def trim_lane(item):
"""
if trim_reads is set with no trimmer specified, default to B-run trimming
only. if trimmer is set to a supported type, perform that trimming
instead.
"""
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
# swap the default to None if trim_reads gets deprecated
if trim_reads == "low_quality" or trim_reads == "true":
logger.info("Trimming low quality ends from %s." %
(", ".join(to_trim)))
out_files = brun_trim_fastq(to_trim, dirs, config)
if trim_reads == "read_through":
logger.info("Trimming low quality ends and read through adapter "
"sequence from %s." % (", ".join(to_trim)))
out_files = trim_read_through(to_trim, dirs, config)
else:
logger.info("Trimming low quality ends from %s." %
(", ".join(to_trim)))
out_files = brun_trim_fastq(to_trim, dirs, config)
item["files"] = out_files
return [[item]]
def trim_lane(item):
"""
if trim_reads is set with no trimmer specified, default to B-run trimming
only. if trimmer is set to a supported type, perform that trimming
instead.
"""
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
# swap the default to None if trim_reads gets deprecated
if trim_reads == "low_quality" or trim_reads == "true":
logger.info("Trimming low quality ends from %s."
% (", ".join(to_trim)))
out_files = brun_trim_fastq(to_trim, dirs, config)
if trim_reads == "read_through":
logger.info("Trimming low quality ends and read through adapter "
"sequence from %s." % (", ".join(to_trim)))
out_files = trim_read_through(to_trim, dirs, config)
else:
logger.info("Trimming low quality ends from %s."
% (", ".join(to_trim)))
out_files = brun_trim_fastq(to_trim, dirs, config)
item["files"] = out_files
return [[item]]
def trim_lane(fastq1, fastq2, info, lane_name, lane_desc, dirs, config):
"""
if trim_reads is set with no trimmer specified, default to B-run trimming
only. if trimmer is set to a supported type, perform that trimming
instead.
"""
to_trim = [x for x in [fastq1, fastq2] if x is not None]
# 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 [(fastq1, fastq2, info, lane_name, lane_desc, dirs, config)]
# swap the default to None if trim_reads gets deprecated
if trim_reads == "low_quality" or trim_reads == "true":
logger.info("Trimming low quality ends from %s."
% (", ".join(to_trim)))
out_files = brun_trim_fastq(to_trim, dirs, config)
if trim_reads == "read_through":
logger.info("Trimming low quality ends and read through adapter "
"sequence from %s." % (", ".join(to_trim)))
out_files = trim_read_through(to_trim, dirs, config)
else:
logger.info("Trimming low quality ends from %s."
% (", ".join(to_trim)))
out_files = brun_trim_fastq(to_trim, dirs, config)
fastq1 = out_files[0]
if fastq2 is not None:
fastq2 = out_files[1]
return [(fastq1, fastq2, info, lane_name, lane_desc, dirs, config)]
def trim_lane(fastq1, fastq2, info, lane_name, lane_desc, dirs, config):
"""
if trim_reads is set with no trimmer specified, default to B-run trimming
only. if trimmer is set to a supported type, perform that trimming
instead.
"""
to_trim = [x for x in [fastq1, fastq2] if x is not None]
# 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 [(fastq1, fastq2, info, lane_name, lane_desc, dirs, config)]
# swap the default to None if trim_reads gets deprecated
if trim_reads == "low_quality" or trim_reads == "true":
logger.info("Trimming low quality ends from %s." %
(", ".join(to_trim)))
out_files = brun_trim_fastq(to_trim, dirs, config)
if trim_reads == "read_through":
logger.info("Trimming low quality ends and read through adapter "
"sequence from %s." % (", ".join(to_trim)))
out_files = trim_read_through(to_trim, dirs, config)
else:
logger.info("Trimming low quality ends from %s." %
(", ".join(to_trim)))
out_files = brun_trim_fastq(to_trim, dirs, config)
fastq1 = out_files[0]
if fastq2 is not None:
fastq2 = out_files[1]
return [(fastq1, fastq2, info, lane_name, lane_desc, dirs, config)]
def test_single(self):
single = self.config["input_single"]
out_file = trim_read_through(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_read_through(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_read_through(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_read_through(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)
