def readLabeledImageSet(collection, tag, tpp='lemm', rootpath=ROOT_PATH):
datafile = os.path.join(rootpath, collection, 'tagged,%s'% tpp, '%s.txt' % tag)
try:
hitset = map(str.strip, open(datafile).readlines())
printStatus('basic.util.readLabeledImageSet', '%s-%s -> %d hits' % (collection, tag, len(hitset)))
except:
printError('basic.util.readLabeledImageSet', 'failed to read %s' % datafile)
hitset = []
return hitset
def readLabeledImageSet(collection, tag, tpp='lemm', rootpath=ROOT_PATH):
datafile = os.path.join(rootpath, collection, 'tagged,%s'% tpp, '%s.txt' % tag)
try:
hitset = map(str.strip, open(datafile).readlines())
printStatus('basic.util.readLabeledImageSet', '%s-%s -> %d hits' % (collection, tag, len(hitset)))
except:
printError('basic.util.readLabeledImageSet', 'failed to read %s' % datafile)
hitset = []
return hitset
def run_vat(arguments, forceVerbose=False):
VAT_BIN_PATH = os.path.join(getScriptDirectory(), "vat-bin")
snpMapperPath = os.path.join(VAT_BIN_PATH, "snpMapper")
indelMapperPath = os.path.join(VAT_BIN_PATH, "indelMapper")
if not os.path.exists(snpMapperPath) or not os.path.exists(indelMapperPath):
printError("VAT is not installed correctly - please see INSTALL")
try:
inputPath = arguments[1]
vatOutputPath = arguments[2]
annotationIntervalPath = arguments[3]
annotationSequencePath = arguments[4]
except:
printError(
"Failed to parse arguments\nUsage is <input_vcf> <vat_output> <annotation_interval_input> <annotation_sequence_input> <verbosity_level>\nThis program will take care of sorting the input_vcf file numerically.\nFor verbosity_level you must pass in 0 (indicating no verbosity) or 1 (indicating verbosity)"
)
verbose = False
if forceVerbose or (5 < len(arguments) and int(arguments[5]) > 0):
verbose = True
if verbose:
print("Parsing VCF file...")
try:
if inputPath.endswith(".gz"):
inputFile = gzip.open(inputPath, "rb")
else:
inputFile = open(inputPath, "rb")
except:
printError("Failed to open %s" % (inputPath))
TEMP_SNP_PATH = os.path.join(os.path.split(vatOutputPath)[0], "snpinput_temp")
TEMP_INDEL_PATH = os.path.join(os.path.split(vatOutputPath)[0], "indelinput_temp")
snpInputFile = open(TEMP_SNP_PATH, "w")
indelInputFile = open(TEMP_INDEL_PATH, "w")
foundHeader = False
foundID = True
numberOfMissingComponents = 0
normalHeaderComponents = ["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"]
for lineBytes in inputFile:
line = lineBytes.decode("utf-8")
lineComponents = line.rstrip("\n").rstrip("\t").split("\t")
if line.startswith("#"):
if line.startswith("#CHR"):
if lineComponents[2] != "ID":
foundID = False
if len(lineComponents) < 8:
numberOfMissingComponents = 8 - len(lineComponents)
if not foundID:
numberOfMissingComponents -= 1
if not foundID:
lineComponents = lineComponents[0:2] + ["ID"] + lineComponents[2:]
if numberOfMissingComponents > 0:
lineComponents += normalHeaderComponents[-numberOfMissingComponents:]
snpInputFile.write("\t".join(lineComponents) + "\n")
indelInputFile.write("\t".join(lineComponents) + "\n")
foundHeader = True
else:
snpInputFile.write(line)
indelInputFile.write(line)
elif not foundHeader:
snpInputFile.write("#" + "\t".join(normalHeaderComponents) + "\n")
indelInputFile.write("#" + "\t".join(normalHeaderComponents) + "\n")
foundHeader = True
if not line.startswith("#"):
if not foundID:
lineComponents = lineComponents[0:2] + ["NA"] + lineComponents[2:]
if numberOfMissingComponents > 0:
lineComponents += ["NA"] * numberOfMissingComponents
refComponents = lineComponents[3].split(",")
altComponents = lineComponents[4].split(",")
foundSnp = False
foundIndel = False
for index in range(len(refComponents)):
refComponent = refComponents[index]
altComponent = altComponents[index]
if len(refComponent) == 1 and len(altComponent) == 1 and not foundSnp:
snpInputFile.write("\t".join(lineComponents) + "\n")
foundSnp = True
if foundIndel:
break
if (len(refComponent) > 1 or len(altComponent) > 1) and not foundIndel:
indelInputFile.write("\t".join(lineComponents) + "\n")
foundIndel = True
if foundSnp:
break
snpInputFile.close()
indelInputFile.close()
snpInputFile = open(TEMP_SNP_PATH, "r")
indelInputFile = open(TEMP_INDEL_PATH, "r")
if verbose:
print("Running snpMapper...")
