/usr/lib/python2.7/dist-packages/pbsuite/utils/VCFIO.py is in python-pbsuite-utils 15.8.24+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 | import sys, re, os
from collections import OrderedDict
from pbsuite.utils.setupLogging import *
#setupLogging(debug=True)
HONTEMPLATE = os.path.join(os.path.dirname(__file__),"vcfTemplate.vcf")
class VCFFile():
"""
Holds all the entries.. no indexing, yet
"""
def __init__(self, filename, template=None, mode='r'):
"""
Either [r]ead , [w]rite, or [a]ppend to a vcf file
"""
#Open or write a file:
self.filename= filename
self.mode = mode
self.filehandler = open(filename, mode)
#INIT the metadata
if template is not None:
self.HEAD = template.HEAD
self.FILTER = template.FILTER
self.INFO = template.INFO
self.ALT = template.ALT
self.FORMAT = template.FORMAT
self.SAMPLES = template.SAMPLES
else:
self.HEAD = OrderedDict()
self.FILTER = OrderedDict()
self.INFO = OrderedDict()
self.ALT = OrderedDict()
self.FORMAT = OrderedDict()
self.SAMPLES = OrderedDict()
if mode in ['r', 'a']:
if template is not None:
logging.warning("Overwriting any META data template has with file's")
self.__parseFile()
else:
self.__entries = []
#Need an iterator
def __iter__(self):
return self.__entries.__iter__()
def __parseFile(self):
self.__entries = []
self.filehandler.seek(0)
for line in self.filehandler.readlines():
if line.startswith("##"):
data = META.fromString(line)
if data.id is None:
self.HEAD[data.key] = data.description
elif data.key == "FILTER":
self.FILTER[data.id] = data
elif data.key == "INFO":
self.INFO[data.id] = data
elif data.key == "ALT":
self.ALT[data.id] = data
elif data.key == "FORMAT":
self.FORMAT[data.id] = data
else:
logging.error("Unrecognized META key %s" % data.key)
elif line.startswith("#"):#Header
for pos, name in enumerate(line.strip().split('\t')[9:]):
self.SAMPLES[name] = pos
else:
self.__parseEntry(line)
def __parseEntry(self, line):
try:
entry = VCFEntry.fromString(line)
self.addEntry(entry)
except ValueError as e:
logging.error("Couldn't parse line %s" % line.strip())
logging.error(e)
exit(1)
def addEntry(self, vcfentry):
##Validation and meta appending...
#meta appending and validation
vcfentry.fileValidate(self)
self.__entries.append(vcfentry)
def write(self, outName):
"""
Output to new file
"""
fout = open(outName, 'w')
for i in self.HEAD:
fout.write(str(self.HEAD[i])+'\n')
for i in self.FILTER:
fout.write(str(self.FILTER[i])+'\n')
for i in self.INFO:
fout.write(str(self.INFO[i])+'\n')
for i in self.ALT:
fout.write(str(self.ALT[i])+'\n')
for i in self.FORMAT:
fout.write(str(self.FORMAT[i])+'\n')
fout.write(VCFEntry.header + "\t" + "\t".join(self.SAMPLES.keys()) + '\n')
for entry in self.__entries:
fout.write(str(entry) + '\n')
METARE = re.compile(('##\s*(?P<key>\w+)\s*=\s*\<\s*ID\s*=\s*(?P<id>\w+)\s*'
',\s*(Number\s*=\s*(?P<number>[0-9.])\s*,'
'\s*Type\s*=\s*(?P<type>\w+)\s*,)?'
