def printConfiguration(fileName=None): configurationText = [] configurationText.append("metAMOS configuration summary:\n") configurationText.append("Time and Date:\t\t%s\n"%(str(datetime.date.today()))) configurationText.append("Working directory:\t%s\n"%(utils.Settings.rundir)) configurationText.append("Prefix:\t\t\t%s\n"%(utils.Settings.PREFIX)) configurationText.append("K-Mer:\t\t\t%d\n"%(utils.Settings.kmer)) configurationText.append("Threads:\t\t%d\n"%(utils.Settings.threads)) configurationText.append("Taxonomic level:\t%s\n"%(utils.Settings.taxa_level)) configurationText.append("Verbose:\t\t%s\n"%(utils.Settings.VERBOSE)) configurationText.append("Steps to skip:\t\t%s\n"%(", ".join(skipsteps))) configurationText.append("Steps to force:\t\t%s\n"%(", ".join(forcesteps))) configurationText.append("\n") configurationText.append("Step-specific configuration:\n") for type in selected_programs.keys(): configurationText.append("[" + type + "]\n") prog = selected_programs[type] if prog == None or prog == "none": configurationText.append("None\n\n") else: (progName, citation) = utils.getProgramCitations(settings, prog) configurationText.append(progName + "\n") try: configurationText.append("\t" + eval("utils.Settings.%s"%(prog.replace("-", "_").upper()))+"\n") except AttributeError: configurationText.append("\tUNKNOWN\n") configurationText.append("\t" + citation + "\n\n") # add step-indepent citations that are always run configurationText.append("[other]\n") for prog in always_run_programs: if prog == None or prog == "none": configurationText.append("None\n\n") else: (progName, citation) = utils.getProgramCitations(settings, prog) configurationText.append(progName + "\n") try: configurationText.append("\t" + eval("utils.Settings.%s"%(prog.upper()))+"\n") except AttributeError: configurationText.append("\tUNKNOWN\n") configurationText.append("\t" + citation + "\n\n") if fileName == "" or fileName == None: print ''.join(configurationText) else: conf = open(fileName, 'w') conf.write(''.join(configurationText)) conf.close()
def printConfiguration(fileName=None): configurationText = [] configurationText.append("metAMOS configuration summary:\n") configurationText.append("metAMOS Version:\t%s\n"%(utils.getVersion())) configurationText.append("Time and Date:\t\t%s\n"%(str(datetime.date.today()))) configurationText.append("Working directory:\t%s\n"%(utils.Settings.rundir)) configurationText.append("Prefix:\t\t\t%s\n"%(utils.Settings.PREFIX)) configurationText.append("K-Mer:\t\t\t%s\n"%(utils.Settings.kmer)) configurationText.append("Threads:\t\t%d\n"%(utils.Settings.threads)) configurationText.append("Taxonomic level:\t%s\n"%(utils.Settings.taxa_level)) configurationText.append("Verbose:\t\t%s\n"%(utils.Settings.VERBOSE)) configurationText.append("Steps to skip:\t\t%s\n"%(", ".join(skipsteps))) configurationText.append("Steps to force:\t\t%s\n"%(", ".join(forcesteps))) # get metamos citations configurationText.append("\n") configurationText.append("[citation]\n") (progName, citation) = utils.getProgramCitations(settings, "metamos") configurationText.append(progName + "\n") configurationText.append("\t" + citation + "\n\n") if isolate_genome == True: (progName, citation) = utils.getProgramCitations(settings, "metamos_isolate") configurationText.append(progName + "\n") configurationText.append("\t" + citation + "\n\n") configurationText.append("\n") configurationText.append("Step-specific configuration:\n") for type in selected_programs.keys(): progs = set(selected_programs[type].split(",")) configurationText.append("[" + type + "]\n") for prog in progs: # special case for validation, orf is a reference to selected orf finder, n50 is nothing if type == "validate" and prog == "n50": continue if type == "validate" and prog == "orf": prog = selected_programs["findorfs"] if type == "preprocess" and prog == "none": configurationText.append(prog.upper() + "\n\tN/A\n\n") continue if type == "preprocess" and prog == "metamos": configurationText.append("metAMOS built-in filtering\n\tN/A\n\n") continue if prog == None or prog == "none": configurationText.append("None\n\n") else: (progName, citation) = utils.getProgramCitations(settings, prog) if progName == "": configurationText.append(prog + "\n") else: configurationText.append(progName + "\n") try: configurationText.append("\t" + eval("utils.Settings.%s"%(prog.replace("-", "_").upper()))+"\n") except AttributeError: try: configurationText.append("\t" + generic.getLocation(utils.STEP_NAMES.mapping[type.upper()], prog) + "\n") except KeyError: configurationText.append("UNKNOWN") if citation != "": configurationText.append("\t" + citation + "\n\n") # add step-indepent citations that are always run configurationText.append("[other]\n") for prog in always_run_programs: if prog == None or prog == "none": configurationText.append("None\n\n") else: (progName, citation) = utils.getProgramCitations(settings, prog) configurationText.append(progName + "\n") try: configurationText.append("\t" + eval("utils.Settings.%s"%(prog.upper()))+"\n") except AttributeError: configurationText.append("\tUNKNOWN\n") configurationText.append("\t" + citation + "\n\n") if fileName == "" or fileName == None: print ''.join(configurationText) else: conf = open(fileName, 'w') conf.write(''.join(configurationText)) conf.close()
