def extractInfoFields(path,max_strings=MAX_INFO_STRINGS,tickFunction=None,numTicks=1000):
infoFields = {}
tickInterval = os.path.getsize(path)/numTicks
nextTick = 0
if path.endswith('gz'):
infile = gzip.open(path,'rb')
else:
infile = open(path,'rb')
for line in infile:
if tickFunction != None:
if infile.tell() > nextTick:
if not tickFunction():
infile.close()
return None
nextTick += tickInterval
line = line.strip()
if len(line) <= 1:
continue
elif line.startswith("##INFO"):
newTag = line[line.find("ID=")+3:]
newTag = newTag[:newTag.find(',')]
if infoFields.has_key(newTag):
raise Exception("Duplicate INFO ID or use of reserved ID:\t%s" % newTag)
infoFields[newTag] = infoDetails(newTag, max_strings, False)
elif line.startswith("#"):
continue
else:
line = vcfLine(line.split('\t'))
line.extractInfo()
for k,v in line.info.iteritems():
if not infoFields.has_key(k):
raise Exception("Missing ##INFO pragma for: %s" % k)
else:
infoFields[k].addArbitraryValue(v)
infile.close()
return infoFields
def run(args):
separateInfoFields = args.separate_info_fields.strip().lower() == "true"
countSeparate = args.count_separate.strip().lower() == "true"
ignoreFields = args.ignore_fields
if ignoreFields == None:
ignoreFields = []
ignoreFields = set(ignoreFields)
posLengthWarned = False
allChrs = []
positions = []
alleleColumn = infoDetails("Ref/Alt", 1, False)
qualColumn = infoDetails("QUAL", 1, False)
filterColumn = infoDetails("FILTER", args.max_strings, False)
infoFields = {"Ref/Alt":alleleColumn,"QUAL":qualColumn,"FILTER":filterColumn}
# TODO: get the numeric ranges, all valid categorical values
infile = open(args.infile,'r')
for line in infile:
line = line.strip()
if len(line) <= 1:
continue
elif line.startswith("#"):
temp = line.lower()
if temp.startswith("##info"):
newTag = line[temp.find("id=")+3:]
newTag = newTag[:newTag.find(',')]
if infoFields.has_key(newTag):
raise Exception("Duplicate INFO ID or use of reserved ID:\t%s" % newTag)
infoFields[newTag] = infoDetails(newTag, args.max_strings, countSeparate)
if newTag in ignoreFields:
infoFields[newTag].maxedOut = True
elif temp.startswith("##filter"):
newTag = line[temp.find("id=")+3:]
newTag = newTag[:newTag.find(',')]
filterColumn.addCategory(newTag, 0)
elif temp.startswith("##contig"):
chrom = line[temp.find("id=")+3:]
chrom = newTag[:chrom.find(',')]
chrom = standardizeChromosome(chrom)
chrLength = line[temp.find("length=")+3:]
chrLength = chrLength[:chrLength.find(',')]
allChrs.append(chrom)
positions.append((0,int(chrLength)))
else:
# a sneaky way of freezing the filter column; if other filters are added (without a .vcf pragma line) or we aren't separating info fields,
# other strings will make this column max out early
filterColumn.maxCategories = len(filterColumn.categories[0])
else:
line = vcfLine(line.split('\t'))
line.extractChrAndPos()
if not line.chromosome not in allChrs:
allChrs.append(line.chromosome)
positions.append((0,0))
chrIndex = allChrs.index(line.chromosome)
if line.position > positions[chrIndex][1]:
positions[chrIndex] = (0,line.position)
if not posLengthWarned:
sys.stderr.write('WARNING: Either ##contig pragma lines aren\'t supplied in your .vcf file or a variant has a position beyond the length of a chromosome.')
sys.stderr.write(' In either case, be aware that chromosome lengths in the .cvf file may not be accurate.')
posLengthWarned = True
line.extractAlleles()
alleles = line.alleles
if not separateInfoFields:
alleles = ",".join(alleles)
alleleColumn.addArbitraryValue(line.alleles)
line.extractQual()
qualColumn.addArbitraryValue(line.qual)
line.extractFilters()
filters = line.filters
if not separateInfoFields:
filters = ",".join(filters)
filterColumn.addArbitraryValue(filters)
line.extractInfo()
for k,v in line.info.iteritems():
if not infoFields.has_key(k):
raise Exception("Missing ##INFO pragma for: %s" % k)
if separateInfoFields:
v = ",".split(v)
infoFields[k].addArbitraryValue(v)
infile.close()
print "Creating file..."
