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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcvcf.pyx @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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1 # cython: embedsignature=True
2 #
3 # Code to read, write and edit VCF files
4 #
5 # VCF lines are encoded as a dictionary with these keys (note: all lowercase):
6 # 'chrom': string
7 # 'pos': integer
8 # 'id': string
9 # 'ref': string
10 # 'alt': list of strings
11 # 'qual': integer
12 # 'filter': None (missing value), or list of keys (strings); empty list parsed as ["PASS"]
13 # 'info': dictionary of values (see below)
14 # 'format': list of keys (strings)
15 # sample keys: dictionary of values (see below)
16 #
17 # The sample keys are accessible through vcf.getsamples()
18 #
19 # A dictionary of values contains value keys (defined in ##INFO or
20 # ##FORMAT lines) which map to a list, containing integers, floats,
21 # strings, or characters. Missing values are replaced by a particular
22 # value, often -1 or .
23 #
24 # Genotypes are not stored as a string, but as a list of 1 or 3
25 # elements (for haploid and diploid samples), the first (and last) the
26 # integer representing an allele, and the second the separation
27 # character. Note that there is just one genotype per sample, but for
28 # consistency the single element is stored in a list.
29 #
30 # Header lines other than ##INFO, ##FORMAT and ##FILTER are stored as
31 # (key, value) pairs and are accessible through getheader()
32 #
33 # The VCF class can be instantiated with a 'regions' variable
34 # consisting of tuples (chrom,start,end) encoding 0-based half-open
35 # segments. Only variants with a position inside the segment will be
36 # parsed. A regions parser is available under parse_regions.
37 #
38 # When instantiated, a reference can be passed to the VCF class. This
39 # may be any class that supports a fetch(chrom, start, end) method.
40 #
41 # NOTE: the position that is returned to Python is 0-based, NOT
42 # 1-based as in the VCF file.
43 # NOTE: There is also preliminary VCF functionality in the VariantFile class.
44 #
45 # TODO:
46 # only v4.0 writing is complete; alleles are not converted to v3.3 format
47 #
48
49 from collections import namedtuple, defaultdict
50 from operator import itemgetter
51 import sys, re, copy, bisect
52
53 from libc.stdlib cimport atoi
54 from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
55 from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
56
57 cimport pysam.libctabix as libctabix
58 cimport pysam.libctabixproxies as libctabixproxies
59
60 from pysam.libcutils cimport force_str
61
62 import pysam
63
64 gtsRegEx = re.compile("[|/\\\\]")
65 alleleRegEx = re.compile('^[ACGTN]+$')
66
67 # Utility function. Uses 0-based coordinates
68 def get_sequence(chrom, start, end, fa):
69 # obtain sequence from .fa file, without truncation
70 if end<=start: return ""
71 if not fa: return "N"*(end-start)
72 if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
73 sequence = fa.fetch(chrom, start, end).upper()
74 if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
75 return sequence
76
77 # Utility function. Parses a region string
78 def parse_regions( string ):
79 result = []
80 for r in string.split(','):
81 elts = r.split(':')
82 chrom, start, end = elts[0], 0, 3000000000
83 if len(elts)==1: pass
84 elif len(elts)==2:
85 if len(elts[1])>0:
86 ielts = elts[1].split('-')
87 if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
88 try: start, end = int(ielts[0])-1, int(ielts[1])
89 except: raise ValueError("Don't understand region string '%s'" % r)
90 else:
91 raise ValueError("Don't understand region string '%s'" % r)
92 result.append( (chrom,start,end) )
93 return result
94
95
96 FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue')
97
98 ###########################################################################################################
99 #
100 # New class
101 #
102 ###########################################################################################################
103
104 cdef class VCFRecord(libctabixproxies.TupleProxy):
105 '''vcf record.
106
107 initialized from data and vcf meta
108 '''
109
110 cdef vcf
111 cdef char * contig
112 cdef uint32_t pos
113
114 def __init__(self, vcf):
115 self.vcf = vcf
116 self.encoding = vcf.encoding
117
118 # if len(data) != len(self.vcf._samples):
119 # self.vcf.error(str(data),
120 # self.BAD_NUMBER_OF_COLUMNS,
121 # "expected %s for %s samples (%s), got %s" % \
122 # (len(self.vcf._samples),
123 # len(self.vcf._samples),
124 # self.vcf._samples,
125 # len(data)))
126
127 def __cinit__(self, vcf):
128 # start indexed access at genotypes
129 self.offset = 9
130
131 self.vcf = vcf
132 self.encoding = vcf.encoding
133
134 def error(self, line, error, opt=None):
135 '''raise error.'''
