entry_num == 1 or ',' not in vals:
if entry_type == 'Integer':
sampdict[fmt] = int(vals)
elif entry_type == 'Float':
sampdict[fmt] = float(vals)
else:
sampdict[fmt] = vals
if entry_num != 1:
sampdict[fmt] = (sampdict[fmt])
continue
vals = vals.split(',')
if entry_type == 'Integer':
sampdict[fmt] = _map(int, vals)
elif entry_type == 'Float' or entry_type == 'Numeric':
sampdict[fmt] = _map(float, vals)
else:
sampdict[fmt] = vals
# create a call object
call = _Call(site, name, sampdict)
samp_data.append(call)
return samp_data
def parseALT(self, str):
if re.search('[\[\]]', str) is not None:
# Paired breakend
items = re.split('[\[\]]', str)
remoteCoords = items[1].split(':')
chr = remoteCoords[0]
if chr[0] == '<':
chr = chr[1:-1]
withinMainAssembly = False
else:
withinMainAssembly = True
pos = remoteCoords[1]
orientation = (str[0] == '[' or str[0] == ']')
remoteOrientation = (re.search('\[', str) is not None)
if orientation:
connectingSequence = items[2]
else:
connectingSequence = items[0]
return _Breakend(chr, pos, orientation, remoteOrientation, connectingSequence, withinMainAssembly)
elif str[0] == '.' and len(str) > 1:
return _SingleBreakend(True, str[1:])
elif str[-1] == '.' and len(str) > 1:
return _SingleBreakend(False, str[:-1])
elif str[0] == "<" and str[-1] == ">":
return _SV(str[1:-1])
else:
return _Substitution(str)
def next(self):
'''Return the next record in the file.'''
line = self.reader.next()
row = re.split('\t| +', line.strip())
chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom
pos = int(row[1])
if row[2] != '.':
ID = row[2]
else:
ID = None
ref = row[3]
alt = self._map(self.parseALT, row[4].split(','))
try:
qual = int(row[5])
except ValueError:
try:
qual = float(row[5])
except ValueError:
qual = None
filt = row[6].split(';') if ';' in row[6] else row[6]
if filt == 'PASS':
filt = None
info = self._parse_info(row[7])
try:
fmt = row[8]
except IndexError:
fmt = None
record = _Record(chrom, pos, ID, ref, alt, qual, filt,
info, fmt, self._sample_indexes)
if fmt is not None:
samples = self._parse_samples(row[9:], fmt, record)
record.samples = samples
return record
def fetch(self, chrom, start, end=None):
""" fetch records from a Tabix indexed VCF, requires pysam
if start and end are specified, return iterator over positions
if end not specified, return individual ``_Call`` at start or None
"""
if not pysam:
raise Exception('pysam not available, try "pip install pysam"?')
if not self.filename:
raise Exception('Please provide a filename (or a "normal" fsock)')
if not self._tabix:
self._tabix = pysam.Tabixfile(self.filename)
if self._prepend_chr and chrom[:3] == 'chr':
chrom = chrom[3:]
# not sure why tabix needs position -1
start = start - 1
if end is None:
self.reader = self._tabix.fetch(chrom, start, start + 1)
try:
return self.next()
except StopIteration:
return None
self.reader = self._tabix.fetch(chrom, start, end)
return self
class Writer(object):
""" VCF Writer """
fixed_fields = "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT".split()
# Reverse keys and values in header field count dictionary
counts = dict((v,k) for k,v in field_counts.iteritems())
def __init__(self, stream, template, lineterminator="\r\n"):
self.writer = csv.writer(stream, delimiter="\t", lineterminator=lineterminator)
self.template = template
self.stream = stream
two = '##{key}=<ID={0},Description="{1}">\n'
four = '##{key}=<ID={0},Number={num},Type={2},Description="{3}">\n'
_num = self._fix_field_count
for (key, vals) in template.metadata.iteritems():
if key in SINGULAR_METADATA:
vals = [vals]
for val in vals:
stream.write('##{0}={1}\n'.format(key, val))
for line in template.infos.itervalues():
stream.write(four.format(key="INFO", *line, num=_num(line.num)))
for line in template.formats.itervalues():
stream.write(four.format(key="FORMAT", *line, num=_num(line.num)))
for line in template.filters.itervalues():
stream.write(two.format(key="FILTER", *line))
for line in template.alts.itervalues():
stream.write(two.format(key="ALT", *line))
self._write_header()
def _write_header(self):
# TODO: write INFO, etc
self.writer.writerow(self.fixed_fields + self.template.samples)
def write_record(self, record):
""" write a record to the file """
ffs = self._map(str, [record.CHROM, record.POS, record.ID, record.REF]) \
+ [self._format_alt(record.ALT), record.QUAL or '.', self._format_filter(record.FILTER),
self._format_info(record.INFO), record.FORMAT]
samples = [self._format_sample(record.FORMAT, sample)
for sample in record.samples]
self.writer.writerow(ffs + samples)
def flush(self):
"""Flush the writer"""
try:
self.stream.flush()
except AttributeError:
pass
def close(self):
"""Close the writer"""
try:
self.stream.close()
except AttributeError:
pass
def _fix_field_count(self, num_str):
"""Restore header number to original state"""
if num_str not in self.counts:
return num_str
else:
return self.counts[num_str]
def _format_alt(self, alt):
return ','.join(self._map(str, alt))
def _format_filter(self, flt):
return self._stringify(flt, none='PASS', delim=';')
def _format_info(self, info):
if not info:
return '.'
return ';'.join([self._stringify_pair(x,y) for x, y in info.iteritems()])
def _format_sample(self, fmt, sample):
if sample.data["GT"] is None:
return "./."
return ':'.join(self._stringify(sample.data[f]) for f in fmt.split(':'))
def _stringify(self, x, none='.', delim=','):
if type(x) == type([]):
return delim.join(self._map(str, x, none))
return str(x) if x is not None else none
def _stringify_pair(self, x, y, none='.', delim=','):
if isinstance(y, bool):
return str(x) if y else ""
return "%s=%s" % (str(x), self._stringify(y, none=none, delim=delim))
def _map(self, func, iterable, none='.'):
'''``map``, but make None values none.'''
return [func(x) if x is not None else none
for x in iterable]
def __update_readme():
import sys, vcf
file('README.rst', 'w').write(vcf.__doc__)
# backwards compatibility
VCFReader = Reader
VCFWriter = Writer
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