outfile = open(args.outfile, 'w')
outfile.write("##\t%s created from %s on %s\n" % (args.outfile,args.infile,str(datetime.datetime.now())))
outfile.write("#\tChromosome\tCHR\t%s\n" % ("\t".join(allChrs)))
outfile.write("#\tPosition\tPOS\t%s\n" % ("\t".join(["(%i,%i)" % p for p in positions])))
outfile.write("#\tID\tID\n")
headers = []
fieldOrder = sorted(infoFields.iterkeys())
for f in fieldOrder:
pragmas = infoFields[f].getPragmas()
for p in pragmas:
outfile.write(p + "\n")
h = p.split("\t")[1]
headers.append(h)
outfile.write('Chromosome\tPosition\tID\t%s\n' % ("\t".join(headers)))
infile = open(args.infile,'r')
for line in infile:
line = line.strip()
if len(line) <= 1 or line.startswith("#"):
continue
line = vcfLine(line.split('\t'))
line.extractChrAndPos()
line.extractInfo()
line.extractAlleles()
line.info["Ref/Alt"] = line.alleles
line.extractQual()
line.info["QUAL"] = str(line.qual)
line.extractFilters()
line.info["FILTER"] = line.filters
outfile.write("%s\t%i\t%s" % (line.chromosome,line.position,line.name))
for f in fieldOrder:
values = line.info[f]
if isinstance(values,list):
if separateInfoFields:
values = "\t".join(values)
else:
values = ",".join(values)
outfile.write("\t%s" % values)
outfile.write("\n")
infile.close()
outfile.close()
def run(args):
separateInfoFields = args.separate_info_fields.strip().lower() == "true"
countSeparate = args.count_separate.strip().lower() == "true"
ignoreFields = args.ignore_fields
if ignoreFields == None:
ignoreFields = []
ignoreFields = set(ignoreFields)
posLengthWarned = False
allChrs = []
positions = []
alleleColumn = infoDetails("Ref/Alt", 1, False)
qualColumn = infoDetails("QUAL", 1, False)
filterColumn = infoDetails("FILTER", args.max_strings, False)
infoFields = {
"Ref/Alt": alleleColumn,
"QUAL": qualColumn,
"FILTER": filterColumn
}
# TODO: get the numeric ranges, all valid categorical values
infile = open(args.infile, 'r')
for line in infile:
line = line.strip()
if len(line) <= 1:
continue
elif line.startswith("#"):
temp = line.lower()
if temp.startswith("##info"):
newTag = line[temp.find("id=") + 3:]
newTag = newTag[:newTag.find(',')]
if infoFields.has_key(newTag):
raise Exception(
"Duplicate INFO ID or use of reserved ID:\t%s" %
newTag)
infoFields[newTag] = infoDetails(newTag, args.max_strings,
countSeparate)
if newTag in ignoreFields:
infoFields[newTag].maxedOut = True
elif temp.startswith("##filter"):
newTag = line[temp.find("id=") + 3:]
newTag = newTag[:newTag.find(',')]
filterColumn.addCategory(newTag, 0)
elif temp.startswith("##contig"):
chrom = line[temp.find("id=") + 3:]
chrom = newTag[:chrom.find(',')]
chrom = standardizeChromosome(chrom)
chrLength = line[temp.find("length=") + 3:]
chrLength = chrLength[:chrLength.find(',')]
allChrs.append(chrom)
positions.append((0, int(chrLength)))
else:
# a sneaky way of freezing the filter column; if other filters are added (without a .vcf pragma line) or we aren't separating info fields,
# other strings will make this column max out early
filterColumn.maxCategories = len(filterColumn.categories[0])
else:
line = vcfLine(line.split('\t'))
line.extractChrAndPos()
if not line.chromosome not in allChrs:
allChrs.append(line.chromosome)
positions.append((0, 0))
chrIndex = allChrs.index(line.chromosome)
if line.position > positions[chrIndex][1]:
positions[chrIndex] = (0, line.position)
if not posLengthWarned:
sys.stderr.write(
'WARNING: Either ##contig pragma lines aren\'t supplied in your .vcf file or a variant has a position beyond the length of a chromosome.'
)
sys.stderr.write(
' In either case, be aware that chromosome lengths in the .cvf file may not be accurate.'
)
posLengthWarned = True
line.extractAlleles()
alleles = line.alleles
if not separateInfoFields:
alleles = ",".join(alleles)
alleleColumn.addArbitraryValue(line.alleles)
line.extractQual()
qualColumn.addArbitraryValue(line.qual)
line.extractFilters()
filters = line.filters
if not separateInfoFields:
filters = ",".join(filters)
filterColumn.addArbitraryValue(filters)
line.extractInfo()
for k, v in line.info.iteritems():
if not infoFields.has_key(k):
raise Exception("Missing ##INFO pragma for: %s" % k)
if separateInfoFields:
v = ",".split(v)
infoFields[k].addArbitraryValue(v)
infile.close()
print "Creating file..."
outfile = open(args.outfile, 'w')
outfile.write("##\t%s created from %s on %s\n" %
(args.outfile, args.infile, str(datetime.datetime.now())))
outfile.write("#\tChromosome\tCHR\t%s\n" % ("\t".join(allChrs)))
outfile.write("#\tPosition\tPOS\t%s\n" %
("\t".join(["(%i,%i)" % p for p in positions])))
outfile.write("#\tID\tID\n")
headers = []
fieldOrder = sorted(infoFields.iterkeys())
for f in fieldOrder:
pragmas = infoFields[f].getPragmas()
for p in pragmas:
outfile.write(p + "\n")
h = p.split("\t")[1]
headers.append(h)
outfile.write('Chromosome\tPosition\tID\t%s\n' % ("\t".join(headers)))
infile = open(args.infile, 'r')
for line in infile:
line = line.strip()
if len(line) <= 1 or line.startswith("#"):
continue
line = vcfLine(line.split('\t'))
line.extractChrAndPos()
line.extractInfo()
line.extractAlleles()
line.info["Ref/Alt"] = line.alleles
line.extractQual()
line.info["QUAL"] = str(line.qual)
line.extractFilters()
line.info["FILTER"] = line.filters
outfile.write("%s\t%i\t%s" %
(line.chromosome, line.position, line.name))
for f in fieldOrder:
values = line.info[f]
if isinstance(values, list):
if separateInfoFields:
values = "\t".join(values)
else:
values = ",".join(values)
outfile.write("\t%s" % values)
outfile.write("\n")
infile.close()
outfile.close()