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 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
