def run_single(self, input_fastq, tophat_options=[], out_dir=None):
if out_dir == None:
out_dir = self.out_dir
if os.path.exists(out_dir):
raise ValueError("Output directory %s already exists!" %
(out_dir, ))
os.mkdir(out_dir)
log_file = os.path.join(out_dir, "tophat.log")
if len(input_fastq) > 2:
raise ValueError("Maximum of two reads per sample!")
phreds = []
for fq in input_fastq:
phreds.append(fastq.fastq_phred(fq))
if len(set(phreds)) <> 1:
raise ValueError("Multiple quality types in reads")
else:
phred_ver = phreds[0]
if phred_ver == 64:
phred_param = ["--phred64-quals"]
elif phred_ver == 59:
phred_param = ["--solexa-quals"]
elif phred_ver == 33:
phred_param = []
else:
raise ValueError("Unrecognized phred version")
with open(log_file, "w") as log_fp:
tophat_cmd = [_common.TOPHAT_PATH,
"-p", str(self.num_threads),
"-o", out_dir,
"-z", "none"] + \
phred_param + \
map(str, tophat_options) + \
[self.bowtie_index] + \
input_fastq
log_fp.write(" ".join(tophat_cmd) + "\n\n")
log_fp.flush()
tophat_proc = subprocess.Popen(tophat_cmd, stderr=log_fp)
while tophat_proc.poll() == None:
time.sleep(1)
if os.path.exists(os.path.join(out_dir, "junctions.bed")):
return True
else:
return False
def run_single(self, input_fastq, tophat_options = [], out_dir = None):
if out_dir == None:
out_dir = self.out_dir
if os.path.exists(out_dir):
raise ValueError("Output directory %s already exists!" % (out_dir,))
os.mkdir(out_dir)
log_file = os.path.join(out_dir, "tophat.log")
if len(input_fastq) > 2:
raise ValueError("Maximum of two reads per sample!")
phreds = []
for fq in input_fastq:
phreds.append(fastq.fastq_phred(fq))
if len(set(phreds)) <> 1:
raise ValueError("Multiple quality types in reads")
else:
phred_ver = phreds[0]
if phred_ver == 64:
phred_param = ["--phred64-quals"]
elif phred_ver == 59:
phred_param = ["--solexa-quals"]
elif phred_ver == 33:
phred_param = []
else:
raise ValueError("Unrecognized phred version")
with open(log_file, "w") as log_fp:
tophat_cmd = [_common.TOPHAT_PATH,
"-p", str(self.num_threads),
"-o", out_dir,
"-z", "none"] + \
phred_param + \
map(str, tophat_options) + \
[self.bowtie_index] + \
input_fastq
log_fp.write(" ".join(tophat_cmd) + "\n\n")
log_fp.flush()
tophat_proc = subprocess.Popen(tophat_cmd, stderr=log_fp)
while tophat_proc.poll() == None:
time.sleep(1)
if os.path.exists(os.path.join(out_dir, "junctions.bed")):
return True
else:
return False
def testPhredVersion(self):
# version 1.4 tests
result = fastq.fastq_phred("./pooled_tophat/v14_p_subset-left.fastq")
self.assertEqual(result, 64)
result = fastq.fastq_phred("./pooled_tophat/v14_p_subset-right.fastq")
self.assertEqual(result, 64)
result = fastq.fastq_phred("./pooled_tophat/v14_s_subset.fastq")
self.assertEqual(result, 64)
# version 1.8 tests
result = fastq.fastq_phred("./pooled_tophat/v18_p_subset-left.fastq")
self.assertEqual(result, 33)
result = fastq.fastq_phred("./pooled_tophat/v18_p_subset-right.fastq")
self.assertEqual(result, 33)
result = fastq.fastq_phred("./pooled_tophat/v18_s_subset.fastq")
self.assertEqual(result, 33)
def testPhredVersion(self):
# version 1.4 tests
result = fastq.fastq_phred("./pooled_tophat/v14_p_subset-left.fastq")
self.assertEqual(result, 64)
result = fastq.fastq_phred("./pooled_tophat/v14_p_subset-right.fastq")
self.assertEqual(result, 64)
result = fastq.fastq_phred("./pooled_tophat/v14_s_subset.fastq")
self.assertEqual(result, 64)
# version 1.8 tests
result = fastq.fastq_phred("./pooled_tophat/v18_p_subset-left.fastq")
self.assertEqual(result, 33)
result = fastq.fastq_phred("./pooled_tophat/v18_p_subset-right.fastq")
self.assertEqual(result, 33)
result = fastq.fastq_phred("./pooled_tophat/v18_s_subset.fastq")
self.assertEqual(result, 33)