def __init__(self, config): self.config = config self.stage_config = get_in(config, ("stage", self.stage), {}) self.chemistry = self.stage_config.get("chemistry", "truseq") if not isinstance(self.chemistry, list): self.chemistry = [self.chemistry] self.options = self.stage_config.get("options", "") self.trim_galore = sh.Command(self.stage_config.get("program", "trim_galore")) self.out_dir_prefix = get_in(config, ("dir", "results"), "results") + self.stage self.trim_polya = self.stage_config.get("trim_polya", True) safe_makedir(self.out_dir_prefix)
def __init__(self, config): self.config = config self.stage_config = get_in(config, ("stage", self.stage), {}) self.chemistry = self.stage_config.get("chemistry", "truseq") if not isinstance(self.chemistry, list): self.chemistry = [self.chemistry] self.options = self.stage_config.get("options", "") self.trim_galore = sh.Command( self.stage_config.get("program", "trim_galore")) self.out_dir_prefix = get_in(config, ("dir", "results"), "results") + self.stage self.trim_polya = self.stage_config.get("trim_polya", True) safe_makedir(self.out_dir_prefix)
def __init__(self, config): self.config = config self.stage_config = get_in(config, ("stage", self.stage), {}) self.chemistry = self.stage_config.get("chemistry", "truseq") if not isinstance(self.chemistry, list): self.chemistry = [self.chemistry] self.options = self.stage_config.get("options", {}) # it is important that we don't drop any reads out during cutadapt self.options["minimum-length"] = 0 self.user_adapters = self.stage_config.get("adapters", []) self.out_dir = os.path.join( get_in(self.config, ("dir", "results"), "results"), self.stage) self.length_cutoff = self.stage_config.get("length_cutoff", 30) self.quality_format = self.stage_config.get("quality_format", None)
def __init__(self, config): self.config = config self.stage_config = get_in(config, ("stage", self.stage), {}) self.chemistry = self.stage_config.get("chemistry", "truseq") if not isinstance(self.chemistry, list): self.chemistry = [self.chemistry] self.options = self.stage_config.get("options", {}) # it is important that we don't drop any reads out during cutadapt self.options["minimum-length"] = 0 self.user_adapters = self.stage_config.get("adapters", []) self.out_dir = os.path.join(get_in(self.config, ("dir", "results"), "results"), self.stage) self.length_cutoff = self.stage_config.get("length_cutoff", 30) self.quality_format = self.stage_config.get("quality_format", None)
def _get_out_file(self, in_file): base, _ = os.path.splitext(os.path.basename(in_file)) out_prefix = os.path.join(get_in(self.config, ("dir", "results"), "results"), self.stage) out_dir = os.path.join(out_prefix, base) out_file = os.path.join(out_dir, base + ".sam") return out_file
def __init__(self, config): self.config = config self.plugins = {} #self.scan(get_in(config, "dir", "plugins")) plugin_dir = get_in(config, ("dir", "plugins")) if plugin_dir: logger.info("Scanning %s for plugins." % plugin_dir) plugins = types.ModuleType("plugins") plugins.__path__ = [plugin_dir] sys.modules["plugins"] = plugins self.scan(plugin_dir) else: self.scan()
def __init__(self, config): self.config = config self.stage_config = config["stage"][self.stage] # defaults = {"q": True, "n": 2, "k": 1, # "X": 2000, "best": True, # "sam": True, # "phred64-quals": True} #self.options = dict(defaults.items() + # self.stage_config.get("options", {}).items()) self.options = self.stage_config.get("options", {}) self.bowtie = sh.Command(self.stage_config.get("program", "bowtie")) self.out_prefix = os.path.join(get_in(self.config, ("dir", "results"), "results"), self.stage) self.ref_file = self.config["ref"] if not any_bowtie_reference_exists(self.ref_file): bowtie_reference_not_found_error()