def setupProgram(): ### Basic Setup of Program
'''
Basic setup of Program:
- Reads sys.argv and augments if appropriate
- Makes Info, Out and Log objects
- Returns [info,out,log,cmd_list]
'''
try:
### Initial Command Setup & Info ###
info = makeInfo()
cmd_list = rje.getCmdList(sys.argv[1:],info=info) ### Load defaults from program.ini
### Out object ###
out = rje.Out(cmd_list=cmd_list)
out.verbose(2,2,cmd_list,1)
out.printIntro(info)
### Additional commands ###
cmd_list = cmdHelp(info,out,cmd_list)
### Log ###
log = rje.setLog(info=info,out=out,cmd_list=cmd_list)
return [info,out,log,cmd_list]
except SystemExit: sys.exit()
except KeyboardInterrupt: sys.exit()
except:
print 'Problem during initial setup.'
raise
def setupProgram(): ### Basic Setup of Program
'''
Basic setup of Program:
- Reads sys.argv and augments if appropriate
- Makes Info, Out and Log objects
- Returns [info,out,log,cmd_list]
'''
### <0> ### Objects setup
try:
## <a> ## Initial Command Setup & Info
cmd_list = sys.argv[1:]
info = makeInfo()
cmd_list = rje.getCmdList(
cmd_list, info=info) ### Load defaults from program.ini
## <b> ## Out object
out = rje.Out(cmd_list=cmd_list)
out.verbose(0, 2, cmd_list, 1)
out.printIntro(info)
## <c> ## Additional commands
cmd_list = cmdHelp(info, out, cmd_list)
## <d> ## Log
log = rje.setLog(info=info, out=out, cmd_list=cmd_list)
return [info, out, log, cmd_list]
except SystemExit:
sys.exit()
except:
print "Problem during initial setup."
raise
def setupProgram(): ### Basic Setup of Program
'''
Basic setup of Program:
- Reads sys.argv and augments if appropriate
- Makes Info, Out and Log objects
- Returns [info,out,log,cmd_list]
'''
try:
### Initial Command Setup & Info ###
info = makeInfo()
cmd_list = rje.getCmdList(
sys.argv[1:], info=info) ### Load defaults from program.ini
### Out object ###
out = rje.Out(cmd_list=cmd_list)
out.verbose(2, 2, cmd_list, 1)
out.printIntro(info)
### Additional commands ###
cmd_list = cmdHelp(info, out, cmd_list)
### Log ###
log = rje.setLog(info=info, out=out, cmd_list=cmd_list)
return [info, out, log, cmd_list]
except SystemExit:
sys.exit()
except KeyboardInterrupt:
sys.exit()
except:
print 'Problem during initial setup.'
raise
def setupProgram(): ### Basic Setup of Program when called from commandline.
'''
Basic Setup of Program when called from commandline:
- Reads sys.argv and augments if appropriate
- Makes Info, Out and Log objects
- Returns [info,out,log,cmd_list]
'''
try: ### ~ [1] ~ Initial Command Setup & Info ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
info = makeInfo() # Sets up Info object with program details
cmd_list = rje.getCmdList(
sys.argv[1:],
info=info) # Reads arguments and load defaults from program.ini
out = rje.Out(cmd_list=cmd_list
) # Sets up Out object for controlling output to screen
out.verbose(2, 2, cmd_list,
1) # Prints full commandlist if verbosity >= 2
out.printIntro(
info) # Prints intro text using details from Info object
cmd_list = cmdHelp(
info, out,
cmd_list) # Shows commands (help) and/or adds commands from user
log = rje.setLog(
info, out,
cmd_list) # Sets up Log object for controlling log file output
return (info, out, log, cmd_list) # Returns objects for use in program
except SystemExit:
sys.exit()
except KeyboardInterrupt:
sys.exit()
except:
print 'Problem during initial setup.'