136 # pass to vcf file for error handling
137 return self.vcf.error(line, error, opt)
138
139 cdef update(self, char * buffer, size_t nbytes):
140 '''update internal data.
141
142 nbytes does not include the terminal '\0'.
143 '''
144 libctabixproxies.TupleProxy.update(self, buffer, nbytes)
145
146 self.contig = self.fields[0]
147 # vcf counts from 1 - correct here
148 self.pos = atoi(self.fields[1]) - 1
149
150 def __len__(self):
151 return max(0, self.nfields - 9)
152
153 property contig:
154 def __get__(self): return self.contig
155
156 property pos:
157 def __get__(self): return self.pos
158
159 property id:
160 def __get__(self): return self.fields[2]
161
162 property ref:
163 def __get__(self):
164 return self.fields[3]
165
166 property alt:
167 def __get__(self):
168 # convert v3.3 to v4.0 alleles below
169 alt = self.fields[4]
170 if alt == ".": alt = []
171 else: alt = alt.upper().split(',')
172 return alt
173
174 property qual:
175 def __get__(self):
176 qual = self.fields[5]
177 if qual == b".": qual = -1
178 else:
179 try: qual = float(qual)
180 except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
181 return qual
182
183 property filter:
184 def __get__(self):
185 f = self.fields[6]
186 # postpone checking that filters exist. Encode missing filter or no filtering as empty list
187 if f == b"." or f == b"PASS" or f == b"0": return []
188 else: return f.split(';')
189
190 property info:
191 def __get__(self):
192 col = self.fields[7]
193 # dictionary of keys, and list of values
194 info = {}
195 if col != b".":
196 for blurp in col.split(';'):
197 elts = blurp.split('=')
198 if len(elts) == 1: v = None
199 elif len(elts) == 2: v = elts[1]
200 else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
201 info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self.vcf))
202 return info
203
204 property format:
205 def __get__(self):
206 return self.fields[8].split(':')
207
208 property samples:
209 def __get__(self):
210 return self.vcf._samples
211
212 def __getitem__(self, key):
213
214 # parse sample columns
215 values = self.fields[self.vcf._sample2column[key]].split(':')
216 alt = self.alt
217 format = self.format
218
219 if len(values) > len(format):
220 self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
221 (len(values),key,len(format)))
222
223 result = {}
224 for idx in range(len(format)):
225 expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
226 if idx < len(values): value = values[idx]
227 else:
228 if expected == -1: value = "."
229 else: value = ",".join(["."]*expected)
230
231 result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
232 if expected != -1 and len(result[format[idx]]) != expected:
233 self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
234 "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
235 if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
236 result[format[idx]] = result[format[idx]][:expected]
237
238 return result
239
240
241 cdef class asVCFRecord(libctabix.Parser):
242 '''converts a :term:`tabix row` into a VCF record.'''
243 cdef vcffile
244 def __init__(self, vcffile):
245 self.vcffile = vcffile
246
247 cdef parse(self, char * buffer, int len):
248 cdef VCFRecord r
249 r = VCFRecord(self.vcffile)
250 r.copy(buffer, len)
251 return r
252
253 class VCF(object):
254
255 # types
256 NT_UNKNOWN = 0
257 NT_NUMBER = 1
258 NT_ALLELES = 2
259 NT_NR_ALLELES = 3
260 NT_GENOTYPES = 4
261 NT_PHASED_GENOTYPES = 5
262
263 _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
264 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
265 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
266 3:"BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)",
267 4:"POS_NOT_NUMERICAL:Position column is not numerical",
268 5:"UNKNOWN_CHAR_IN_REF:Unknown character in reference field",
269 6:"V33_BAD_REF:Reference should be single-character in v3.3 VCF",
270 7:"V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF",
271 8:"POS_NOT_POSITIVE:Position field must be >0",
272 9:"QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'",
273 10:"ERROR_INFO_STRING:Error while parsing info field",
274 11:"ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)",
275 12:"ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s",
276 13:"ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string",
277 14:"FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header",
278 15:"FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header",
279 16:"BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)",
280 17:"BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)",
281 18:"BAD_GENOTYPE:Cannot parse genotype (%s)",
282 19:"V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)",
283 20:"MISSING_REF:Reference allele missing",
284 21:"V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)",
285 22:"V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets",