try:
snpMapperPipe = Popen(
[snpMapperPath, annotationIntervalPath, annotationSequencePath], stdout=PIPE, stdin=snpInputFile
)
except:
printError("Failed to open snpMapper")
numSnp = 0
numIndel = 0
sortedLines = []
vcfOutputFile = open(vatOutputPath, "w")
for lineBytes in snpMapperPipe.stdout:
line = lineBytes.decode("utf-8")
if line.startswith("#"):
vcfOutputFile.write(line)
else:
numSnp += 1
sortedLines.append(line.rstrip("\n"))
snpInputFile.close()
os.remove(TEMP_SNP_PATH)
if verbose:
print("Running indelMapper...")
try:
indelMapperPipe = Popen(
[indelMapperPath, annotationIntervalPath, annotationSequencePath], stdout=PIPE, stdin=indelInputFile
)
except:
printError("Failed to open indelMapper")
for lineBytes in indelMapperPipe.stdout:
line = lineBytes.decode("utf-8")
if not line.startswith("#"):
sortedLines.append(line.rstrip("\n"))
numIndel += 1
indelInputFile.close()
os.remove(TEMP_INDEL_PATH)
if verbose:
print("Writing out VAT file...")
# Sort and remove duplicate entries
sortVCFLines(sortedLines)
lastLine = None
for line in sortedLines:
if line != lastLine:
vcfOutputFile.write(line + "\n")
lastLine = line
vcfOutputFile.close()
if verbose:
print("Finishing VAT. There were %d snp lines and %d indel lines in the output" % (numSnp, numIndel))
def run_vat(arguments, forceVerbose=False):
VAT_BIN_PATH = os.path.join(getScriptDirectory(), 'vat-bin')
snpMapperPath = os.path.join(VAT_BIN_PATH, 'snpMapper')
indelMapperPath = os.path.join(VAT_BIN_PATH, 'indelMapper')
if not os.path.exists(snpMapperPath) or not os.path.exists(
indelMapperPath):
printError("VAT is not installed correctly - please see INSTALL")
try:
inputPath = arguments[1]
vatOutputPath = arguments[2]
annotationIntervalPath = arguments[3]
annotationSequencePath = arguments[4]
except:
printError(
"Failed to parse arguments\nUsage is <input_vcf> <vat_output> <annotation_interval_input> <annotation_sequence_input> <verbosity_level>\nThis program will take care of sorting the input_vcf file numerically.\nFor verbosity_level you must pass in 0 (indicating no verbosity) or 1 (indicating verbosity)"
)
verbose = False
if forceVerbose or (5 < len(arguments) and int(arguments[5]) > 0):
verbose = True
if verbose: print('Parsing VCF file...')
