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"):
