def __init__(self,
gene_name="not_a_gene",
fedit=2,
redit=0,
use_reverse_primer=True,
keep_primers=False,
max_ns=0,
min_length=300,
min_qual=20,
framebot_ref_ident=0.3,
framebot_minlength=100,
nucl_control=None,
prot_control=None,
decontam_cutoff=0.1,
process_notag=True):
self.gene_name = gene_name
self.fedit = str(fedit)
self.redit = str(redit)
self.min_length = str(min_length)
self.max_ns = str(max_ns)
self.min_qual = str(min_qual)
self.keep_primers = keep_primers
self.framebot_ref_ident = str(framebot_ref_ident)
self.framebot_minlength = str(framebot_minlength)
self.decontamination_cutoff = str(decontam_cutoff)
self.use_reverse = use_reverse_primer
self.process_notag = process_notag
pipeline.setup_controls(self, nucl_control, prot_control)
def __init__(self, gene_name = "not_a_gene", fedit = 2, redit = 0, use_reverse_primer = True, keep_primers = False, max_ns = 0, min_length = 300, min_qual = 20, framebot_ref_ident = 0.3, framebot_minlength = 100, nucl_control = None, prot_control = None, decontam_cutoff = 0.1, process_notag=True): self.gene_name = gene_name self.fedit = str(fedit) self.redit = str(redit) self.min_length = str(min_length) self.max_ns = str(max_ns) self.min_qual = str(min_qual) self.keep_primers = keep_primers self.framebot_ref_ident = str(framebot_ref_ident) self.framebot_minlength = str(framebot_minlength) self.decontamination_cutoff = str(decontam_cutoff) self.use_reverse = use_reverse_primer self.process_notag = process_notag pipeline.setup_controls(self, nucl_control, prot_control)
def parse_section(default_opts, config, section):
nucl_control = None
prot_control = None
ret = copy.deepcopy(default_opts)
ret.gene_name = section
if not config or not config.has_section(section):
pipeline.setup_controls(ret, nucl_control, prot_control)
return ret
if config.has_option(section, "nucl_control"):
nucl_control = config.get(section, "nucl_control")
config.remove_option(section, "nucl_control")
if config.has_option(section, "prot_control"):
prot_control = config.get(section, "prot_control")
config.remove_option(section, "prot_control")
pipeline.setup_controls(ret, nucl_control, prot_control)
if config.has_option(section, "fedit"):
ret.fedit = config.get(section, "fedit")
config.remove_option(section, "fedit")
if config.has_option(section, "redit"):
ret.redit = config.get(section, "redit")
config.remove_option(section, "redit")
if config.has_option(section, "min_length"):
ret.min_length = config.get(section, "min_length")
config.remove_option(section, "min_length")
if config.has_option(section, "min_qual"):
ret.min_qual = config.get(section, "min_qual")
config.remove_option(section, "min_qual")
if config.has_option(section, "max_ns"):
ret.max_ns = config.get(section, "max_ns")
config.remove_option(section, "max_ns")
if config.has_option(section, "keep_primers"):
ret.keep_primers = config.get(section,
"keep_primers").lower() == "true"
config.remove_option(section, "keep_primers")
if config.has_option(section, "gene_name"):
ret.gene_name = config.get(section, "gene_name")
config.remove_option(section, "gene_name")
if config.has_option(section, "framebot_ref_ident"):
ret.framebot_ref_ident = config.get(section, "framebot_ref_ident")
config.remove_option(section, "framebot_ref_ident")
if config.has_option(section, "framebot_minlength"):
ret.framebot_minlength = config.get(section, "framebot_minlength")
config.remove_option(section, "framebot_minlength")
if config.has_option(section, "decontam_cutoff"):
ret.decontam_cutoff = config.get(section, "decontam_cutoff")
config.remove_option(section, "decontam_cutoff")
if config.has_option(section, "chop"):
ret.chop = config.get(section, "chop").lower() == "true"
config.remove_option(section, "chop")
if config.has_option(section, "model_chop_start"):
ret.model_chop_start = int(config.get(section, "model_chop_start"))
config.remove_option(section, "model_chop_start")
else:
ret.model_chop_end = 0
if config.has_option(section, "model_chop_end"):
ret.model_chop_end = int(config.get(section, "model_chop_end"))
config.remove_option(section, "model_chop_end")
else:
raise IOError(
"Must specify model chop end if you turn on chopping")
else:
ret.chop = False
if config.has_option(section, "use_reverse"):
ret.use_reverse = config.get(section, "use_reverse") == "true"
config.remove_option(section, "use_reverse")
if len(config.items(section)) != 0:
raise IOError("Unknown options %s in section %s" %
(config.items(section), section))
return ret
def parse_section(default_opts, config, section):
nucl_control = None
prot_control = None
ret = copy.deepcopy(default_opts)
ret.gene_name = section
if not config or not config.has_section(section):
pipeline.setup_controls(ret, nucl_control, prot_control)
return ret
if config.has_option(section, "nucl_control"):
nucl_control = config.get(section, "nucl_control")
config.remove_option(section, "nucl_control")
if config.has_option(section, "prot_control"):
prot_control = config.get(section, "prot_control")
config.remove_option(section, "prot_control")
pipeline.setup_controls(ret, nucl_control, prot_control)
if config.has_option(section, "fedit"):
ret.fedit = config.get(section, "fedit")
config.remove_option(section, "fedit")
if config.has_option(section, "redit"):
ret.redit = config.get(section, "redit")
config.remove_option(section, "redit")
if config.has_option(section, "min_length"):
ret.min_length = config.get(section, "min_length")
config.remove_option(section, "min_length")
if config.has_option(section, "min_qual"):
ret.min_qual = config.get(section, "min_qual")
config.remove_option(section, "min_qual")
if config.has_option(section, "max_ns"):
ret.max_ns = config.get(section, "max_ns")
config.remove_option(section, "max_ns")
if config.has_option(section, "keep_primers"):
ret.keep_primers = config.get(section, "keep_primers").lower() == "true"
config.remove_option(section, "keep_primers")
if config.has_option(section, "gene_name"):
ret.gene_name = config.get(section, "gene_name")
config.remove_option(section, "gene_name")
if config.has_option(section, "framebot_ref_ident"):
ret.framebot_ref_ident = config.get(section, "framebot_ref_ident")
config.remove_option(section, "framebot_ref_ident")
if config.has_option(section, "framebot_minlength"):
ret.framebot_minlength = config.get(section, "framebot_minlength")
config.remove_option(section, "framebot_minlength")
if config.has_option(section, "decontam_cutoff"):
ret.decontam_cutoff = config.get(section, "decontam_cutoff")
config.remove_option(section, "decontam_cutoff")
if config.has_option(section, "chop"):
ret.chop = config.get(section, "chop").lower() == "true"
config.remove_option(section, "chop")
if config.has_option(section, "model_chop_start"):
ret.model_chop_start = int(config.get(section, "model_chop_start"))
config.remove_option(section, "model_chop_start")
else:
ret.model_chop_end = 0
if config.has_option(section, "model_chop_end"):
ret.model_chop_end = int(config.get(section, "model_chop_end"))
config.remove_option(section, "model_chop_end")
else:
raise IOError("Must specify model chop end if you turn on chopping")
else:
ret.chop = False
if config.has_option(section, "use_reverse"):
ret.use_reverse = config.get(section, "use_reverse") == "true"
config.remove_option(section, "use_reverse")
if len(config.items(section)) != 0:
raise IOError("Unknown options %s in section %s" % (config.items(section), section))
return ret
