forked from rdpstaff/fungene_pipeline
/
titanium_options.py
166 lines (137 loc) · 6.46 KB
/
titanium_options.py
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#!/usr/bin/python
import sys
import pipeline
import ConfigParser
import os
import copy
def options_from_file(filename):
config = ConfigParser.ConfigParser()
config.read(filename)
if not config.has_section("general"):
raise IOError("Option file must have a general section")
if not config.has_option("general", "genes_of_interest"):
raise IOError("general section must have genes_of_interest option")
if not config.has_option("general", "seq_file_pattern"):
raise IOError("general section must have seq_file_pattern option")
if not config.has_option("general", "qual_file_pattern"):
raise IOError("general section must have qual_file_pattern option")
opts = dict()
opts["genes_of_interest"] = [t.strip() for t in config.get("general", "genes_of_interest").split(",")]
opts["seq_file_pattern" ] = config.get("general", "seq_file_pattern")
opts["qual_file_pattern" ] = config.get("general", "qual_file_pattern")
process_notag = True
default_fprimer = "fake_primer"
default_rprimer = None
max_ns = "0"
if config.has_option("general", "default_fprimer"):
default_fprimer = config.get("general", "default_fprimer").replace(" ", "")
config.remove_option("general", "default_fprimer")
if config.has_option("general", "default_rprimer"):
default_rprimer = config.get("general", "default_rprimer").replace(" ", "")
config.remove_option("general", "default_rprimer")
if config.has_option("general", "process_notag"):
process_notag = config.get("general", "process_notag") == "true"
config.remove_option("general", "process_notag")
if config.has_option("general", "max_ns"):
max_ns = config.get("general", "max_ns")
config.remove_option("general", "max_ns")
config.remove_option("general", "genes_of_interest")
config.remove_option("general", "seq_file_pattern")
config.remove_option("general", "qual_file_pattern")
opts["general"] = parse_section(Opts(), config, "general")
for section in config.sections():
if section == "general":
continue
if not section in opts["genes_of_interest"]:
print "WARNING: gene %s present in options but not listed as gene of interest" % section
opts[section] = parse_section(opts["general"], config, section)
for gene_of_interest in opts["genes_of_interest"]:
if gene_of_interest not in opts:
print "WARNING: gene %s is listed as a gene of interest but not listed in option file, default options will be used" % gene_of_interest
opts[gene_of_interest] = parse_section(opts["general"], None, gene_of_interest)
opts["general"].process_notag = process_notag
opts["general"].forward_primers = default_fprimer
opts["general"].reverse_primers = default_rprimer
opts["general"].max_ns = max_ns
return opts
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
class Opts:
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)