286 23:"FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes",
287 24:"V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields",
288 25:"HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs",
289 26:"WRONG_REF:Wrong reference %s",
290 27:"ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data",
291 28:"BAD_CHR_TAG:Error calculating chr tag for %s",
292 29:"ZERO_LENGTH_ALLELE:Found zero-length allele",
293 30:"MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base",
294 31:"ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'",
295 32:"ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s",
296 33:"ERROR_FLAG_HAS_VALUE:Flag fields should not have a value",
297 }
298
299 # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
300 _header = []
301
302 # version number; 33=v3.3; 40=v4.0
303 _version = 40
304
305 # info, filter and format data
306 _info = {}
307 _filter = {}
308 _format = {}
309
310 # header; and required columns
311 _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
312 _samples = []
313
314 # control behaviour
315 _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD
316 _warn_errors = set([])
317 _leftalign = False
318
319 # reference sequence
320 _reference = None
321
322 # regions to include; None includes everything
323 _regions = None
324
325 # statefull stuff
326 _lineno = -1
327 _line = None
328 _lines = None
329
330 def __init__(self, _copy=None, reference=None, regions=None,
331 lines=None, leftalign=False):
332 # make error identifiers accessible by name
333 for id in self._errors.keys():
334 self.__dict__[self._errors[id].split(':')[0]] = id
335 if _copy != None:
336 self._leftalign = _copy._leftalign
337 self._header = _copy._header[:]
338 self._version = _copy._version
339 self._info = copy.deepcopy(_copy._info)
340 self._filter = copy.deepcopy(_copy._filter)
341 self._format = copy.deepcopy(_copy._format)
342 self._samples = _copy._samples[:]
343 self._sample2column = copy.deepcopy(_copy._sample2column)
344 self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
345 self._warn_errors = copy.deepcopy(_copy._warn_errors)
346 self._reference = _copy._reference
347 self._regions = _copy._regions
348 if reference: self._reference = reference
349 if regions: self._regions = regions
350 if leftalign: self._leftalign = leftalign
351 self._lines = lines
352 self.encoding = "ascii"
353 self.tabixfile = None
354
355 def error(self,line,error,opt=None):
356 if error in self._ignored_errors: return
357 errorlabel, errorstring = self._errors[error].split(':')
358 if opt: errorstring = errorstring % opt
359 errwarn = ["Error","Warning"][error in self._warn_errors]
360 errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
361 if error in self._warn_errors: return
362 raise ValueError(errorstring)
363
364 def parse_format(self,line,format,filter=False):
365 if self._version == 40:
366 if not format.startswith('<'):
367 self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
368 format = "<"+format
369 if not format.endswith('>'):
370 self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
371 format += ">"
372 format = format[1:-1]
373 data = {'id':None,'number':None,'type':None,'descr':None}
374 idx = 0
375 while len(format.strip())>0:
376 elts = format.strip().split(',')
377 first, rest = elts[0], ','.join(elts[1:])
378 if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
379 if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
380 if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
381 first = ["ID=","Number=","Type=","Description="][idx] + first
382 if first.startswith('ID='): data['id'] = first.split('=')[1]
383 elif first.startswith('Number='): data['number'] = first.split('=')[1]
384 elif first.startswith('Type='): data['type'] = first.split('=')[1]
385 elif first.startswith('Description='):
386 elts = format.split('"')
387 if len(elts)<3:
388 self.error(line,self.FORMAT_MISSING_QUOTES)
389 elts = first.split('=') + [rest]
390 data['descr'] = elts[1]
391 rest = '"'.join(elts[2:])
392 if rest.startswith(','): rest = rest[1:]
393 else:
394 self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
395 format = rest
396 idx += 1
397 if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
398 if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
399 if 'descr' not in data:
400 # missing description
401 self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
402 data['descr'] = ""
403 if not data['type'] and not data['number']:
404 # fine, ##filter format
405 return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
406 if not data['type'] in ["Integer","Float","Character","String","Flag"]:
407 self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
408 # I would like a missing-value field, but it isn't there
409 if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
410 else: data['missing'] = '.'