raise
def setupProgram(): ### Basic Setup of Program
"""
Basic setup of Program:
- Reads sys.argv and augments if appropriate
- Makes Info, Out and Log objects
- Returns [info,out,log,cmd_list]
"""
### <0> ### Objects setup
try:
## <a> ## Initial Command Setup & Info
cmd_list = sys.argv[1:]
info = makeInfo()
cmd_list = rje.getCmdList(cmd_list, info=info) ### Load defaults from program.ini
## <b> ## Out object
out = rje.Out(cmd_list=cmd_list)
out.verbose(0, 2, cmd_list, 1)
out.printIntro(info)
## <c> ## Additional commands
cmd_list = cmdHelp(info, out, cmd_list)
## <d> ## Log
log = rje.setLog(info=info, out=out, cmd_list=cmd_list)
return [info, out, log, cmd_list]
except SystemExit:
sys.exit()
except KeyboardInterrupt:
sys.exit()
except:
print "Problem during initial setup."
raise
def batchRun(self,returnobj=False): ### Execute batch mode runs
'''Execute batch mode runs.'''
try:### ~ [0] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
barg = self.getStrLC('BatchArg')
if not barg: raise ValueError('Cannot use batchrun=FILELIST if batcharg=None.')
batchfiles = self.list['BatchRun'][0:]
self.list['BatchRun'] = [] # Avoid recursive running!
blog = self.getStr('BatchLog')
if not blog.startswith('.'): blog = '.%s' % blog
if not blog.endswith('.log'): blog = '%s.log' % blog
rawcmd = self.cmd_list[0:]
rawlog = self.log
batchobj = []
### ~ [1] Batch Run ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
bx = 0
for bfile in batchfiles:
bx += 1
self.printLog('#BATCH','Batch running %s of %s: %s=%s' % (rje.iStr(bx),rje.iLen(batchfiles),barg,bfile))
## Setup parameters
bbase = rje.baseFile(bfile,strip_path=True)
bcmd = ['%s=%s' % (barg,bfile)]
if self.getBool('BatchBase'):
if blog == '.log': bcmd += ['basefile=%s' % bbase]
else: bcmd += ['basefile=%s%s' % (bbase,rje.baseFile(blog))]
elif self.getStrLC('BatchLog'): bcmd += ['log=%s%s' % (bbase,blog)]
else: bcmd += ['newlog=F']
#self.debug(bcmd)
## Setup Seqsuite object
self.cmd_list = rawcmd + bcmd
self.log = rje.setLog(self.log.obj['Info'],self,self.cmd_list) # Sets up Log object for controlling log file output
## Run
batchobj.append(self.run())
## Finish and Tidy
self.log = rawlog
runobj = batchobj[-1]
if runobj:
if not returnobj: batchobj[-1] = True
info = runobj.log.obj['Info']
self.printLog('#RUN','%s V%s run finished.' % (info.program,info.version))
else: self.warnLog('Batch run failed (%s=%s).' % (barg,bfile))
### ~ [2] Finish and Return ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
failx = batchobj.count(False)
self.printLog('#BATCH','%s batch runs complete: %s failed.' % (rje.iLen(batchfiles),rje.iStr(failx)))
self.list['BatchRun'] = batchfiles
return batchobj
except: self.errorLog('%s.batchRun error' % self); return False
def setupProgram(): ### Basic Setup of Program when called from commandline.
'''
Basic Setup of Program when called from commandline:
- Reads sys.argv and augments if appropriate
- Makes Info, Out and Log objects
- Returns [info,out,log,cmd_list]
'''
try:### ~ [1] ~ Initial Command Setup & Info ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
info = makeInfo() # Sets up Info object with program details
cmd_list = rje.getCmdList(sys.argv[1:],info=info) # Reads arguments and load defaults from program.ini
out = rje.Out(cmd_list=cmd_list) # Sets up Out object for controlling output to screen
out.verbose(2,2,cmd_list,1) # Prints full commandlist if verbosity >= 2
out.printIntro(info) # Prints intro text using details from Info object
cmd_list = cmdHelp(info,out,cmd_list) # Shows commands (help) and/or adds commands from user
log = rje.setLog(info,out,cmd_list) # Sets up Log object for controlling log file output
return (info,out,log,cmd_list) # Returns objects for use in program
except SystemExit: sys.exit()
except KeyboardInterrupt: sys.exit()
except: print 'Problem during initial setup.'; raise
def multiHAQ(self,secondrun=False): ### Executes main HAQESAC runs
'''Executes main HAQESAC runs.'''
