atexit.register(cleanFile, lockName)
if mode == "sra":
sraName = os.path.join(tmpDir, expName + "_original.sra")
atexit.register(cleanFile, sraName)
ret = os.system(
"wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR{2}/{0}/{0}.sra -O {1}"
.format(expName, sraName,
str(sraNum)[:3]))
if ret != 0:
raise RuntimeError(
"Download failed with return code {0}".format(ret))
counters = mapping.splitSRA(
sraName,
os.path.join(fastqFolder,
expName + "_chunk{0:04d}_fhtagn_side{1}.fastq.gz"),
chunkSize) # creating unique IDs requires creativity
os.remove(sraName)
pickle.dump(counters, open(os.path.join(saveFolder, "read_counts"),
'w'))
elif mode == "fastq":
firstSide = os.path.join(inFastqDir,
expName + sidePrefixes[0] + ".fastq.gz")
secondSide = os.path.join(inFastqDir,
expName + sidePrefixes[1] + ".fastq.gz")
counter = mapping.splitSingleFastq(
firstSide,
os.path.join(fastqFolder,
expName + "_chunk{0:04d}_fhtagn_side1.fastq.gz"),
lock = open(lockName, "w")
lock.close()
atexit.register(cleanFile, lockName)
if mode == "sra":
sraName = os.path.join(tmpDir, expName + "_original.sra")
atexit.register(cleanFile, sraName)
# ret = os.system("wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR{2}/{0}/{0}.sra -O {1}".format(expName, sraName, str(sraNum)[:3]))
# if ret != 0:
# raise RuntimeError("Download failed with return code {0}".format(ret))
print sra_folder + expName + ".sra"
counters = mapping.splitSRA(
sra_folder + expName + ".sra",
os.path.join(fastqFolder,
expName + "_chunk{0:04d}_fhtagn_side{1}.fastq.gz"),
chunkSize,
FASTQ_BINARY="/mnt/storage/home/vsfishman/HiC/bin/sra/bin/fastq-dump"
) # creating unique IDs requires creativity
# os.remove(sraName)
pickle.dump(counters, open(os.path.join(saveFolder, "read_counts"),
'w'))
elif mode == "fastq":
firstSide = os.path.join(inFastqDir,
expName + sidePrefixes[0] + ".fastq.gz")
secondSide = os.path.join(inFastqDir,
expName + sidePrefixes[1] + ".fastq.gz")
counter = mapping.splitSingleFastq(
firstSide,
os.path.join(fastqFolder,