411 if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
412 try:
413 n = int(data['number'])
414 t = self.NT_NUMBER
415 except ValueError:
416 n = -1
417 if data['number'] == '.': t = self.NT_UNKNOWN
418 elif data['number'] == '#alleles': t = self.NT_ALLELES
419 elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
420 elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
421 elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
422 elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
423 # abbreviations added in VCF version v4.1
424 elif data['number'] == 'A': t = self.NT_ALLELES
425 elif data['number'] == 'G': t = self.NT_GENOTYPES
426 else:
427 self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
428 # if number is 0 - type must be Flag
429 if n == 0 and data['type'] != 'Flag':
430 self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
431 # force type 'Flag' if no number
432 data['type'] = 'Flag'
433
434 return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
435
436 def format_format( self, fmt, filter=False ):
437 values = [('ID',fmt.id)]
438 if fmt.number != None and not filter:
439 if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
440 elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
441 elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
442 elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
443 elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
444 elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
445 else:
446 raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
447 values.append( ('Number',nmb) )
448 values.append( ('Type', fmt.type) )
449 values.append( ('Description', '"' + fmt.description + '"') )
450 if self._version == 33:
451 format = ",".join([v for k,v in values])
452 else:
453 format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">"
454 return format
455
456 def get_expected(self, format, formatdict, alt):
457 fmt = formatdict[format]
458 if fmt.numbertype == self.NT_UNKNOWN: return -1
459 if fmt.numbertype == self.NT_NUMBER: return fmt.number
460 if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
461 if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
462 if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
463 if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
464 return 0
465
466
467 def _add_definition(self, formatdict, key, data, line ):
468 if key in formatdict: return
469 self.error(line,self.ERROR_UNKNOWN_KEY,key)
470 if data == None:
471 formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
472 return
473 if data == []: data = [""] # unsure what type -- say string
474 if type(data[0]) == type(0.0):
475 formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
476 return
477 if type(data[0]) == type(0):
478 formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
479 return
480 formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
481
482
483 # todo: trim trailing missing values
484 def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
485 output, sdata = [], []
486 if type(data) == type([]): # for FORMAT field, make data with dummy values
487 d = {}
488 for k in data: d[k] = []
489 data = d
490 # convert missing values; and silently add definitions if required
491 for k in data:
492 self._add_definition( format, k, data[k], "(output)" )
493 for idx,v in enumerate(data[k]):
494 if v == format[k].missingvalue: data[k][idx] = "."
495 # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
496 for k in data:
497 if k != 'GT': sdata.append( (k,data[k]) )
498 sdata.sort()
499 if 'GT' in data:
500 sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
501 for k,v in sdata:
502 if v == []: v = None
503 if key and value:
504 if v != None: output.append( k+"="+','.join(map(str,v)) )
505 else: output.append( k )
506 elif key: output.append(k)
507 elif value:
508 if v != None: output.append( ','.join(map(str,v)) )
509 else: output.append( "." ) # should not happen
510 # snip off trailing missing data
511 while len(output) > 1:
512 last = output[-1].replace(',','').replace('.','')
513 if len(last)>0: break
514 output = output[:-1]
515 return separator.join(output)
516
517
518 def enter_default_format(self):
519 for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
520 FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
521 FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
522 FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
523 FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
524 FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
525 FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
526 FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
527 FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
528 FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
529 FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
530 FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
531 FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1),
532 FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
533 ]:
534 if f.id not in self._format:
535 self._format[f.id] = f
536
537 def parse_header(self, line):
538
539 assert line.startswith('##')
540 elts = line[2:].split('=')
541 key = elts[0].strip()
542 value = '='.join(elts[1:]).strip()
543 if key == "fileformat":
544 if value == "VCFv3.3":
545 self._version = 33
546 elif value == "VCFv4.0":
547 self._version = 40
548 elif value == "VCFv4.1":
549 # AH - for testing
550 self._version = 40
551 elif value == "VCFv4.2":
552 # AH - for testing
553 self._version = 40
554 else:
555 self.error(line,self.UNKNOWN_FORMAT_STRING)
556 elif key == "INFO":
557 f = self.parse_format(line, value)
558 self._info[ f.id ] = f
559 elif key == "FILTER":
560 f = self.parse_format(line, value, filter=True)
561 self._filter[ f.id ] = f
562 elif key == "FORMAT":
563 f = self.parse_format(line, value)
564 self._format[ f.id ] = f
565 else:
566 # keep other keys in the header field
567 self._header.append( (key,value) )
568
569
570 def write_header( self, stream ):
571 stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
572 for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
573 for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
574 for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
575
576
577 def parse_heading( self, line ):
578 assert line.startswith('#')
579 assert not line.startswith('##')
580 headings = line[1:].split('\t')
581 # test for 8, as FORMAT field might be missing
582 if len(headings)==1 and len(line[1:].split()) >= 8:
583 self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
584 headings = line[1:].split()
585
586 for i,s in enumerate(self._required):
587
588 if len(headings)<=i or headings[i] != s:
589
590 if len(headings) <= i:
591 err = "(%sth entry not found)" % (i+1)
592 else:
593 err = "(found %s, expected %s)" % (headings[i],s)
594
595 #self.error(line,self.BADLY_FORMATTED_HEADING,err)
596 # allow FORMAT column to be absent
597 if len(headings) == 8:
598 headings.append("FORMAT")
599 else:
600 self.error(line,self.BADLY_FORMATTED_HEADING,err)
601
602 self._samples = headings[9:]
603 self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
604
605 def write_heading( self, stream ):
606 stream.write("#" + "\t".join(self._required + self._samples) + "\n")
607
608 def convertGT(self, GTstring):
609 if GTstring == ".": return ["."]
