--- /dev/null
+#
+# Code to read, write and edit VCF files
+#
+# VCF lines are encoded as a dictionary with these keys (note: all lowercase):
+# 'chrom': string
+# 'pos': integer
+# 'id': string
+# 'ref': string
+# 'alt': list of strings
+# 'qual': integer
+# 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"]
+# 'info': dictionary of values (see below)
+# 'format': list of keys (strings)
+# sample keys: dictionary of values (see below)
+#
+# The sample keys are accessible through vcf.getsamples()
+#
+# A dictionary of values contains value keys (defined in ##INFO or ##FORMAT lines) which map
+# to a list, containign integers, floats, strings, or characters. Missing values are replaced
+# by a particular value, often -1 or .
+#
+# Genotypes are not stored as a string, but as a list of 1 or 3 elements (for haploid and diploid samples),
+# the first (and last) the integer representing an allele, and the second the separation character.
+# Note that there is just one genotype per sample, but for consistency the single element is stored in a list.
+#
+# Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as (key, value) pairs and are accessible
+# through getheader()
+#
+# The VCF class can be instantiated with a 'regions' variable consisting of tuples (chrom,start,end) encoding
+# 0-based half-open segments. Only variants with a position inside the segment will be parsed. A regions
+# parser is available under parse_regions.
+#
+# When instantiated, a reference can be passed to the VCF class. This may be any class that supports a
+# fetch(chrom, start, end) method.
+#
+#
+#
+# NOTE: the position that is returned to Python is 0-based, NOT 1-based as in the VCF file.
+#
+#
+#
+# TODO:
+# only v4.0 writing is complete; alleles are not converted to v3.3 format
+#
+
+from collections import namedtuple, defaultdict
+from operator import itemgetter
+import sys, re, copy, bisect
+
+import pysam
+
+gtsRegEx = re.compile("[|/\\\\]")
+alleleRegEx = re.compile('^[ACGTN]+$')
+
+# Utility function. Uses 0-based coordinates
+def get_sequence(chrom, start, end, fa):
+ # obtain sequence from .fa file, without truncation
+ if end<=start: return ""
+ if not fa: return "N"*(end-start)
+ if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
+ sequence = fa.fetch(chrom, start, end).upper()
+ if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
+ return sequence
+
+# Utility function. Parses a region string
+def parse_regions( string ):
+ result = []
+ for r in string.split(','):
+ elts = r.split(':')
+ chrom, start, end = elts[0], 0, 3000000000
+ if len(elts)==1: pass
+ elif len(elts)==2:
+ if len(elts[1])>0:
+ ielts = elts[1].split('-')
+ if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
+ try: start, end = int(ielts[0])-1, int(ielts[1])
+ except: raise ValueError("Don't understand region string '%s'" % r)
+ else:
+ raise ValueError("Don't understand region string '%s'" % r)
+ result.append( (chrom,start,end) )
+ return result
+
+
+FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue')
+
+###########################################################################################################
+#
+# New class
+#
+###########################################################################################################
+
+class VCFRecord:
+ '''vcf record.
+
+ initialized from data and vcf meta
+ '''
+
+ data = None
+ vcf = None
+
+ def __init__(self, data, vcf):
+ self.data, self.vcf = data, vcf
+
+ if len(data) != len(self.vcf._samples):
+ self.error(str(data),
+ self.BAD_NUMBER_OF_COLUMNS,
+ "expected %s for %s samples (%s), got %s" % \
+ (len(self.vcf._samples),
+ len(self.vcf._samples),
+ self.vcf._samples,
+ len(data)))
+
+ property contig:
+ def contig( self ): return self.data[0]
+
+ property pos:
+ def __get__( self ):
+ return self.data.pos
+
+ property id:
+ def __get__( self ): return self.data[2]
+
+ property ref:
+ def __get__(self ):
+ # note: gerton substitutes reference if it can be fixed.