#skipsteps.append("Abundance") skipsteps.add("FunctionalAnnotation") #skip nofcpblast = True elif o in ("-y","--lowcpu"): nofcpblast = True elif o in ("-w","--what"): utils.Settings.OUTPUT_ONLY = True elif o in ("-j","--justprogs"): output_programs = 1 print "\n======Supported programs and citations (if available)=======\n" for type in supported_programs.keys(): print "[" + type + "]" ccnt = 1 for prog in supported_programs[type]: (progName, citation) = utils.getProgramCitations(settings, prog) #citation = "NA" try: citation = pub_dict[prog] except KeyError: citation = "NA" print " %d)"%(ccnt)+" "+progName print " "+citation+"\n" ccnt +=1 sys.exit(0) elif o in ("-u","--unassembledreads"): utils.Settings.annotate_unmapped = 1 elif o in ("-x","--xcov"): min_ctg_cvg = int(a) elif o in ("-l","--lencontigorf"):
def printConfiguration(fileName=None): configurationText = [] configurationText.append("metAMOS configuration summary:\n") configurationText.append("metAMOS Version:\t%s\n" % (utils.getVersion())) configurationText.append("Time and Date:\t\t%s\n" % (str(datetime.date.today()))) configurationText.append("Working directory:\t%s\n" % (utils.Settings.rundir)) configurationText.append("Prefix:\t\t\t%s\n" % (utils.Settings.PREFIX)) configurationText.append("K-Mer:\t\t\t%s\n" % (utils.Settings.kmer)) configurationText.append("Threads:\t\t%d\n" % (utils.Settings.threads)) configurationText.append("Taxonomic level:\t%s\n" % (utils.Settings.taxa_level)) configurationText.append("Verbose:\t\t%s\n" % (utils.Settings.VERBOSE)) configurationText.append("Steps to skip:\t\t%s\n" % (", ".join(skipsteps))) configurationText.append("Steps to force:\t\t%s\n" % (", ".join(forcesteps))) # get metamos citations configurationText.append("\n") configurationText.append("[citation]\n") (progName, citation) = utils.getProgramCitations(settings, "metamos") configurationText.append(progName + "\n") configurationText.append("\t" + citation + "\n\n") if isolate_genome == True: (progName, citation) = utils.getProgramCitations(settings, "metamos_isolate") configurationText.append(progName + "\n") configurationText.append("\t" + citation + "\n\n") configurationText.append("\n") configurationText.append("Step-specific configuration:\n") for type in selected_programs.keys(): progs = set(selected_programs[type].split(",")) configurationText.append("[" + type + "]\n") for prog in progs: # special case for validation, orf is a reference to selected orf finder, n50 is nothing if type == "validate" and prog == "n50": continue if type == "validate" and prog == "orf": prog = selected_programs["findorfs"] if type == "preprocess" and prog == "none": configurationText.append(prog.upper() + "\n\tN/A\n\n") continue if type == "preprocess" and prog == "metamos": configurationText.append( "metAMOS built-in filtering\n\tN/A\n\n") continue if prog == None or prog == "none": configurationText.append("None\n\n") else: (progName, citation) = utils.getProgramCitations(settings, prog) if progName == "": configurationText.append(prog + "\n") else: configurationText.append(progName + "\n") try: configurationText.append( "\t" + eval("utils.Settings.%s" % (prog.replace("-", "_").upper())) + "\n") except AttributeError: try: configurationText.append("\t" + generic.getLocation( utils.STEP_NAMES.mapping[type.upper()], prog) + "\n") except KeyError: configurationText.append("UNKNOWN") if citation != "": configurationText.append("\t" + citation + "\n\n") # add step-indepent citations that are always run configurationText.append("[other]\n") for prog in always_run_programs: if prog == None or prog == "none": configurationText.append("None\n\n") else: (progName, citation) = utils.getProgramCitations(settings, prog) configurationText.append(progName + "\n") try: configurationText.append("\t" + eval("utils.Settings.%s" % (prog.upper())) + "\n") except AttributeError: configurationText.append("\tUNKNOWN\n") configurationText.append("\t" + citation + "\n\n") if fileName == "" or fileName == None: print ''.join(configurationText) else: conf = open(fileName, 'w') conf.write(''.join(configurationText)) conf.close()
skipsteps.add("FunctionalAnnotation") #skip nofcpblast = True elif o in ("-y", "--lowcpu"): nofcpblast = True elif o in ("-w", "--what"): utils.Settings.OUTPUT_ONLY = True elif o in ("-j", "--justprogs"): output_programs = 1 print "\n======Supported programs and citations (if available)=======\n" for type in supported_programs.keys(): print "[" + type + "]" ccnt = 1 for prog in supported_programs[type]: (progName, citation) = utils.getProgramCitations(settings, prog) #citation = "NA" try: citation = pub_dict[prog] except KeyError: citation = "NA" print " %d)" % (ccnt) + " " + progName print " " + citation + "\n" ccnt += 1 sys.exit(0) elif o in ("-u", "--unassembledreads"): utils.Settings.classify_unmapped = 1 elif o in ("-x", "--xcov"): min_ctg_cvg = int(a) elif o in ("-l", "--lencontigorf"):