610 try:
611 gts = gtsRegEx.split(GTstring)
612 if len(gts) == 1: return [int(gts[0])]
613 if len(gts) != 2: raise ValueError()
614 if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
615 return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
616 except ValueError:
617 self.error(self._line,self.BAD_GENOTYPE,GTstring)
618 return [".","|","."]
619
620 def convertGTback(self, GTdata):
621 return ''.join(map(str,GTdata))
622
623 def parse_formatdata( self, key, value, formatdict, line ):
624 # To do: check that the right number of values is present
625 f = formatdict.get(key,None)
626 if f == None:
627 self._add_definition(formatdict, key, value, line )
628 f = formatdict[key]
629 if f.type == "Flag":
630 if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
631 return []
632 values = value.split(',')
633 # deal with trailing data in some early VCF files
634 if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
635 self.error(line,self.ERROR_TRAILING_DATA,values[-1])
636 values[-1] = values[-1].split(';')[0]
637 if f.type == "Integer":
638 for idx,v in enumerate(values):
639 try:
640 if v == ".": values[idx] = f.missingvalue
641 else: values[idx] = int(v)
642 except:
643 self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
644 return [0] * len(values)
645 return values
646 elif f.type == "String":
647 self._line = line
648 if f.id == "GT": values = list(map( self.convertGT, values ))
649 return values
650 elif f.type == "Character":
651 for v in values:
652 if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
653 return values
654 elif f.type == "Float":
655 for idx,v in enumerate(values):
656 if v == ".": values[idx] = f.missingvalue
657 try: return list(map(float,values))
658 except:
659 self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values)))
660 return [0.0] * len(values)
661 else:
662 # can't happen
663 self.error(line,self.ERROR_INFO_STRING)
664
665 def inregion(self, chrom, pos):
666 if not self._regions: return True
667 for r in self._regions:
668 if r[0] == chrom and r[1] <= pos < r[2]: return True
669 return False
670
671 def parse_data( self, line, lineparse=False ):
672 cols = line.split('\t')
673 if len(cols) != len(self._samples)+9:
674 # gracefully deal with absent FORMAT column
675 # and those missing samples
676 if len(cols) == 8:
677 cols.append("")
678 else:
679 self.error(line,
680 self.BAD_NUMBER_OF_COLUMNS,
681 "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
682
683 chrom = cols[0]
684
685 # get 0-based position
686 try: pos = int(cols[1])-1
687 except: self.error(line,self.POS_NOT_NUMERICAL)
688 if pos < 0: self.error(line,self.POS_NOT_POSITIVE)
689
690 # implement filtering
691 if not self.inregion(chrom,pos): return None
692
693 # end of first-pass parse for sortedVCF
694 if lineparse: return chrom, pos, line
695
696 id = cols[2]
697
698 ref = cols[3].upper()
699 if ref == ".":
700 self.error(line,self.MISSING_REF)
701 if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
702 else: ref = ""
703 else:
704 for c in ref:
705 if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
706 if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
707
708 # make sure reference is sane
709 if self._reference:
710 left = max(0,pos-100)
711 faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
712 faref = faref_leftflank[pos-left:]
713 if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
714 ref = faref
715
716 # convert v3.3 to v4.0 alleles below
717 if cols[4] == ".": alt = []
718 else: alt = cols[4].upper().split(',')
719
720 if cols[5] == ".": qual = -1
721 else:
722 try: qual = float(cols[5])
723 except: self.error(line,self.QUAL_NOT_NUMERICAL)
724
725 # postpone checking that filters exist. Encode missing filter or no filtering as empty list
726 if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
727 else: filter = cols[6].split(';')
728
729 # dictionary of keys, and list of values
730 info = {}
731 if cols[7] != ".":
732 for blurp in cols[7].split(';'):
733 elts = blurp.split('=')
734 if len(elts) == 1: v = None
735 elif len(elts) == 2: v = elts[1]
736 else: self.error(line,self.ERROR_INFO_STRING)
737 info[elts[0]] = self.parse_formatdata(elts[0],
738 v,
739 self._info,
740 line)
741
742 # Gracefully deal with absent FORMAT column
743 if cols[8] == "": format = []
744 else: format = cols[8].split(':')
745
746 # check: all filters are defined
747 for f in filter:
748 if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f)
749
750 # check: format fields are defined
751 if self._format:
752 for f in format:
753 if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
754
755 # convert v3.3 alleles
756 if self._version == 33:
757 if len(ref) != 1: self.error(line,self.V33_BAD_REF)
758 newalts = []
