forked from jdoughertyii/PyVCF
/
parser.py
765 lines (632 loc) · 26.5 KB
/
parser.py
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import codecs
import collections
import csv
import gzip
import itertools
import os
import re
import sys
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
from model import _Call, _Record, make_calldata_tuple
from model import _Substitution, _Breakend, _SingleBreakend, _SV
# 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', 'H3': 'Flag', 'MQ': 'Float',
'MQ0': 'Integer', 'NS': 'Integer', 'SB': 'String', 'SOMATIC': 'Flag',
'VALIDATED': 'Flag', '1000G': 'Flag',
# Keys used for structural variants
'IMPRECISE': 'Flag', 'NOVEL': 'Flag', 'SVTYPE': 'String',
'SVLEN': 'Integer', 'CIPOS': 'Integer', 'CIEND': 'Integer',
'HOMLEN': 'Integer', 'HOMSEQ': 'String', 'BKPTID': 'String',
'MEINFO': 'String', 'METRANS': 'String', 'DGVID': 'String',
'DBVARID': 'String', 'DBRIPID': 'String', 'MATEID': 'String',
'PARID': 'String', 'EVENT': 'String', 'CILEN': 'Integer',
'DPADJ': 'Integer', 'CN': 'Integer', 'CNADJ': 'Integer',
'CICN': 'Integer', 'CICNADJ': 'Integer'
}
RESERVED_FORMAT = {
'GT': 'String', 'DP': 'Integer', 'FT': 'String', 'GL': 'Float',
'GLE': 'String', 'PL': 'Integer', 'GP': 'Float', 'GQ': 'Integer',
'HQ': 'Integer', 'PS': 'Integer', 'PQ': 'Integer', 'EC': 'Integer',
'MQ': 'Integer',
# Keys used for structural variants
'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 alternate alleles in a given record
'G': -2, # Equal to the number of genotypes in a given record
'R': -3, # Equal to the number of alleles including reference in a given record
}
_Info = collections.namedtuple('Info', ['id', 'num', 'type', 'desc', 'source', 'version'])
_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'])
_Contig = collections.namedtuple('Contig', ['id', 'length'])
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>[^,]+),\s*
Number=(?P<number>-?\d+|\.|[AGR]),\s*
Type=(?P<type>Integer|Float|Flag|Character|String),\s*
Description="(?P<desc>[^"]*)"
(?:,\s*Source="(?P<source>[^"]*)")?
(?:,\s*Version="?(?P<version>[^"]*)"?)?
>''', re.VERBOSE)
self.filter_pattern = re.compile(r'''\#\#FILTER=<
ID=(?P<id>[^,]+),\s*
Description="(?P<desc>[^"]*)"
>''', re.VERBOSE)
self.alt_pattern = re.compile(r'''\#\#ALT=<
ID=(?P<id>[^,]+),\s*
Description="(?P<desc>[^"]*)"
>''', re.VERBOSE)
self.format_pattern = re.compile(r'''\#\#FORMAT=<
ID=(?P<id>.+),\s*
Number=(?P<number>-?\d+|\.|[AGR]),\s*
Type=(?P<type>.+),\s*
Description="(?P<desc>.*)"
>''', re.VERBOSE)
self.contig_pattern = re.compile(r'''\#\#contig=<
ID=(?P<id>[^>,]+)
(,.*length=(?P<length>-?\d+))?
.*
>''', 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 is None:
return None
elif 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'),
match.group('source'), match.group('version'))
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_contig(self, contig_string):
'''Read a meta-contigrmation INFO line.'''
match = self.contig_pattern.match(contig_string)
if not match:
raise SyntaxError(
"One of the contig lines is malformed: %s" % contig_string)
length = self.vcf_field_count(match.group('length'))
contig = _Contig(match.group('id'), length)
return (match.group('id'), contig)
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]
# N.B., items can have quoted values, so cannot just split on comma
val = OrderedDict()
state = 0
k = ''
v = ''
for c in items[1]:
if state == 0: # reading item key
if c == '=':
state = 1 # end of key, start reading value
else:
k += c # extend key
elif state == 1: # reading item value
if v == '' and c == '"':
v += c # include quote mark in value
state = 2 # start reading quoted value
elif c == ',':
val[k] = v # store parsed item
state = 0 # read next key
k = ''
v = ''
else:
v += c
elif state == 2: # reading quoted item value
if c == '"':
v += c # include quote mark in value
state = 1 # end quoting
else:
v += c
if k != '':
val[k] = v
return key, val
def read_meta(self, meta_string):
if re.match("##.+=<", meta_string):
return self.read_meta_hash(meta_string)
match = self.meta_pattern.match(meta_string)
if not match:
# Spec only allows key=value, but we try to be liberal and
# interpret anything else as key=none (and all values are parsed
# as strings).
return meta_string.lstrip('#'), 'none'
return match.group('key'), match.group('val')
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,
strict_whitespace=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``
'prepend_chr=True' will put 'chr' before all the CHROM values, useful
for different sources.
'strict_whitespace=True' will split records on tabs only (as with VCF
spec) which allows you to parse files with spaces in the sample names.
