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 _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.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()
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()