759 have_deletions = False
760 for a in alt:
761 if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
762 elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
763 elif a.startswith('D'): # allow D<seq> and D<num>
764 have_deletions = True
765 try:
766 l = int(a[1:]) # throws ValueError if sequence
767 if len(ref) < l: # add to reference if necessary
768 addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
769 ref += addns
770 for i,na in enumerate(newalts): newalts[i] = na+addns
771 a = ref[l:] # new deletion, deleting pos...pos+l
772 except ValueError:
773 s = a[1:]
774 if len(ref) < len(s): # add Ns to reference if necessary
775 addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
776 if not s.endswith(addns) and addns != 'N'*len(addns):
777 self.error(line,self.V33_UNMATCHED_DELETION,
778 "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
779 ref += addns
780 for i,na in enumerate(newalts): newalts[i] = na+addns
781 a = ref[len(s):] # new deletion, deleting from pos
782 else:
783 self.error(line,self.V33_BAD_ALLELE)
784 newalts.append(a)
785 alt = newalts
786 # deletion alleles exist, add dummy 1st reference allele, and account for leading base
787 if have_deletions:
788 if pos == 0:
789 # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
790 addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
791 ref += addn
792 alt = [allele+addn for allele in alt]
793 else:
794 addn = get_sequence(chrom,pos-1,pos,self._reference)
795 ref = addn + ref
796 alt = [addn + allele for allele in alt]
797 pos -= 1
798 else:
799 # format v4.0 -- just check for nucleotides
800 for allele in alt:
801 if not alleleRegEx.match(allele):
802 self.error(line,self.V40_BAD_ALLELE,allele)
803
804 # check for leading nucleotide in indel calls
805 for allele in alt:
806 if len(allele) != len(ref):
807 if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
808 if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
809 self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
810
811 # trim trailing bases in alleles
812 # AH: not certain why trimming this needs to be added
813 # disabled now for unit testing
814 # if alt:
815 # for i in range(1,min(len(ref),min(map(len,alt)))):
816 # if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
817 # break
818 # ref, alt = ref[:-1], [allele[:-1] for allele in alt]
819
820 # left-align alleles, if a reference is available
821 if self._leftalign and self._reference:
822 while left < pos:
823 movable = True
824 for allele in alt:
825 if len(allele) > len(ref):
826 longest, shortest = allele, ref
827 else:
828 longest, shortest = ref, allele
829 if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
830 movable = False
831 if longest[-1].upper() != longest[len(shortest)-1].upper():
832 movable = False
833 if not movable:
834 break
835 ref = ref[:-1]
836 alt = [allele[:-1] for allele in alt]
837 if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
838 ref = faref_leftflank[pos-left-1] + ref
839 alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
840 pos -= 1
841
842 # parse sample columns
843 samples = []
844 for sample in cols[9:]:
845 dict = {}
846 values = sample.split(':')
847 if len(values) > len(format):
848 self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
849 for idx in range(len(format)):
850 expected = self.get_expected(format[idx], self._format, alt)
851 if idx < len(values): value = values[idx]
852 else:
853 if expected == -1: value = "."
854 else: value = ",".join(["."]*expected)
855
856 dict[format[idx]] = self.parse_formatdata(format[idx],
857 value,
858 self._format,
859 line)
860 if expected != -1 and len(dict[format[idx]]) != expected:
861 self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
862 "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
863 if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
864 dict[format[idx]] = dict[format[idx]][:expected]
865 samples.append( dict )
866
867 # done
868 d = {'chrom':chrom,
869 'pos':pos, # return 0-based position
870 'id':id,
871 'ref':ref,
872 'alt':alt,
873 'qual':qual,
874 'filter':filter,
875 'info':info,
876 'format':format}
877 for key,value in zip(self._samples,samples):
878 d[key] = value
879
880 return d
881
882
883 def write_data(self, stream, data):
884 required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
885 for k in required:
886 if k not in data: raise ValueError("Required key %s not found in data" % str(k))
887 if data['alt'] == []: alt = "."
888 else: alt = ",".join(data['alt'])
889 if data['filter'] == None: filter = "."
890 elif data['filter'] == []:
891 if self._version == 33: filter = "0"
892 else: filter = "PASS"
893 else: filter = ';'.join(data['filter'])
894 if data['qual'] == -1: qual = "."