"""
super(Reader, 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)
if strict_whitespace:
self._separator = '\t'
else:
self._separator = '\t| +'
self.reader = (line.strip() for line in self._reader if line.strip())
#: 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
#: contig fields from header
self.contigs = None
self.samples = None
self._sample_indexes = None
self._header_lines = []
self._column_headers = []
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', 'contigs', 'formats'):
setattr(self, attr, OrderedDict())
parser = _vcf_metadata_parser()
line = self.reader.next()
while line.startswith('##'):
self._header_lines.append(line)
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
elif line.startswith('##contig'):
key, val = parser.read_contig(line)
self.contigs[key] = val
else:
key, val = parser.read_meta(line)
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(self._separator, line[1:])
self._column_headers = fields[:9]
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 = {}
for entry in entries:
entry = entry.split('=', 1)
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(',')
try:
val = self._map(int, vals)
# Allow specified integers to be flexibly parsed as floats.
# Handles cases with incorrectly specified header types.
except ValueError:
val = self._map(float, vals)
elif entry_type == 'Float':
vals = entry[1].split(',')
val = self._map(float, vals)
elif entry_type == 'Flag':
val = True
elif entry_type in ('String', 'Character'):
try:
vals = entry[1].split(',') # commas are reserved characters indicating multiple values
val = self._map(str, vals)
except IndexError:
entry_type = 'Flag'
val = True
try:
if self.infos[ID].num == 1 and entry_type not in ( 'Flag', ):
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 = make_calldata_tuple(samp_fmt.split(':'))
for fmt in samp_fmt._fields:
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
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 not in self._format_cache:
self._format_cache[samp_fmt] = self._parse_sample_format(samp_fmt)
samp_fmt = self._format_cache[samp_fmt]
if cparse:
return cparse.parse_samples(
self.samples, samples, samp_fmt, samp_fmt._types, samp_fmt._nums, site)
samp_data = []
_map = self._map
nfields = len(samp_fmt._fields)
for name, sample in itertools.izip(self.samples, samples):
# parse the data for this sample
sampdat = [None] * nfields
for i, vals in enumerate(sample.split(':')):
# short circuit the most common
if samp_fmt._fields[i] == 'GT':
sampdat[i] = vals
continue
elif vals == ".":
sampdat[i] = None
continue
entry_num = samp_fmt._nums[i]
entry_type = samp_fmt._types[i]
# we don't need to split single entries
if entry_num == 1 or ',' not in vals:
if entry_type == 'Integer':
try:
sampdat[i] = int(vals)
except ValueError:
sampdat[i] = float(vals)
elif entry_type == 'Float':
sampdat[i] = float(vals)
else:
sampdat[i] = vals
if entry_num != 1:
sampdat[i] = (sampdat[i])
continue
vals = vals.split(',')
if entry_type == 'Integer':
try:
sampdat[i] = _map(int, vals)
except ValueError:
sampdat[i] = _map(float, vals)
elif entry_type == 'Float' or entry_type == 'Numeric':
sampdat[i] = _map(float, vals)
else:
sampdat[i] = vals
# create a call object
call = _Call(site, name, samp_fmt(*sampdat))
samp_data.append(call)
return samp_data
def _parse_alt(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(self._separator, line.rstrip())
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._parse_alt, row[4].split(','))
try:
qual = int(row[5])
except ValueError:
try:
qual = float(row[5])
except ValueError:
qual = None
filt = row[6]
if filt == '.':
filt = None
elif filt == 'PASS':
filt = []
else:
filt = filt.split(';')
info = self._parse_info(row[7])
try:
fmt = row[8]
except IndexError:
fmt = None
else:
if fmt == '.':
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=None, end=None):
""" Fetches records from a tabix-indexed VCF file and returns an
iterable of ``_Record`` instances
chrom must be specified.
The start and end coordinates are in the zero-based,
half-open coordinate system, similar to ``_Record.start`` and
``_Record.end``. The very first base of a chromosome is
index 0, and the the region includes bases up to, but not
including the base at the end coordinate. For example
``fetch('4', 10, 20)`` would include all variants
overlapping a 10 base pair region from the 11th base of
through the 20th base (which is at index 19) of chromosome
4. It would not include the 21st base (at index 20). See
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms
for more information on the zero-based, half-open coordinate
system.
If end is omitted, all variants from start until the end of
the chromosome chrom will be included.
If start and end are omitted, all variants on chrom will be
returned.
requires pysam
"""
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:]
self.reader = self._tabix.fetch(chrom, start, end)
return self
class Writer(object):
"""VCF Writer. On Windows Python 2, open stream with 'wb'."""
# 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="\n"):
self.writer = csv.writer(stream, delimiter="\t",
lineterminator=lineterminator,
quotechar='', quoting=csv.QUOTE_NONE)
self.template = template
self.stream = stream
# Order keys for INFO fields defined in the header (undefined fields
# get a maximum key).
self.info_order = collections.defaultdict(
lambda: len(template.infos),
dict(zip(template.infos.iterkeys(), itertools.count())))
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:
if isinstance(val, dict):
values = ','.join('{0}={1}'.format(key, value)
for key, value in val.items())
stream.write('##{0}=<{1}>\n'.format(key, values))
else:
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))
for line in template.contigs.itervalues():
if line.length:
stream.write('##contig=<ID={0},length={1}>\n'.format(*line))
else:
stream.write('##contig=<ID={0}>\n'.format(*line))
self._write_header()
def _write_header(self):
# TODO: write INFO, etc
self.stream.write('#' + '\t'.join(self.template._column_headers
+ self.template.samples) + '\n')
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)]
if record.FORMAT:
ffs.append(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):
if flt == []:
return 'PASS'
return self._stringify(flt, none='.', delim=';')
def _format_info(self, info):
if not info:
return '.'
def order_key(field):
# Order by header definition first, alphabetically second.
return self.info_order[field], field
return ';'.join(self._stringify_pair(f, info[f]) for f in
sorted(info, key=order_key))
def _format_sample(self, fmt, sample):
if hasattr(sample.data, 'GT'):
gt = sample.data.GT
else:
gt = './.' if 'GT' in fmt else ''
if not gt:
return ':'.join([self._stringify(x) for x in sample.data])
# Following the VCF spec, GT is always the first item whenever it is present.
else:
return ':'.join([gt] + [self._stringify(x) for x in sample.data[1:]])
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