+ return self.data[3].upper()
+
+ property alt:
+ def __get__(self):
+ # convert v3.3 to v4.0 alleles below
+ alt = self.data[4]
+ if alt == ".": alt = []
+ else: alt = alt.upper().split(',')
+ return alt
+
+ property qual:
+ def __get__(self):
+ qual = self.data[5]
+ if qual == ".": qual = -1
+ else:
+ try: qual = float(qual)
+ except: self.error(line,self.QUAL_NOT_NUMERICAL)
+
+ property filter:
+ def __get__(self):
+ # postpone checking that filters exist. Encode missing filter or no filtering as empty list
+ if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
+ else: filter = cols[6].split(';')
+
+ return filter
+
+ property info:
+ def __get__(self):
+ col = self.data[7]
+ # dictionary of keys, and list of values
+ info = {}
+ if col != ".":
+ for blurp in col.split(';'):
+ elts = blurp.split('=')
+ if len(elts) == 1: v = None
+ elif len(elts) == 2: v = elts[1]
+ else: self.error(str(self.data),self.ERROR_INFO_STRING)
+ info[elts[0]] = self.parse_formatdata(elts[0], v, self.vcf._info, line)
+ return info
+
+ property format:
+ def __get__(self):
+ return self.data[8].split(':')
+
+ def __getitem__(self, key):
+
+ # parse sample columns
+ values = self.data[self.vcf._sample2column[key]].split(':')
+ alt = self.alt
+ format = self.format
+
+ if len(values) > len(format):
+ self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
+
+ result = {}
+ for idx in range(len(format)):
+ expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
+ if idx < len(values): value = values[idx]
+ else:
+ if expected == -1: value = "."
+ else: value = ",".join(["."]*expected)
+
+ result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, line)
+ if expected != -1 and len(result[format[idx]]) != expected:
+ self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
+ "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
+ if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
+ result[format[idx]] = result[format[idx]][:expected]
+
+ return result
+
+ def __str__(self):
+ return str(self.data)
+
+class VCF:
+
+ # types
+ NT_UNKNOWN = 0
+ NT_NUMBER = 1
+ NT_ALLELES = 2
+ NT_NR_ALLELES = 3
+ NT_GENOTYPES = 4
+ NT_PHASED_GENOTYPES = 5
+
+ _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
+ 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
+ 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
+ 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)",
+ 4:"POS_NOT_NUMERICAL:Position column is not numerical",
+ 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field",
+ 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF",
+ 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF",
+ 8:"POS_NOT_POSITIVE:Position field must be >0",
+ 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'",
+ 10:"ERROR_INFO_STRING:Error while parsing info field",
+ 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)",
+ 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s",
+ 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string",
+ 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header",
+ 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header",
+ 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)",
+ 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)",
+ 18:"BAD_GENOTYPE:Cannot parse genotype (%s)",
+ 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)",
+ 20:"MISSING_REF:Reference allele missing",
+ 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)",
+ 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets",
+ 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes",
+ 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields",
+ 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs",
+ 26:"WRONG_REF:Wrong reference %s",
+ 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data",
+ 28:"BAD_CHR_TAG:Error calculating chr tag for %s",
+ 29:"ZERO_LENGTH_ALLELE:Found zero-length allele",
+ 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base"
+ }
+
+ # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
+ _header = []
+
+ # version number; 33=v3.3; 40=v4.0
+ _version = 40
+
+ # info, filter and format data
+ _info = {}
+ _filter = {}
+ _format = {}
+
+ # header; and required columns
+ _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
+ _samples = []
+
+ # control behaviour
+ _ignored_errors = set([11]) # ERROR_UNKNOWN_KEY
+ _warn_errors = set([])
+ _leftalign = False
+
+ # reference sequence
+ _reference = None
+
+ # regions to include; None includes everything
+ _regions = None
+
+ # statefull stuff
+ _lineno = -1
+ _line = None
+ _lines = None
+
+ def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False):
+ # make error identifiers accessible by name
+ for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id
+ if _copy != None:
+ self._leftalign = _copy._leftalign
+ self._header = _copy._header[:]
+ self._version = _copy._version
+ self._info = copy.deepcopy(_copy._info)
+ self._filter = copy.deepcopy(_copy._filter)
+ self._format = copy.deepcopy(_copy._format)
+ self._samples = _copy._samples[:]
+ self._sample2column = copy.deepcopy(_copy._sample2column)
+ self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
+ self._warn_errors = copy.deepcopy(_copy._warn_errors)
+ self._reference = _copy._reference
+ self._regions = _copy._regions