895 else: qual = str(data['qual'])
896
897 output = [data['chrom'],
898 str(data['pos']+1), # change to 1-based position
899 data['id'],
900 data['ref'],
901 alt,
902 qual,
903 filter,
904 self.format_formatdata(
905 data['info'], self._info, separator=";"),
906 self.format_formatdata(
907 data['format'], self._format, value=False)]
908
909 for s in self._samples:
910 output.append(self.format_formatdata(
911 data[s], self._format, key=False))
912
913 stream.write( "\t".join(output) + "\n" )
914
915 def _parse_header(self, stream):
916 self._lineno = 0
917 for line in stream:
918 line = force_str(line, self.encoding)
919 self._lineno += 1
920 if line.startswith('##'):
921 self.parse_header(line.strip())
922 elif line.startswith('#'):
923 self.parse_heading(line.strip())
924 self.enter_default_format()
925 else:
926 break
927 return line
928
929 def _parse(self, line, stream):
930 # deal with files with header only
931 if line.startswith("##"): return
932 if len(line.strip()) > 0:
933 d = self.parse_data( line.strip() )
934 if d: yield d
935 for line in stream:
936 self._lineno += 1
937 if self._lines and self._lineno > self._lines: raise StopIteration
938 d = self.parse_data( line.strip() )
939 if d: yield d
940
941 ######################################################################################################
942 #
943 # API follows
944 #
945 ######################################################################################################
946
947 def getsamples(self):
948 """ List of samples in VCF file """
949 return self._samples
950
951 def setsamples(self,samples):
952 """ List of samples in VCF file """
953 self._samples = samples
954
955 def getheader(self):
956 """ List of header key-value pairs (strings) """
957 return self._header
958
959 def setheader(self,header):
960 """ List of header key-value pairs (strings) """
961 self._header = header
962
963 def getinfo(self):
964 """ Dictionary of ##INFO tags, as VCF.FORMAT values """
965 return self._info
966
967 def setinfo(self,info):
968 """ Dictionary of ##INFO tags, as VCF.FORMAT values """
969 self._info = info
970
971 def getformat(self):
972 """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
973 return self._format
974
975 def setformat(self,format):
976 """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
977 self._format = format
978
979 def getfilter(self):
980 """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
981 return self._filter
982
983 def setfilter(self,filter):
984 """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
985 self._filter = filter
986
987 def setversion(self, version):
988 if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
989 self._version = version
990
991 def setregions(self, regions):
992 self._regions = regions
993
994 def setreference(self, ref):
995 """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
996 self._reference = ref
997
998 def ignoreerror(self, errorstring):
999 try: self._ignored_errors.add(self.__dict__[errorstring])
1000 except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
1001
1002 def warnerror(self, errorstring):
1003 try: self._warn_errors.add(self.__dict__[errorstring])
1004 except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
1005
1006 def parse(self, stream):
1007 """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
1008 last_line = self._parse_header(stream)
1009 # now return a generator that does the actual work. In this way the pre-processing is done
1010 # before the first piece of data is yielded
1011 return self._parse(last_line, stream)
1012
1013 def write(self, stream, datagenerator):
1014 """ Writes a VCF file to a stream, using a data generator (or list) """
1015 self.write_header(stream)
1016 self.write_heading(stream)
1017 for data in datagenerator: self.write_data(stream,data)
1018
1019 def writeheader(self, stream):
1020 """ Writes a VCF header """
1021 self.write_header(stream)
1022 self.write_heading(stream)
1023
1024 def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2):
1025 """ Utility function: compares two calls for equality """
1026 # a variant should always be assigned to a unique position, one base before
1027 # the leftmost position of the alignment gap. If this rule is implemented
1028 # correctly, the two positions must be equal for the calls to be identical.
1029 if pos1 != pos2: return False
1030 # from both calls, trim rightmost bases when identical. Do this safely, i.e.
1031 # only when the reference bases are not Ns
1032 while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
1033 ref1 = ref1[:-1]
1034 alt1 = alt1[:-1]
1035 while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
1036 ref2 = ref2[:-1]
1037 alt2 = alt2[:-1]
1038 # now, the alternative alleles must be identical
1039 return alt1 == alt2
1040
1041 ###########################################################################################################
1042 ###########################################################################################################
1043 ## API functions added by Andreas
1044 ###########################################################################################################
1045
1046 def connect(self, filename, encoding="ascii"):
1047 '''connect to tabix file.'''
1048 self.encoding=encoding
1049 self.tabixfile = pysam.Tabixfile(filename, encoding=encoding)
1050 self._parse_header(self.tabixfile.header)
1051
1052 def __del__(self):
1053 self.close()
1054 self.tabixfile = None
1055
1056 def close(self):
1057 if self.tabixfile:
1058 self.tabixfile.close()
1059 self.tabixfile = None
1060
1061 def fetch(self,
1062 reference=None,
1063 start=None,
1064 end=None,
1065 region=None ):
1066 """ Parse a stream of VCF-formatted lines.
1067 Initializes class instance and return generator """
1068 return self.tabixfile.fetch(
1069 reference,
1070 start,
1071 end,
1072 region,
1073 parser = asVCFRecord(self))
1074
1075 def validate(self, record):
1076 '''validate vcf record.
