def read(self, comment = "#"):
# populate from file
self.isValid = True
workflow_file = None
for p in self.path:
if os.path.exists("%s%s%s.ini"%(p, os.sep, self.name.lower())):
workflow_file = open("%s%s%s.ini"%(p, os.sep, self.name.lower()), 'r')
if workflow_file == None:
print "Error: cannot open workflow %s"%(self.name)
raise(JobSignalledBreak)
lastPos = 0
while True:
lastPos = workflow_file.tell()
line = workflow_file.readline()
(line, sep, commentLine) = line.partition(comment)
if len(commentLine) != 0:
continue
if "programs:" in line:
splitLine = line.replace("programs:", "").strip().split()
for prog in splitLine:
self.programList.add(prog.lower())
elif "md5:" in line:
self.md5 = line.replace("md5:", "").strip()
elif "inherit:" in line:
splitLine = line.replace("inherit:", "").strip().split()
for master in splitLine:
self.super.append(master)
masterFlow = None
if master in _workflows:
masterFlow = _workflows[master]
else:
masterFlow = Workflow(line.replace("inherit:", "").strip(), self.path)
masterFlow.read()
self.programList.update(masterFlow.programList)
self.readlibs.extend(masterFlow.readlibs)
self.commandList = (masterFlow.commandList + " " + self.commandList).strip()
self.asmcontigs.extend(masterFlow.asmcontigs)
self.isModifiable = masterFlow.isModifiable or self.isModifiable
elif "modify:" in line:
splitLine = line.replace("modify:", "").strip()
self.isModifiable = self.isModifiable or str2bool(splitLine)
elif "command:" in line:
splitLine = line.replace("command:", "").strip()
self.commandList = (self.commandList + " " + splitLine).strip()
else:
break
workflow_file.seek(lastPos)
# now read the library info
(readasm, readl, ignore) = readConfigInfo(workflow_file)
self.readlibs.extend(readl)
self.asmcontigs.extend(readasm)
workflow_file.close()
if self.md5 != None:
if self.md5 != getMD5():
self.isValid = False
if _verbose:
print "Read workflow %s"%(self.name)
print "Inherits from %s"%(",".join(self.super))
print "Supported programs %s"%(",".join(self.programList))
print "Asm contigs %s"%(",".join(self.asmcontigs))
for lib in self.readlibs:
print "Lib %s %s %s %s %s %s %s %s %s"%(lib.id, lib.format, lib.mean, lib.stdev, lib.mmin, lib.mmax, lib.mated, lib.interleaved, lib.innie)
elif o in ("-d", "--projectdir"):
utils.Settings.rundir = os.path.abspath(a)
if not os.path.exists(a):
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 workflow %s specified. Please choose one of %s." % (
wfName, ",".join(availableWorkflows.keys()))
sys.exit(1)
wf = availableWorkflows[wfName]
sys.exit()
elif o in ("-d", "--projectdir"):
utils.Settings.rundir = os.path.abspath(a)
if not os.path.exists(a):
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)
def read(self, comment="#"):
# populate from file
self.isValid = True
workflow_file = None
for p in self.path:
if os.path.exists("%s%s%s.ini" % (p, os.sep, self.name.lower())):
workflow_file = open(
"%s%s%s.ini" % (p, os.sep, self.name.lower()), 'r')
if workflow_file == None:
print "Error: cannot open workflow %s" % (self.name)
raise (JobSignalledBreak)
lastPos = 0
while True:
lastPos = workflow_file.tell()
line = workflow_file.readline()
(line, sep, commentLine) = line.partition(comment)
if len(commentLine) != 0:
continue
if "programs:" in line:
splitLine = line.replace("programs:", "").strip().split()
for prog in splitLine:
self.programList.add(prog.lower())
if "steps:" in line:
self.stepList = []
splitLine = line.replace("steps:", "").strip().split()
for step in splitLine:
if step not in stepList:
self.stepList.append(step.lower())
elif "md5:" in line:
self.md5 = line.replace("md5:", "").strip()
elif "inherit:" in line:
splitLine = line.replace("inherit:", "").strip().split()
for master in splitLine:
self.super.append(master)
masterFlow = None
if master in _workflows:
masterFlow = _workflows[master]
else:
masterFlow = Workflow(
line.replace("inherit:", "").strip(), self.path)
masterFlow.read()
self.programList.update(masterFlow.programList)
self.readlibs.extend(masterFlow.readlibs)
self.commandList = (masterFlow.commandList + " " +
self.commandList).strip()
self.asmcontigs.extend(masterFlow.asmcontigs)
self.isModifiable = masterFlow.isModifiable or self.isModifiable
elif "modify:" in line:
splitLine = line.replace("modify:", "").strip()
self.isModifiable = self.isModifiable or str2bool(splitLine)
elif "command:" in line:
splitLine = line.replace("command:", "").strip()
self.commandList = (self.commandList + " " + splitLine).strip()
else:
break
workflow_file.seek(lastPos)
# now read the library info
(readasm, readl, ignore) = readConfigInfo(workflow_file)
self.readlibs.extend(readl)
self.asmcontigs.extend(readasm)
workflow_file.close()
if self.md5 != None:
if self.md5 != getMD5():
self.isValid = False
if _verbose:
print "Read workflow %s" % (self.name)
print "Inherits from %s" % (",".join(self.super))
print "Supported programs %s" % (",".join(self.programList))
print "Asm contigs %s" % (",".join(self.asmcontigs))
for lib in self.readlibs:
print "Lib %s %s %s %s %s %s %s %s %s" % (
lib.id, lib.format, lib.mean, lib.stdev, lib.mmin,
lib.mmax, lib.mated, lib.interleaved, lib.innie)