+ if reference: self._reference = reference
+ if regions: self._regions = regions
+ if leftalign: self._leftalign = leftalign
+ self._lines = lines
+
+ def error(self,line,error,opt=None):
+ if error in self._ignored_errors: return
+ errorlabel, errorstring = self._errors[error].split(':')
+ if opt: errorstring = errorstring % opt
+ errwarn = ["Error","Warning"][error in self._warn_errors]
+ sys.stderr.write("Line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring))
+ if error in self._warn_errors: return
+ raise ValueError(errorstring)
+
+ def parse_format(self,line,format,filter=False):
+ if self._version == 40:
+ if not format.startswith('<'):
+ self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+ format = "<"+format
+ if not format.endswith('>'):
+ self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
+ format += ">"
+ format = format[1:-1]
+ data = {'id':None,'number':None,'type':None,'descr':None}
+ idx = 0
+ while len(format.strip())>0:
+ elts = format.strip().split(',')
+ first, rest = elts[0], ','.join(elts[1:])
+ if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
+ if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
+ if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ first = ["ID=","Number=","Type=","Description="][idx] + first
+ if first.startswith('ID='): data['id'] = first.split('=')[1]
+ elif first.startswith('Number='): data['number'] = first.split('=')[1]
+ elif first.startswith('Type='): data['type'] = first.split('=')[1]
+ elif first.startswith('Description='):
+ elts = format.split('"')
+ if len(elts)<3:
+ self.error(line,self.FORMAT_MISSING_QUOTES)
+ elts = first.split('=') + [rest]
+ data['descr'] = elts[1]
+ rest = '"'.join(elts[2:])
+ if rest.startswith(','): rest = rest[1:]
+ else:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ format = rest
+ idx += 1
+ if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
+ if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ if not data['descr']:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ data['descr'] = '<none>'
+ if not data['type'] and not data['number']:
+ # fine, ##filter format
+ return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
+ if not data['type'] in ["Integer","Float","Character","String","Flag"]:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ # I would like a missing-value field, but it isn't there
+ if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
+ else: data['missing'] = '.'
+ if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ try:
+ n = int(data['number'])
+ t = self.NT_NUMBER
+ except ValueError:
+ n = -1
+ if data['number'] == '.': t = self.NT_UNKNOWN
+ elif data['number'] == '#alleles': t = self.NT_ALLELES
+ elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
+ elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
+ elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
+ else:
+ self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
+ return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
+
+
+ def format_format( self, fmt, filter=False ):
+ values = [('ID',fmt.id)]
+ if fmt.number != None and not filter:
+ if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
+ elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
+ elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
+ elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
+ elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
+ elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
+ else:
+ raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
+ values.append( ('Number',nmb) )
+ values.append( ('Type', fmt.type) )
+ values.append( ('Description', '"' + fmt.description + '"') )
+ if self._version == 33:
+ format = ",".join(v for k,v in values)
+ else:
+ format = "<" + (",".join( "%s=%s" % (k,v) for (k,v) in values )) + ">"
+ return format
+
+ def get_expected(self, format, formatdict, alt):
+ fmt = formatdict[format]
+ if fmt.numbertype == self.NT_UNKNOWN: return -1
+ if fmt.numbertype == self.NT_NUMBER: return fmt.number
+ if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
+ if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
+ if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
+ if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
+ return 0
+
+
+ def _add_definition(self, formatdict, key, data, line ):
+ if key in formatdict: return
+ self.error(line,self.ERROR_UNKNOWN_KEY,key)
+ if data == None:
+ formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
+ return
+ if data == []: data = [""] # unsure what type -- say string
+ if type(data[0]) == type(0.0):
+ formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
+ return
+ if type(data[0]) == type(0):
+ formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
+ return
+ formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
+
+
+ # todo: trim trailing missing values
+ def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
+ output, sdata = [], []
+ if type(data) == type([]): # for FORMAT field, make data with dummy values
+ d = {}
+ for k in data: d[k] = []
+ data = d
+ # convert missing values; and silently add definitions if required
+ for k in data:
+ self._add_definition( format, k, data[k], "(output)" )
+ for idx,v in enumerate(data[k]):
+ if v == format[k].missingvalue: data[k][idx] = "."
+ # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
+ for k in data:
+ if k != 'GT': sdata.append( (k,data[k]) )
+ sdata.sort()
+ if 'GT' in data:
+ sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
+ for k,v in sdata:
+ if v == []: v = None
+ if key and value:
+ if v != None: output.append( k+"="+','.join(map(str,v)) )
+ else: output.append( k )
+ elif key: output.append(k)
+ elif value:
+ if v != None: output.append( ','.join(map(str,v)) )
+ else: output.append( "." ) # should not happen
+ # snip off trailing missing data
+ while len(output) > 1:
+ last = output[-1].replace(',','').replace('.','')
+ if len(last)>0: break
+ output = output[:-1]
+ return separator.join(output)
+
+
+ def enter_default_format(self):
+ for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
+ FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
+ FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
+ FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
+ FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.')]:
+ if f.id not in self._format:
+ self._format[f.id] = f
+
+ def parse_header( self, line ):
+ assert line.startswith('##')
+ elts = line[2:].split('=')
+ key = elts[0].strip()
+ value = '='.join(elts[1:]).strip()
+ if key == "fileformat":
+ if value == "VCFv3.3":
+ self._version = 33
+ elif value == "VCFv4.0":
+ self._version = 40
+ elif value == "VCFv4.1":
+ # AH - for testing
+ self._version = 40
+ else:
+ self.error(line,self.UNKNOWN_FORMAT_STRING)
+ elif key == "INFO":
+ f = self.parse_format(line, value)
+ self._info[ f.id ] = f
+ elif key == "FILTER":
+ f = self.parse_format(line, value, filter=True)
+ self._filter[ f.id ] = f
+ elif key == "FORMAT":
+ f = self.parse_format(line, value)
+ self._format[ f.id ] = f
+ else:
+ # keep other keys in the header field
+ self._header.append( (key,value) )
+
+
+ def write_header( self, stream ):
+ stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
+ for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
+ for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
+ for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
+
+
+ def parse_heading( self, line ):
+ assert line.startswith('#')
+ assert not line.startswith('##')
+ headings = line[1:].split('\t')
+ if len(headings)==1 and len(line[1:].split()) >= 9:
+ self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
+ headings = line[1:].split()
+
+ for i,s in enumerate(self._required):
+
+ if len(headings)<=i or headings[i] != s:
+
+ if len(headings) <= i:
+ err = "(%sth entry not found)" % (i+1)
+ else:
+ err = "(found %s, expected %s)" % (headings[i],s)
+
+ #self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+ # allow FORMAT column to be absent
+ if len(headings) == 8:
+ headings.append("FORMAT")
+ else:
+ self.error(line,self.BADLY_FORMATTED_HEADING,err)
+
+ self._samples = headings[9:]
+ self._sample2column = dict( [(y,x) for x,y in enumerate( self._samples ) ] )
+
+ def write_heading( self, stream ):
+ stream.write("#" + "\t".join(self._required + self._samples) + "\n")
+
+ def convertGT(self, GTstring):
+ if GTstring == ".": return ["."]
+ try:
+ gts = gtsRegEx.split(GTstring)
+ if len(gts) == 1: return [int(gts[0])]
+ if len(gts) != 2: raise ValueError()
+ if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
+ return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
+ except ValueError:
+ self.error(self._line,self.BAD_GENOTYPE,GTstring)
+ return [".","|","."]
