def main(argv):
# parse arguments
opts, args = getopt.getopt(argv[1:-1], 'ho:q:', longopts = ['help'])
qmin = 30
outputName = ''
for option, val in opts:
if option in ['-h', '--help']:
print(helpString)
sys.exit()
elif option == '-o':
outputName = val
elif option == '-q':
qmin = float(val)
else:
sys.exit('Unsupported parameter.')
# deal with invalid paths
if (len(argv) == 1) or (not os.path.isfile(argv[-1])):
print(helpString)
sys.exit('Valid input file required.')
else:
inputName = argv[-1]
parser = FASTQParser(inputName)
if outputName != '':
outFile = open(outputName, 'w')
# read file and print back lines that pass the filter
while True:
read = parser.nextRead()
# stop at EOF
if read['quals'] == '':
break
numQual = encoding2num(read['quals'], parser.encoding)
# get first index of acceptable quality
start = -1
for baseq in numQual:
start += 1
if baseq >= qmin:
break
# now get last index
end = -1
for baseq in reversed(numQual):
end += 1
if baseq >= qmin:
break
# only print back reads where there was at least one decent base call
end = len(numQual) - end - 1
if start < end:
if outputName == '':
print(read['header'], read['bases'][start:end], '\n', read['qheader'], read['quals'][start:end], '\n',\
sep='', end='')
else:
outFile.writelines([read['header'], read['bases'][start:end], '\n', \
read['qheader'], read['quals'][start:end], '\n'])
parser.file.close()
if outputName != '':
outFile.close()
def indexFile(fileName):
idxParser = FASTQParser(fileName)
IDStore = {}
try:
while True:
# process individual reads
pos = idxParser.file.tell()
read = idxParser.nextRead()
# break at EOF
if read["quals"] == "":
break
# get tile X/Y position and use as key for dictionary that stores file position for later read
IDStore[regex.findall(read["header"])[0]] = pos
finally:
idxParser.close()
return IDStore
def main(argv):
# parse arguments
opts, args = getopt.getopt(argv[1:-1], 'ho:q:', longopts = ['help'])
qmin = 30
outputName = ''
for option, val in opts:
if option in ['-h', '--help']:
print(helpString)
sys.exit()
elif option == '-o':
outputName = val
elif option == '-q':
qmin = float(val)
else:
sys.exit('Unsupported parameter.')
# deal with invalid paths
if (len(argv) == 1) or (not os.path.isfile(argv[-1])):
print(helpString)
sys.exit('Valid input file required.')
else:
inputName = argv[-1]
parser = FASTQParser(inputName)
if outputName != '':
outFile = open(outputName, 'w')
# read file and print back lines that pass the filter
while True:
read = parser.nextRead()
# stop at EOF
if read['quals'] == '':
break
meanQual = mean(encoding2num(read['quals'], parser.encoding))
if meanQual >= qmin:
if outputName == '':
print(read['header'], read['bases'], read['qheader'], read['quals'], sep = '', end = '')
else:
outFile.writelines([read['header'], read['bases'], read['qheader'], read['quals']])
parser.file.close()
if outputName != '':
outFile.close()
def matchReads(fastq1, fastq2):
idxStore = indexFile(fastq2)
# open file handles
fastq1_common = open(fastq1 + ".common", "w")
fastq1_unique = open(fastq1 + ".unique", "w")
fastq2_common = open(fastq2 + ".common", "w")
fastq1_parser = FASTQParser(fastq1)
fastq2_parser = FASTQParser(fastq2)
while True:
read = fastq1_parser.nextRead()
# EOF
if read["quals"] == "":
break
ID = regex.findall(read["header"])[0]
if ID in idxStore.keys():
# write both reads out to common files, remove key from index
fastq1_common.writelines([read["header"], read["bases"], read["qheader"], read["quals"]])
fastq2_parser.file.seek(idxStore.pop(ID))
readMatch = fastq2_parser.nextRead()
fastq2_common.writelines(
[readMatch["header"], readMatch["bases"], readMatch["qheader"], readMatch["quals"]]
)
else:
# write out to unique file for fastq1
fastq1_unique.writelines([read["header"], read["bases"], read["qheader"], read["quals"]])
# close file handles
fastq1_common.close()
fastq1_unique.close()
fastq2_common.close()
# all remaining keys in dictionary are the unique reads for fastq2
with open(fastq2 + ".unique", "w") as fastq2_unique:
for remaining in idxStore:
fastq2_parser.file.seek(idxStore[remaining])
read = fastq2_parser.nextRead()
fastq2_unique.writelines([read["header"], read["bases"], read["qheader"], read["quals"]])
fastq1_parser.close()
fastq2_parser.close()
return