'\s*Description\s*=\s*"(?P<description>.*)"\s*\>\s*'),\
re.IGNORECASE)
class META():
"""
Key=<ID=x,Number=y,Type=z,Description="everything has one of these">
or
Key=some text description
Holds the rules on how to parse the various META types
If id == None, we assume some simple text passed in through
description
"""
def __init__(self, key, id=None, number=None, type=None, description=None):
self.key = key
self.id = id
self.number = number
self.type = type
self.description = description
@classmethod
def fromString(cls, line):
match = METARE.match(line)
if match is None:
try:
key,val = line.lstrip("#").strip().split('=')
key = key.strip()
val = val.strip()
return cls(key=key, description=val)
except Exception as e:
logging.error("Error parsing %s\n" % line)
logging.error(str(e)+'\n')
exit(1)
g = match.groupdict()
if g['number'] == '':
g['number'] = None
return cls(**g)
def convert(self, data):
"""
Based on the meta tag's rules, convert this data
"""
if self.type is None:
return data
if self.number == '1':
items = [data]
else:
items = data.split(',')
if self.type.lower() == 'integer':
convert = int
elif self.type.lower() == 'float':
convert = float
elif self.type.lower() == 'flag':
convert = bool
elif self.type.lower() == 'string':
convert = str
else:
convert = lambda x: x
newItems = []
for i in items:
newItems.append(convert(i))
return newItems
def __str__(self):
if self.id is None:
return "##%s=%s" % (self.id, self.description)
return '##{0}=<ID={1},Number={2},Type={3},Description="{4}">'\
.format(self.key, self.id, self.number, self.type, self.description)
class VCFEntry():
"""
CHROM the chromosome.
POS the genome coordinate of the first base in the variant. Within a chromosome, VCF
records are sorted in order of increasing position.
ID a semicolon-separated list of marker identifiers.
REF the reference allele expressed as a sequence of one or more A/C/G/T nucleotides
(e.g. "A" or "AAC")
ALT the alternate allele expressed as a sequence of one or more A/C/G/T nucleotides
(e.g. "A" or "AAC"). If there is more than one alternate alleles, the field should
be a comma-separated list of alternate alleles.
QUAL probability that the ALT allele is incorrectly specified, expressed on the the
phred scale (-10log10(probability)).
FILTER Either "PASS" or a semicolon-separated list of failed quality control filters.
INFO additional information (no white space, tabs, or semi-colons permitted).
FORMAT colon-separated list of data subfields reported for each sample. The format
fields in the Example are explained below.
Only CHROM and POS are required. Everything else will be blank if necessicary
"""
header = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"
def __init__(self, CHROM, POS, ID=None, REF=None, ALT=None, QUAL=None, \
FILTER=None, INFO=None, FORMAT=None, SAMPLES=None):
"""
#CHROM str
#POS int
#ID str or None
#REF str or None
#ALT list or None
#QUAL float or None
#FILTER list or None
#INFO dict or None
#FORMAT list or None
#SAMPLE dict or None
"""
#Populate VCF Entry
self.CHROM = str(CHROM)
self.POS = int(POS)
self.ID = str(ID) if ID is not None else '.'
self.REF = str(REF) if REF is not None else '.'
if ALT is not None:
if type(ALT) == list:
self.ALT = [re.sub('[<>]', '', x) for x in ALT if x != '']
else:
raise ValueError("Expected ALT to be list")
else:
self.ALT = []
self.QUAL = float(QUAL) if QUAL not in [None, '.'] else '.'