+
+
+ def convertGTback(self, GTdata):
+ return ''.join(map(str,GTdata))
+
+ def parse_formatdata( self, key, value, formatdict, line ):
+ # To do: check that the right number of values is present
+ f = formatdict.get(key,None)
+ if f == None:
+ self._add_definition(formatdict, key, value, line )
+ f = formatdict[key]
+ if f.type == "Flag":
+ if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
+ return []
+ values = value.split(',')
+ # deal with trailing data in some early VCF files
+ if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
+ self.error(line,self.ERROR_TRAILING_DATA,values[-1])
+ values[-1] = values[-1].split(';')[0]
+ if f.type == "Integer":
+ for idx,v in enumerate(values):
+ try:
+ if v == ".": values[idx] = f.missingvalue
+ else: values[idx] = int(v)
+ except:
+ self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
+ return [0] * len(values)
+ return values
+ elif f.type == "String":
+ self._line = line
+ if f.id == "GT": values = map( self.convertGT, values )
+ return values
+ elif f.type == "Character":
+ for v in values:
+ if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
+ return values
+ elif f.type == "Float":
+ for idx,v in enumerate(values):
+ if v == ".": values[idx] = f.missingvalue
+ try: return map(float,values)
+ except:
+ self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,values)
+ return [0.0] * len(values)
+ else:
+ # can't happen
+ self.error(line,self.ERROR_INFO_STRING)
+
+
+ def inregion(self, chrom, pos):
+ if not self._regions: return True
+ for r in self._regions:
+ if r[0] == chrom and r[1] <= pos < r[2]: return True
+ return False
+
+
+ def parse_data( self, line, lineparse=False ):
+ cols = line.split('\t')
+ if len(cols) != len(self._samples)+9:
+ # gracefully deal with absent FORMAT column
+ if len(cols) == 8 and len(self._samples)==0:
+ cols.append("")
+ else:
+ self.error(line,
+ self.BAD_NUMBER_OF_COLUMNS,
+ "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
+
+ chrom = cols[0]
+
+ # get 0-based position
+ try: pos = int(cols[1])-1
+ except: self.error(line,self.POS_NOT_NUMERICAL)
+ if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
+
+ # implement filtering
+ if not self.inregion(chrom,pos): return None
+
+ # end of first-pass parse for sortedVCF
+ if lineparse: return chrom, pos, line
+
+ id = cols[2]
+
+ ref = cols[3].upper()
+ if ref == ".":
+ self.error(line,self.MISSING_REF)
+ if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
+ else: ref = ""
+ else:
+ for c in ref:
+ if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
+ if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
+
+ # make sure reference is sane
+ if self._reference:
+ left = max(0,pos-100)
+ faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
+ faref = faref_leftflank[pos-left:]
+ if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
+ ref = faref
+
+ # convert v3.3 to v4.0 alleles below
+ if cols[4] == ".": alt = []
+ else: alt = cols[4].upper().split(',')
+
+ if cols[5] == ".": qual = -1
+ else:
+ try: qual = float(cols[5])
+ except: self.error(line,self.QUAL_NOT_NUMERICAL)
+
+ # postpone checking that filters exist. Encode missing filter or no filtering as empty list
+ if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
+ else: filter = cols[6].split(';')
+
+ # dictionary of keys, and list of values
+ info = {}
+ if cols[7] != ".":
+ for blurp in cols[7].split(';'):
+ elts = blurp.split('=')
+ if len(elts) == 1: v = None
+ elif len(elts) == 2: v = elts[1]
+ else: self.error(line,self.ERROR_INFO_STRING)
+ info[elts[0]] = self.parse_formatdata(elts[0], v, self._info, line)
+
+ # Gracefully deal with absent FORMAT column
+ if cols[8] == "": format = []
+ else: format = cols[8].split(':')
+
+ # check: all filters are defined
+ for f in filter:
+ if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f)
+
+ # check: format fields are defined
+ for f in format:
+ if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
+
+ # convert v3.3 alleles
+ if self._version == 33:
+ if len(ref) != 1: self.error(line,self.V33_BAD_REF)
+ newalts = []
+ have_deletions = False
+ for a in alt:
+ if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
+ elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
