os.system("bunzip2 -c %s > %s"%(inFile, dest))
elif base.endswith("gz"):
os.system("gunzip -c %s > %s"%(inFile, dest))
else:
os.system("cp %s %s"%(inFile, dest))
if doremove:
os.system("rm -f %s"%(base))
if len(sys.argv) < 2:
usage()
sys.exit(1)
selectedWorkflow = ""
selectedCommands = ""
availableWf = workflow.getSupportedWorkflows("%s/workflows"%(UTILS_DIR), True)
availableWf.extend(workflow.getSupportedWorkflows(os.getcwd(), True))
availableWorkflows = dict()
for wf in availableWf:
availableWorkflows[wf.name] = wf
allsteps = ["Preprocess","Assemble","Validate","MultiAlign","FindORFS","FindRepeats","Abundance","Annotate","FunctionalAnnotation","Scaffold","Propagate","FindScaffoldORFS","Classify","Postprocess"]
today = datetime.datetime.now()
#todaytime = date.fromtimestamp(time.time())
timestamp = "P_"+today.isoformat().replace("-","_").replace(".","").replace(":","").replace("T","_")
#print timestamp
try:
opts, args = getopt.getopt(sys.argv[1:], "hfsq1:2:m:c:i:d:or:l:VW:", ["help", "fasta","fastq","sff","f1=","f2=","matelib=","asmcontig=","insertlen=","dir=","outtie=","readlen=","version", "workflow"])
except getopt.GetoptError, err:
# print help information and exit:
usage()
sys.exit(1)
if not os.path.exists(settings.rundir) or settings.rundir == "":
print "project dir %s does not exist!" % (settings.rundir)
usage()
sys.exit(1)
inifile = settings.rundir + os.sep + "pipeline.ini"
inf = open(inifile, 'r')
(asmcontigs, readlibs,
wfName) = utils.readConfigInfo(inf, "%s/Preprocess/in/" % (settings.rundir))
if wfName != "":
#parse frag/libs out of pipeline.ini out of rundir
availableWf = workflow.getSupportedWorkflows(
"%s/workflows" % (utils.INITIAL_UTILS), True)
availableWf.extend(workflow.getSupportedWorkflows(os.getcwd(), True))
availableWorkflows = dict()
for wf in availableWf:
availableWorkflows[wf.name] = wf
if wfName.lower() not in availableWorkflows.keys():
print "Error: unknown workflow %s specified. Please choose one of %s." % (
wfName, ",".join(availableWorkflows.keys()))
sys.exit(1)
wf = availableWorkflows[wfName]
try:
wfopts, wfargs = getopt.getopt(wf.commandList.strip().split(),
shortOptions, longOptions)
if wf.canModify():
wfopts.extend(opts)
print "project dir %s does not exist!"%(settings.rundir)
usage()
sys.exit(1)
if not os.path.exists(settings.rundir) or settings.rundir == "":
print "project dir %s does not exist!"%(settings.rundir)
usage()
sys.exit(1)
inifile = settings.rundir+os.sep+"pipeline.ini"
inf = open(inifile,'r')
(asmcontigs, readlibs, wfName) = utils.readConfigInfo(inf, "%s/Preprocess/in/"%(settings.rundir))
if wfName != "":
#parse frag/libs out of pipeline.ini out of rundir
availableWf = workflow.getSupportedWorkflows("%s/workflows"%(utils.INITIAL_UTILS), True)
availableWf.extend(workflow.getSupportedWorkflows(os.getcwd(), True))
availableWorkflows = dict()
for wf in availableWf:
availableWorkflows[wf.name] = wf
if wfName.lower() not in availableWorkflows.keys():
print "Error: unknown wofkflow %s specified. Please choose one of %s."%(wfName, ",".join(availableWorkflows.keys()))
sys.exit(1)
wf = availableWorkflows[wfName]
try:
wfopts, wfargs = getopt.getopt(wf.commandList.strip().split(), shortOptions, longOptions)
if wf.canModify():
wfopts.extend(opts)
wfargs.extend(args)
opts = wfopts
elif base.endswith("gz"):
os.system("gunzip -c %s > %s" % (inFile, dest))
else:
os.system("cp %s %s" % (inFile, dest))
if doremove:
os.system("rm -f %s" % (base))
if len(sys.argv) < 2:
usage()
sys.exit(1)
selectedWorkflow = ""
selectedCommands = ""
availableWf = workflow.getSupportedWorkflows("%s/workflows" % (UTILS_DIR),
True)
availableWf.extend(workflow.getSupportedWorkflows(os.getcwd(), True))
availableWorkflows = dict()
for wf in availableWf:
availableWorkflows[wf.name] = wf
allsteps = [
"Preprocess", "Assemble", "Validate", "MultiAlign", "FindORFS",
"FindRepeats", "Abundance", "Classify", "ClassifyReads", "Benchmark",
"FunctionalAnnotation", "Scaffold", "Propagate", "FindScaffoldORFS", "Bin",
"Postprocess"
]
today = datetime.datetime.now()
#todaytime = date.fromtimestamp(time.time())
timestamp = "P_" + today.isoformat().replace("-", "_").replace(