def annotate(options, refGene):
with open(options.output, 'w') as output:
csvWriter = csv.writer(output, delimiter='\t', quotechar='|')
# Read the rows of the variants TSV file into a list.
with open(options.variants) as variants:
for row in csv.reader(variants, delimiter='\t', quotechar='|'):
if len(row) >= 1:
coords = row[0].split(',')
if len(coords) >= 4 and coords[1].isdigit():
chrName = "chr" + coords[0]
pos = safeReadInt(coords[1])
searchResult = search(chrName, pos, refGene)
if searchResult != None:
csvWriter.writerow(row + [searchResult])
else:
csvWriter.writerow(row)
def annotate(options, refGene):
with open(options.output, 'w') as output:
csvWriter = csv.writer(output, delimiter='\t', quotechar='|')
# Read the rows of the variants TSV file into a list.
with open(options.variants) as variants:
for row in csv.reader(variants, delimiter='\t', quotechar='|'):
if len(row) >= 1:
coords = row[0].split(',')
if len(coords) >= 4 and coords[1].isdigit():
chrName = "chr" + coords[0]
pos = safeReadInt(coords[1])
searchResult = search(chrName, pos, refGene)
if searchResult != None:
csvWriter.writerow(row + [searchResult])
else:
csvWriter.writerow(row)
def readRefGene(options):
with open(options.refGene) as refs:
refGene = {}
for row in csv.reader(refs, delimiter='\t'):
if len(row) >= 11:
chr = row[2]
if chr not in refGene:
refGene[chr] = []
direction = row[3]
transcriptStart = safeReadInt(row[4]) + 1
transcriptEnd = safeReadInt(row[5])
# All coordinates for all fields in the refGene file
# are 0-based start and 1-based end, including the transcript, CDS and exons.
# see: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
codingRegionStart = safeReadInt(row[6]) + 1 # add one to fix up zero-based start coordinate
codingRegionEnd = safeReadInt(row[7])
# For non-coding genes (who, by definition, have a coding region size of
# 0), cdsStart will always equal cdsEnd in the genePred format.
# As a convention to help with standardization, we
# have made the cdsStart equal the txtStart for non-coding genes.
# check if this is a coding gene
if codingRegionStart < (codingRegionEnd + 1):
codingStart = CodingRegionStart(direction, options.startslack, codingRegionStart, codingRegionEnd)
refGene[chr].append(codingStart)
exonStarts = map(lambda x: safeReadInt(x) + 1, row[9].rstrip(',').split(',')) # add one to fix up zero-based start coordinate
exonEnds = map(lambda x: safeReadInt(x), row[10].rstrip(',').split(','))
# if the gene is on the reverse strand then we swap the start and end coordinates.
if direction == '-':
(exonStarts, exonEnds) = (exonEnds, exonStarts)
# we classify the start and ends of exons depending on whether they fall
# inside or outside the coding region, including the partial case where
# one end is inside and the other end is outside.
for start,end in zip(exonStarts, exonEnds):
isStartCoding = isCoding(codingRegionStart, codingRegionEnd, start)
isEndCoding = isCoding(codingRegionStart, codingRegionEnd, end)
if isStartCoding and isEndCoding:
refGene[chr].append(CodingExonBoundary(options.spliceslack, direction, start, 'start'))
refGene[chr].append(CodingExonBoundary(options.spliceslack, direction, end, 'end'))
elif not isStartCoding and not isEndCoding:
refGene[chr].append(NonCodingExonBoundary(options.spliceslack, direction, start, 'start'))
refGene[chr].append(NonCodingExonBoundary(options.spliceslack, direction, end, 'end'))
elif isStartCoding and not isEndCoding:
refGene[chr].append(CodingExonBoundary(options.spliceslack, direction, start, 'start'))
refGene[chr].append(PartialCodingExonBoundary(options.spliceslack, direction, end, 'end'))
elif not isStartCoding and isEndCoding:
refGene[chr].append(PartialCodingExonBoundary(options.spliceslack, direction, start, 'start'))
refGene[chr].append(CodingExonBoundary(options.spliceslack, direction, end, 'end'))
return refGene
except getopt.GetoptError, err:
print str(err)
usage()
sys.exit(2)
options = Options()
for o, a in opts:
if o == "--variants":
options.variants = a
elif o == "--bin":
options.bin = a
elif o == "--keep":
options.keep = a
elif o == "--log":
options.log = a
elif o == "--varLikeThresh":
options.varLikeThresh = safeReadInt(a)
elif o == "--samplesPercent":
options.samplesPercent = safeReadInt(a)
elif o in ('-h', '--help'):
usage()
sys.exit(0)
if not options.check():
print('Incorrect arguments')
usage()
exit(2)