+ elif a.startswith('D'): # allow D<seq> and D<num>
+ have_deletions = True
+ try:
+ l = int(a[1:]) # throws ValueError if sequence
+ if len(ref) < l: # add to reference if necessary
+ addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
+ ref += addns
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ a = ref[l:] # new deletion, deleting pos...pos+l
+ except ValueError:
+ s = a[1:]
+ if len(ref) < len(s): # add Ns to reference if necessary
+ addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
+ if not s.endswith(addns) and addns != 'N'*len(addns):
+ self.error(line,self.V33_UNMATCHED_DELETION,
+ "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
+ ref += addns
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ a = ref[len(s):] # new deletion, deleting from pos
+ else:
+ self.error(line,self.V33_BAD_ALLELE)
+ newalts.append(a)
+ alt = newalts
+ # deletion alleles exist, add dummy 1st reference allele, and account for leading base
+ if have_deletions:
+ if pos == 0:
+ # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
+ addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
+ ref += addn
+ alt = [allele+addn for allele in alt]
+ else:
+ addn = get_sequence(chrom,pos-1,pos,self._reference)
+ ref = addn + ref
+ alt = [addn + allele for allele in alt]
+ pos -= 1
+ else:
+ # format v4.0 -- just check for nucleotides
+ for allele in alt:
+ if not alleleRegEx.match(allele):
+ self.error(line,self.V40_BAD_ALLELE,allele)
+
+ # check for leading nucleotide in indel calls
+ for allele in alt:
+ if len(allele) != len(ref):
+ if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
+ if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
+ self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
+
+ # trim trailing bases in alleles
+ for i in range(1,min(len(ref),min(map(len,alt)))):
+ if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
+ break
+ ref, alt = ref[:-1], [allele[:-1] for allele in alt]
+
+ # left-align alleles, if a reference is available
+ if self._leftalign and self._reference:
+ while left < pos:
+ movable = True
+ for allele in alt:
+ if len(allele) > len(ref):
+ longest, shortest = allele, ref
+ else:
+ longest, shortest = ref, allele
+ if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
+ movable = False
+ if longest[-1].upper() != longest[len(shortest)-1].upper():
+ movable = False
+ if not movable:
+ break
+ ref = ref[:-1]
+ alt = [allele[:-1] for allele in alt]
+ if min(len(allele) for allele in alt) == 0 or len(ref) == 0:
+ ref = faref_leftflank[pos-left-1] + ref
+ alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+ pos -= 1
+
+ # parse sample columns
+ samples = []
+ for sample in cols[9:]:
+ dict = {}
+ values = sample.split(':')
+ if len(values) > len(format):
+ self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
+ for idx in range(len(format)):
+ expected = self.get_expected(format[idx], self._format, alt)
+ if idx < len(values): value = values[idx]
+ else:
+ if expected == -1: value = "."
+ else: value = ",".join(["."]*expected)
+ dict[format[idx]] = self.parse_formatdata(format[idx], value, self._format, line)
+ if expected != -1 and len(dict[format[idx]]) != expected:
+ self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
+ "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
+ if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
+ dict[format[idx]] = dict[format[idx]][:expected]
+ samples.append( dict )
+
+ # done
+ d = {'chrom':chrom,
+ 'pos':pos, # return 0-based position
+ 'id':id,
+ 'ref':ref,
+ 'alt':alt,
+ 'qual':qual,
+ 'filter':filter,
+ 'info':info,
+ 'format':format}
+ for key,value in zip(self._samples,samples):
+ d[key] = value
+
+ return d
+
+
+ def write_data(self, stream, data):
+ required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
+ for k in required:
+ if k not in data: raise ValueError("Required key %s not found in data" % str(k))
+ if data['alt'] == []: alt = "."
+ else: alt = ",".join(data['alt'])
+ if data['filter'] == None: filter = "."
+ elif data['filter'] == []:
+ if self._version == 33: filter = "0"
+ else: filter = "PASS"
+ else: filter = ';'.join(data['filter'])
+ if data['qual'] == -1: qual = "."