if FILTER is not None:
if type(FILTER) == list:
self.FILTER = FILTER
else:
raise ValueError("Invalid Value for FILTER")
else:
self.FILTER = []
if INFO is not None:
if type(INFO) == dict:
self.INFO = INFO
else:
raise ValueError("Invalid Value for INFO")
else:
self.INFO = {}
if FORMAT is not None:
if type(FORMAT) == list:
self.FORMAT = FORMAT
else:
raise ValueError("Invalid Value for INFO")
else:
self.FORMAT = []
if SAMPLES is not None:
self.SAMPLES = SAMPLES
if type(SAMPLES) == dict:
self.SAMPLES = SAMPLES
else:
raise ValueError("Invalid Value for SAMPLE")
else:
self.SAMPLES = {}
@classmethod
def fromString(cls, line):
data = line.strip().split('\t')
chrom = data[0]
pos = int(data[1])
id = data[2]
ref = data[3]
alt = data[4].split(',') if data[4] != '.' else []
qual = float(data[5]) if data[5] != '.' else None
filter = data[6].split(';') if data[6] != '.' else []
info = {}
for i in data[7].split(';'):
k,v = i.split('=')
info[k] = v
format = data[8].split(':') if data[8] != '.' else []
samples = {}
for idx, samp in enumerate(data[9:]):
samples[idx] = samp.split(':')
return cls(chrom, pos, id, ref, alt, qual, filter, info, format, samples)
def fileValidate(self, vcffile):
"""
validates entry as if it's from vcffile .. so all info must exist
in header
updates any blanks (e.g. indexed samples) with metadata info
makes a dict out of the samples information
This is super useful for when you're reading in a file
If you're creating new entries, use VCFFile.addEntry()
and it'll ensure that everything you're adding from that entry is
already documented within the VCFFile's metadata
"""
self.__myparent = vcffile
for i in self.ALT:
if i.upper() not in vcffile.ALT and len(re.sub(i.upper(), "[ATCGN.]", '')) != 0:
raise ValueError("Unknown ALT %s in entry %s" % (i, str(self)))
for i in self.FILTER:
if i not in vcffile.FILTER and i != "PASS":
raise ValueError("Unknown FILTER %s in entry %s" % (str(i), str(self)))
for i in self.INFO:
if i not in vcffile.INFO:
raise ValueError("Unknown INFO %s in entry %s" % (i, str(self)))
self.INFO[i] = vcffile.INFO[i].convert(self.INFO[i])
for i in self.FORMAT:
if i not in vcffile.FORMAT:
raise ValueError("Unknown FORMAT %s in entry %s" % (i, str(self)))
newSamp = {}
for key in self.SAMPLES:
if type(key) == int:
try:
newKey = vcffile.SAMPLES.keys()[key]
newSamp[newKey] = self.SAMPLES[key]
except IndexError:
raise ValueError("More SAMPLES than VCFFile has in entry %s" % (str(self)))
elif key not in vcffile.SAMPLES:
raise ValueError("Unknown SAMPLE %s" % (str(key)))
else:
newSamp[key] = self.SAMPLES[key]
self.SAMPLES = newSamp
def __str__(self):
if self.__myparent is None:
logging.warning("Writing entry without parent. Sample order may suffer")
nALT = ",".join(self.ALT) if len(self.ALT) != 0 else "."
nINFO = ";".join(["%s=%s" % (x,",".join([str(y) for y in self.INFO[x]])) for x in self.INFO])
nFORMAT = ':'.join(self.FORMAT)
nSAMPLES = []
for s in self.SAMPLES:
dat = []
for i in nFORMAT:
dat.append(i)
else:
nALT = []
for i in self.ALT:
if i in self.__myparent.ALT:
nALT.append("<%s>" % i)
else:
nALT.append(i)
nALT = ",".join(nALT)
nINFO = []
for i in self.__myparent.INFO:
if i in self.INFO:
if self.__myparent.INFO[i].number == '1':
nINFO.append("%s=%s" % (i, self.INFO[i][0]))
else:
nINFO.append("%s=%s" % (i, ",".join([str(y) for y in self.INFO[i]])))
nINFO = ";".join(nINFO)
nFORMATd = []
for i in self.__myparent.FORMAT:
if i in self.FORMAT:
nFORMATd.append(i)
nSAMPLES = []
for i in self.__myparent.SAMPLES:
if i in self.SAMPLES:
nSAMPLES.append(":".join([str(x) for x in self.SAMPLES[i]]))
else:
nSAMPLES.append(':'.join(['.']*len(nFORMATd)))
if len(nFORMATd) == 0:
nFORMAT = '.'; nSAMPLES = ['.']
else:
nFORMAT = ':'.join(nFORMATd)
return "\t".join([self.CHROM, \
str(self.POS),\
self.ID, \
self.REF, \
nALT, \
str(self.QUAL), \
";".join(self.FILTER), \
nINFO, \
nFORMAT, \
"\t".join(nSAMPLES)])
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
#otherwise we'll format correctly
#for i in self.__myparent:
#Need . for unknown samples
#
def test(filename):
f = VCFFile(filename, 'r')
for i in f:
print str(i)
return f
if __name__ == '__main__':
test(sys.argv[1])
test(sys.argv[1])
|