def trim_lane(item):
"""Trim reads with the provided trimming method.
Support methods: read_through.
"""
to_trim = [x for x in item["files"] if x is not None]
dirs = item["dirs"]
config = item["config"]
# this block is to maintain legacy configuration files
trim_reads = config["algorithm"].get("trim_reads", False)
if not trim_reads:
logger.info("Skipping trimming of %s." % (", ".join(to_trim)))
return [[item]]
if trim_reads == "read_through":
logger.info("Trimming low quality ends and read through adapter " "sequence from %s." % (", ".join(to_trim)))
out_files = trim_adapters(to_trim, dirs, config)
item["files"] = out_files
return [[item]]
def trim_lane(item):
"""Trim reads with the provided trimming method.
Support methods: read_through.
"""
to_trim = [x for x in item["files"] if x is not None]
dirs = item["dirs"]
config = item["config"]
# this block is to maintain legacy configuration files
trim_reads = config["algorithm"].get("trim_reads", False)
if not trim_reads:
logger.info("Skipping trimming of %s." % (", ".join(to_trim)))
return [[item]]
if trim_reads == "read_through":
logger.info("Trimming low quality ends and read through adapter "
"sequence from %s." % (", ".join(to_trim)))
out_files = trim_adapters(to_trim, dirs, config)
item["files"] = out_files
return [[item]]
def trim_sample(data):
"""Trim from a sample with the provided trimming method.
Support methods: read_through.
"""
to_trim = [x for x in data["files"] if x is not None]
dirs = data["dirs"]
config = data["config"]
# this block is to maintain legacy configuration files
trim_reads = config["algorithm"].get("trim_reads", False)
if not trim_reads:
logger.info("Skipping trimming of %s." % (", ".join(to_trim)))
return [[data]]
out_dir = os.path.join(dd.get_work_dir(data), "trimmed")
utils.safe_makedir(out_dir)
if trim_reads == "read_through":
logger.info("Trimming low quality ends and read through adapter " "sequence from %s." % (", ".join(to_trim)))
out_files = trim_adapters(to_trim, out_dir, config)
data["files"] = out_files
return [[data]]
def trim_sample(data):
"""Trim from a sample with the provided trimming method.
Support methods: read_through.
"""
to_trim = [x for x in data["files"] if x is not None]
config = data["config"]
# this block is to maintain legacy configuration files
trim_reads = config["algorithm"].get("trim_reads", False)
if not trim_reads:
logger.info("Skipping trimming of %s." % (", ".join(to_trim)))
return [[data]]
out_dir = os.path.join(dd.get_work_dir(data), "trimmed")
utils.safe_makedir(out_dir)
if trim_reads == "read_through":
logger.info("Trimming low quality ends and read through adapter "
"sequence from %s." % (", ".join(to_trim)))
out_files = trim_adapters(to_trim, out_dir, config)
data["files"] = out_files
return [[data]]
def test_single(self):
single = self.config["input_single"]
out_file = trim_adapters(single, self.config["dir"], self.config)
correct_file = self._trim_single_correct(out_file)
self.assertTrue(filecmp.cmp(correct_file, out_file))
shutil.rmtree(self.root_work)
def test_pairedend(self):
paired = self.config["input_paired"]
out_files = trim_adapters(paired, self.config["dir"], self.config)
correct_files = map(self._trim_paired_correct, out_files)
self.assertTrue(all(map(filecmp.cmp, correct_files, out_files)))
shutil.rmtree(self.root_work)
def test_single(self):
single = self.config["input_single"]
out_file = trim_adapters(single, self.config["dir"], self.config)
correct_file = self._trim_single_correct(out_file)
self.assertTrue(filecmp.cmp(correct_file, out_file))
shutil.rmtree(self.root_work)
def test_pairedend(self):
paired = self.config["input_paired"]
out_files = trim_adapters(paired, self.config["dir"], self.config)
correct_files = map(self._trim_paired_correct, out_files)
self.assertTrue(all(map(filecmp.cmp, correct_files, out_files)))
shutil.rmtree(self.root_work)