+ else: qual = str(data['qual'])
+
+ output = [data['chrom'],
+ str(data['pos']+1), # change to 1-based position
+ data['id'],
+ data['ref'],
+ alt,
+ qual,
+ filter,
+ self.format_formatdata( data['info'], self._info, separator=";" ),
+ self.format_formatdata( data['format'], self._format, value=False ) ]
+
+ for s in self._samples:
+ output.append( self.format_formatdata( data[s], self._format, key=False ) )
+
+ stream.write( "\t".join(output) + "\n" )
+
+ def _parse_header(self, stream):
+ self._lineno = 0
+ for line in stream:
+ self._lineno += 1
+ if line.startswith('##'):
+ self.parse_header( line.strip() )
+ elif line.startswith('#'):
+ self.parse_heading( line.strip() )
+ self.enter_default_format()
+ else:
+ break
+ return line
+
+ def _parse(self, line, stream):
+ if len(line.strip()) > 0:
+ d = self.parse_data( line.strip() )
+ if d: yield d
+ for line in stream:
+ self._lineno += 1
+ if self._lines and self._lineno > self._lines: raise StopIteration
+ d = self.parse_data( line.strip() )
+ if d: yield d
+
+ ######################################################################################################
+ #
+ # API follows
+ #
+ ######################################################################################################
+
+ def getsamples(self):
+ """ List of samples in VCF file """
+ return self._samples
+
+ def setsamples(self,samples):
+ """ List of samples in VCF file """
+ self._samples = samples
+
+ def getheader(self):
+ """ List of header key-value pairs (strings) """
+ return self._header
+
+ def setheader(self,header):
+ """ List of header key-value pairs (strings) """
+ self._header = header
+
+ def getinfo(self):
+ """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+ return self._info
+
+ def setinfo(self,info):
+ """ Dictionary of ##INFO tags, as VCF.FORMAT values """
+ self._info = info
+
+ def getformat(self):
+ """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+ return self._format
+
+ def setformat(self,format):
+ """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
+ self._format = format
+
+ def getfilter(self):
+ """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+ return self._filter
+
+ def setfilter(self,filter):
+ """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
+ self._filter = filter
+
+ def setversion(self, version):
+ if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
+ self._version = version
+
+ def setregions(self, regions):
+ self._regions = regions
+
+ def setreference(self, ref):
+ """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
+ self._reference = ref
+
+ def ignoreerror(self, errorstring):
+ try: self._ignored_errors.add(self.__dict__[errorstring])
+ except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
+
+ def warnerror(self, errorstring):
+ try: self._warn_errors.add(self.__dict__[errorstring])
+ except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
+
+ def parse(self, stream):
+ """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
+ last_line = self._parse_header(stream)
+ # now return a generator that does the actual work. In this way the pre-processing is done
+ # before the first piece of data is yielded
+ return self._parse(last_line, stream)
+
+ def write(self, stream, datagenerator):
+ """ Writes a VCF file to a stream, using a data generator (or list) """
+ self.write_header(stream)
+ self.write_heading(stream)
+ for data in datagenerator: self.write_data(stream,data)
+
+ def writeheader(self, stream):
+ """ Writes a VCF header """
+ self.write_header(stream)
+ self.write_heading(stream)
+
+ def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2):
+ """ Utility function: compares two calls for equality """
+ # a variant should always be assigned to a unique position, one base before
+ # the leftmost position of the alignment gap. If this rule is implemented
+ # correctly, the two positions must be equal for the calls to be identical.
+ if pos1 != pos2: return False
+ # from both calls, trim rightmost bases when identical. Do this safely, i.e.
+ # only when the reference bases are not Ns
+ while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
+ ref1 = ref1[:-1]
+ alt1 = alt1[:-1]
+ while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
+ ref2 = ref2[:-1]
+ alt2 = alt2[:-1]
+ # now, the alternative alleles must be identical
+ return alt1 == alt2
+
+###########################################################################################################
+###########################################################################################################
+## API functions added by Andreas
+###########################################################################################################
+
+ def connect( self, filename ):
+ '''connect to tabix file.'''