try:
if inputPath.endswith(".gz"):
inputFile = gzip.open(inputPath, 'rb')
else:
inputFile = open(inputPath, 'rb')
except:
printError("Failed to open %s" % (inputPath))
TEMP_SNP_PATH = os.path.join(
os.path.split(vatOutputPath)[0], "snpinput_temp")
TEMP_INDEL_PATH = os.path.join(
os.path.split(vatOutputPath)[0], "indelinput_temp")
snpInputFile = open(TEMP_SNP_PATH, "w")
indelInputFile = open(TEMP_INDEL_PATH, "w")
foundHeader = False
foundID = True
numberOfMissingComponents = 0
normalHeaderComponents = [
'CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO'
]
for lineBytes in inputFile:
line = lineBytes.decode("utf-8")
lineComponents = line.rstrip("\n").rstrip("\t").split("\t")
if line.startswith("#"):
if line.startswith("#CHR"):
if lineComponents[2] != 'ID':
foundID = False
if len(lineComponents) < 8:
numberOfMissingComponents = 8 - len(lineComponents)
if not foundID:
numberOfMissingComponents -= 1
if not foundID:
lineComponents = lineComponents[0:2] + [
'ID'
] + lineComponents[2:]
if numberOfMissingComponents > 0:
lineComponents += normalHeaderComponents[
-numberOfMissingComponents:]
snpInputFile.write('\t'.join(lineComponents) + "\n")
indelInputFile.write('\t'.join(lineComponents) + "\n")
foundHeader = True
else:
snpInputFile.write(line)
indelInputFile.write(line)
elif not foundHeader:
snpInputFile.write("#" + "\t".join(normalHeaderComponents) + "\n")
indelInputFile.write("#" + "\t".join(normalHeaderComponents) +
"\n")
foundHeader = True
if not line.startswith("#"):
if not foundID:
lineComponents = lineComponents[0:2] + ['NA'
] + lineComponents[2:]
if numberOfMissingComponents > 0:
lineComponents += ['NA'] * numberOfMissingComponents
refComponents = lineComponents[3].split(",")
altComponents = lineComponents[4].split(",")
foundSnp = False
foundIndel = False
for index in range(len(refComponents)):
refComponent = refComponents[index]
altComponent = altComponents[index]
if len(refComponent) == 1 and len(
altComponent) == 1 and not foundSnp:
snpInputFile.write("\t".join(lineComponents) + "\n")
foundSnp = True
if foundIndel:
break
if (len(refComponent) > 1
or len(altComponent) > 1) and not foundIndel:
indelInputFile.write("\t".join(lineComponents) + "\n")
foundIndel = True
if foundSnp:
break
snpInputFile.close()
indelInputFile.close()
snpInputFile = open(TEMP_SNP_PATH, "r")
indelInputFile = open(TEMP_INDEL_PATH, "r")
if verbose: print("Running snpMapper...")
try:
snpMapperPipe = Popen(
[snpMapperPath, annotationIntervalPath, annotationSequencePath],
stdout=PIPE,
stdin=snpInputFile)
except:
printError("Failed to open snpMapper")
numSnp = 0
numIndel = 0
sortedLines = []
vcfOutputFile = open(vatOutputPath, "w")
for lineBytes in snpMapperPipe.stdout:
line = lineBytes.decode("utf-8")
if line.startswith("#"):
vcfOutputFile.write(line)
else:
numSnp += 1
sortedLines.append(line.rstrip("\n"))
snpInputFile.close()
os.remove(TEMP_SNP_PATH)
if verbose: print("Running indelMapper...")
try:
indelMapperPipe = Popen(
[indelMapperPath, annotationIntervalPath, annotationSequencePath],
stdout=PIPE,
stdin=indelInputFile)
except:
printError("Failed to open indelMapper")
for lineBytes in indelMapperPipe.stdout:
line = lineBytes.decode("utf-8")
if not line.startswith("#"):
sortedLines.append(line.rstrip("\n"))
numIndel += 1
indelInputFile.close()
os.remove(TEMP_INDEL_PATH)
if verbose: print("Writing out VAT file...")
#Sort and remove duplicate entries
sortVCFLines(sortedLines)
lastLine = None
for line in sortedLines:
if line != lastLine:
vcfOutputFile.write(line + "\n")
lastLine = line
vcfOutputFile.close()
if verbose:
print(
"Finishing VAT. There were %d snp lines and %d indel lines in the output"
% (numSnp, numIndel))