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)