1077
1078 returns a validated record.
1079 '''
1080
1081 raise NotImplementedError("needs to be checked")
1082
1083 chrom, pos = record.chrom, record.pos
1084
1085 # check reference
1086 ref = record.ref
1087 if ref == ".":
1088 self.error(str(record),self.MISSING_REF)
1089 if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
1090 else: ref = ""
1091 else:
1092 for c in ref:
1093 if c not in "ACGTN": self.error(str(record),self.UNKNOWN_CHAR_IN_REF)
1094 if "N" in ref: ref = get_sequence(chrom,
1095 pos,
1096 pos+len(ref),
1097 self._reference)
1098
1099 # make sure reference is sane
1100 if self._reference:
1101 left = max(0,self.pos-100)
1102 faref_leftflank = get_sequence(chrom,left,self.pos+len(ref),self._reference)
1103 faref = faref_leftflank[pos-left:]
1104 if faref != ref: self.error(str(record),self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
1105 ref = faref
1106
1107 # check: format fields are defined
1108 for f in record.format:
1109 if f not in self._format: self.error(str(record),self.FORMAT_NOT_DEFINED, f)
1110
1111 # check: all filters are defined
1112 for f in record.filter:
1113 if f not in self._filter: self.error(str(record),self.FILTER_NOT_DEFINED, f)
1114
1115 # convert v3.3 alleles
1116 if self._version == 33:
1117 if len(ref) != 1: self.error(str(record),self.V33_BAD_REF)
1118 newalts = []
1119 have_deletions = False
1120 for a in alt:
1121 if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
1122 elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
1123 elif a.startswith('D'): # allow D<seq> and D<num>
1124 have_deletions = True
1125 try:
1126 l = int(a[1:]) # throws ValueError if sequence
1127 if len(ref) < l: # add to reference if necessary
1128 addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
1129 ref += addns
1130 for i,na in enumerate(newalts): newalts[i] = na+addns
1131 a = ref[l:] # new deletion, deleting pos...pos+l
1132 except ValueError:
1133 s = a[1:]
1134 if len(ref) < len(s): # add Ns to reference if necessary
1135 addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
1136 if not s.endswith(addns) and addns != 'N'*len(addns):
1137 self.error(str(record),self.V33_UNMATCHED_DELETION,
1138 "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
1139 ref += addns
1140 for i,na in enumerate(newalts): newalts[i] = na+addns
1141 a = ref[len(s):] # new deletion, deleting from pos
1142 else:
1143 self.error(str(record),self.V33_BAD_ALLELE)
1144 newalts.append(a)
1145 alt = newalts
1146 # deletion alleles exist, add dummy 1st reference allele, and account for leading base
1147 if have_deletions:
1148 if pos == 0:
1149 # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
1150 addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
1151 ref += addn
1152 alt = [allele+addn for allele in alt]
1153 else:
1154 addn = get_sequence(chrom,pos-1,pos,self._reference)
1155 ref = addn + ref
1156 alt = [addn + allele for allele in alt]
1157 pos -= 1
1158 else:
1159 # format v4.0 -- just check for nucleotides
1160 for allele in alt:
1161 if not alleleRegEx.match(allele):
1162 self.error(str(record),self.V40_BAD_ALLELE,allele)
1163
1164
1165 # check for leading nucleotide in indel calls
1166 for allele in alt:
1167 if len(allele) != len(ref):
1168 if len(allele) == 0: self.error(str(record),self.ZERO_LENGTH_ALLELE)
1169 if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
1170 self.error(str(record),self.MISSING_INDEL_ALLELE_REF_BASE)
1171
1172 # trim trailing bases in alleles
1173 # AH: not certain why trimming this needs to be added
1174 # disabled now for unit testing
1175 # for i in range(1,min(len(ref),min(map(len,alt)))):
1176 # if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
1177 # break
1178 # ref, alt = ref[:-1], [allele[:-1] for allele in alt]
1179
1180 # left-align alleles, if a reference is available
1181 if self._leftalign and self._reference:
1182 while left < pos:
1183 movable = True
1184 for allele in alt:
1185 if len(allele) > len(ref):
1186 longest, shortest = allele, ref
1187 else:
1188 longest, shortest = ref, allele
1189 if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
1190 movable = False
1191 if longest[-1].upper() != longest[len(shortest)-1].upper():
1192 movable = False
1193 if not movable:
1194 break
1195 ref = ref[:-1]
1196 alt = [allele[:-1] for allele in alt]
1197 if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
1198 ref = faref_leftflank[pos-left-1] + ref
1199 alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
1200 pos -= 1
1201
1202 __all__ = [
1203 "VCF", "VCFRecord", ]