bamFilenames = args
# Read the rows of the variants TSV file into a list.
with open(options.variants) as variants:
variantList = list(csv.reader(variants, delimiter='\t', quotechar='|'))
# compute the presence/absence of each variant in the bam files
evidence = getEvidence(variantList, bamFilenames)
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], shortOptionsFlags, longOptionsFlags)
except getopt.GetoptError, err:
print str(err)
usage()
sys.exit(2)
options = Options()
for o, a in opts:
if o == "--refGene":
options.refGene = a
elif o == "--variants":
options.variants = a
elif o == "--spliceslack":
options.spliceslack = safeReadInt(a)
elif o == "--startslack":
options.startslack = safeReadInt(a)
elif o == "--output":
options.output = a
elif o in ('-h', '--help'):
usage()
sys.exit(0)
if not options.check():
print('Incorrect arguments')
usage()
exit(2)
refGene = readRefGene(options)
#showRefGene(refGene)
annotate(options, refGene)
except getopt.GetoptError, err:
print str(err)
usage()
sys.exit(2)
options = Options()
for o, a in opts:
if o == "--variants":
options.variants = a
elif o == "--bin":
options.bin = a
elif o == "--keep":
options.keep = a
elif o == "--log":
options.log = a
elif o == "--varLikeThresh":
options.varLikeThresh = safeReadInt(a)
elif o == "--samplesPercent":
options.samplesPercent = safeReadInt(a)
elif o in ('-h', '--help'):
usage()
sys.exit(0)
if not options.check():
print('Incorrect arguments')
usage()
exit(2)
bamFilenames = args
# Read the rows of the variants TSV file into a list.
with open(options.variants) as variants:
variantList = list(csv.reader(variants, delimiter='\t', quotechar='|'))
# compute the presence/absence of each variant in the bam files
evidence = getEvidence(variantList, bamFilenames)
def readRefGene(options):
with open(options.refGene) as refs:
refGene = {}
for row in csv.reader(refs, delimiter='\t'):
if len(row) >= 11:
chr = row[2]
if chr not in refGene:
refGene[chr] = []
direction = row[3]
transcriptStart = safeReadInt(row[4]) + 1
transcriptEnd = safeReadInt(row[5])
# All coordinates for all fields in the refGene file
# are 0-based start and 1-based end, including the transcript, CDS and exons.
# see: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
codingRegionStart = safeReadInt(
row[6]
) + 1 # add one to fix up zero-based start coordinate
codingRegionEnd = safeReadInt(row[7])
# For non-coding genes (who, by definition, have a coding region size of
# 0), cdsStart will always equal cdsEnd in the genePred format.
# As a convention to help with standardization, we
# have made the cdsStart equal the txtStart for non-coding genes.
# check if this is a coding gene
if codingRegionStart < (codingRegionEnd + 1):
codingStart = CodingRegionStart(direction,
options.startslack,
codingRegionStart,
codingRegionEnd)
refGene[chr].append(codingStart)
exonStarts = map(
lambda x: safeReadInt(x) + 1, row[9].rstrip(',').split(
',')) # add one to fix up zero-based start coordinate
exonEnds = map(lambda x: safeReadInt(x),
row[10].rstrip(',').split(','))
# if the gene is on the reverse strand then we swap the start and end coordinates.
if direction == '-':
(exonStarts, exonEnds) = (exonEnds, exonStarts)
# we classify the start and ends of exons depending on whether they fall
# inside or outside the coding region, including the partial case where
# one end is inside and the other end is outside.
for start, end in zip(exonStarts, exonEnds):
isStartCoding = isCoding(codingRegionStart,
codingRegionEnd, start)
isEndCoding = isCoding(codingRegionStart, codingRegionEnd,
end)
if isStartCoding and isEndCoding:
refGene[chr].append(
CodingExonBoundary(options.spliceslack, direction,
start, 'start'))
refGene[chr].append(
CodingExonBoundary(options.spliceslack, direction,
end, 'end'))
elif not isStartCoding and not isEndCoding:
refGene[chr].append(
NonCodingExonBoundary(options.spliceslack,
direction, start, 'start'))
refGene[chr].append(
NonCodingExonBoundary(options.spliceslack,
direction, end, 'end'))
elif isStartCoding and not isEndCoding:
refGene[chr].append(
CodingExonBoundary(options.spliceslack, direction,
start, 'start'))
refGene[chr].append(
PartialCodingExonBoundary(options.spliceslack,
direction, end, 'end'))
elif not isStartCoding and isEndCoding:
refGene[chr].append(
PartialCodingExonBoundary(options.spliceslack,
direction, start,
'start'))
refGene[chr].append(
CodingExonBoundary(options.spliceslack, direction,
end, 'end'))
return refGene
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], shortOptionsFlags,
longOptionsFlags)
except getopt.GetoptError, err:
print str(err)
usage()
sys.exit(2)
options = Options()
for o, a in opts:
if o == "--refGene":
options.refGene = a
elif o == "--variants":
options.variants = a
elif o == "--spliceslack":
options.spliceslack = safeReadInt(a)
elif o == "--startslack":
options.startslack = safeReadInt(a)
elif o == "--output":
options.output = a
elif o in ('-h', '--help'):
usage()
sys.exit(0)
if not options.check():
print('Incorrect arguments')
usage()
exit(2)
refGene = readRefGene(options)
#showRefGene(refGene)
annotate(options, refGene)