+ self.tabixfile = pysam.Tabixfile( filename )
+ self._parse_header(self.tabixfile.header)
+
+ def fetch(self,
+ reference = None,
+ start = None,
+ end = None,
+ region = None ):
+ """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
+
+ iter = self.tabixfile.fetch( reference, start, end, region, parser = pysam.asVCF() )
+ for x in iter:
+ yield VCFRecord( x, self )
+
+ def validate( self, record ):
+ '''validate vcf record.
+
+ returns a validated record.
+ '''
+
+ chrom, pos = record.chrom, record.pos
+
+ # check reference
+ ref = record.ref
+ if ref == ".":
+ self.error(str(record),self.MISSING_REF)
+ if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
+ else: ref = ""
+ else:
+ for c in ref:
+ if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF)
+ if "N" in ref: ref = get_sequence(chrom,
+ pos,
+ pos+len(ref),
+ self._reference)
+
+ # make sure reference is sane
+ if self._reference:
+ left = max(0,self.pos-100)
+ faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference)
+ faref = faref_leftflank[pos-left:]
+ if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
+ ref = faref
+
+ # check: format fields are defined
+ for f in record.format:
+ if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f)
+
+ # check: all filters are defined
+ for f in record.filter:
+ if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f)
+
+ # convert v3.3 alleles
+ if self._version == 33:
+ if len(ref) != 1: self.error(line,self.V33_BAD_REF)
+ newalts = []
+ have_deletions = False
+ for a in alt:
+ if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
+ elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
+ elif a.startswith('D'): # allow D<seq> and D<num>
+ have_deletions = True
+ try:
+ l = int(a[1:]) # throws ValueError if sequence
+ if len(ref) < l: # add to reference if necessary
+ addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
+ ref += addns
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ a = ref[l:] # new deletion, deleting pos...pos+l
+ except ValueError:
+ s = a[1:]
+ if len(ref) < len(s): # add Ns to reference if necessary
+ addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
+ if not s.endswith(addns) and addns != 'N'*len(addns):
+ self.error(line,self.V33_UNMATCHED_DELETION,
+ "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
+ ref += addns
+ for i,na in enumerate(newalts): newalts[i] = na+addns
+ a = ref[len(s):] # new deletion, deleting from pos
+ else:
+ self.error(line,self.V33_BAD_ALLELE)
+ newalts.append(a)
+ alt = newalts
+ # deletion alleles exist, add dummy 1st reference allele, and account for leading base
+ if have_deletions:
+ if pos == 0:
+ # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
+ addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
+ ref += addn
+ alt = [allele+addn for allele in alt]
+ else:
+ addn = get_sequence(chrom,pos-1,pos,self._reference)
+ ref = addn + ref
+ alt = [addn + allele for allele in alt]
+ pos -= 1
+ else:
+ # format v4.0 -- just check for nucleotides
+ for allele in alt:
+ if not alleleRegEx.match(allele):
+ self.error(line,self.V40_BAD_ALLELE,allele)
+
+
+ # check for leading nucleotide in indel calls
+ for allele in alt:
+ if len(allele) != len(ref):
+ if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
+ if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
+ self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
+
+ # trim trailing bases in alleles
+ for i in range(1,min(len(ref),min(map(len,alt)))):
+ if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
+ break
+ ref, alt = ref[:-1], [allele[:-1] for allele in alt]
+
+ # left-align alleles, if a reference is available
+ if self._leftalign and self._reference:
+ while left < pos:
+ movable = True
+ for allele in alt:
+ if len(allele) > len(ref):
+ longest, shortest = allele, ref
+ else:
+ longest, shortest = ref, allele
+ if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
+ movable = False
+ if longest[-1].upper() != longest[len(shortest)-1].upper():
+ movable = False
+ if not movable:
+ break
+ ref = ref[:-1]
+ alt = [allele[:-1] for allele in alt]
+ if min(len(allele) for allele in alt) == 0 or len(ref) == 0:
+ ref = faref_leftflank[pos-left-1] + ref
+ alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
+ pos -= 1
+
+
+
+
projects / pysam.git / blobdiff