try:### ~ [0] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
finalrun = secondrun == self.opt['MultiHAQ'] # Whether this is the manual HAQESAC phase
qryacc = self.obj['SeqList'].accList() # Full list of Query accession numbers
processed = [] # List of processed sequence accession numbers
### ~ [1] Peform HAQESAC runs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for seq in self.seqs():
## ~ [1a] Check AutoSkip ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
acc = seq.info['AccNum']
if finalrun and acc in processed and (self.opt['AutoSkip'] or (self.i() >=0 and rje.yesNo('%s already covered by previous HAQESAC. Skip?' % seq.shortName()))):
self.printLog('#SKIP','%s already covered by previous HAQESAC: Skipped' % seq.shortName()); continue
## ~ [1b] Check Whether to run (re-runs and low sequence number) ~~~~~~~~~~~~~~~~~~ ##
logfile = rje.makePath('%s%s.log' % (self.info['HaqDir'],acc),wholepath=True)
infile = rje.makePath('%s%s.fas' % (self.info['HaqDir'],acc),wholepath=True)
pkfile = rje.makePath('%s%s.pickle' % (self.info['HaqDir'],acc),wholepath=True)
pkzfile = rje.makePath('%s%s.pickle.gz' % (self.info['HaqDir'],acc),wholepath=True)
if not os.path.exists(infile): self.printLog('#SKIP','%s input file %s not found: Skipped' % (seq.shortName(),infile)); continue
if not finalrun and not self.opt['Force'] and rje.isYounger(pkzfile,infile) == pkzfile:
self.printLog('#SKIP','%s run detected: Skipped' % seq.shortName()); continue
if not finalrun and not self.opt['Force'] and rje.isYounger(pkfile,infile) == pkfile:
self.printLog('#SKIP','%s run detected: Skipped' % seq.shortName()); continue
inseqx = rje_seq.SeqCount(self,infile)
if inseqx < 2: self.printLog('#SKIP','Only one sequence found in %s: Skipped' % (infile)); continue
## ~ [1c] Pause if running in Chaser Mode and no Pickle ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
pickled = os.path.exists(pkfile) or os.path.exists('%s.gz' % pkfile); tm = 0
while secondrun and self.opt['Chaser'] and not pickled:
self.progLog('#WAIT','No %s pickle. Sleeping for %d min.' % (acc,tm))
time.sleep(60*tm); tm += 1
pickled = os.path.exists(pkfile) or os.path.exists('%s.gz' % pkfile)
if not pickled:
try: rje.choice('Press <ENTER> to try again, or <CTRL+C> to Quit')
except:
self.printLog('#PICKLE','No %s pickle.' % (acc,tm))
self.printLog('\r#MULTI','Exiting multiHAQ "Chaser" run.'); return
## ~ [1d] Run HAQESAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
runhaqesac = True
pngfile = rje.makePath('%s%s.png' % (self.info['HaqDir'],acc),wholepath=True)
if not self.force() and rje.exists(pngfile):
self.printLog('#SKIP','Found evidence of completed run: %s (force=F). Skipping.' % pngfile)
runhaqesac = False
ancfile = rje.makePath('%s%s.anc.fas' % (self.info['HaqDir'],acc),wholepath=True)
if not self.force() and rje.exists(ancfile):
self.printLog('#SKIP','Found evidence of completed run: %s (force=F). Skipping.' % ancfile)
runhaqesac = False
#if not finalrun or self.opt['Force'] or rje.isYounger(logfile,nsfile) != logfile:
if runhaqesac:
haqcmd = ['ini=haqesac.ini','seqin=%s.fas' % acc, 'query=%s' % acc, 'basefile=%s' % acc, 'newlog=F']
self.printLog('#HAQ','Running HAQESAC for %s - will have own log etc.' % seq.shortName(),log=False)
os.chdir(self.info['HaqDir'])
info = haqesac.makeInfo()
haqcmd = rje.getCmdList(haqcmd,info=info)
out = rje.Out(cmd_list=haqcmd) # Sets up Out object for controlling output to screen
out.printIntro(info) # Prints intro text using details from Info object
haqlog = rje.setLog(info,out,haqcmd) # Sets up Log object for controlling log file output
try: haqesac.HAQESAC(log=haqlog, cmd_list=haqcmd).run(setobjects=True)
except:
os.chdir(self.info['RunPath'])
if self.i() >= 0 and rje.yesNo('Problem with %s HAQESAC run. Abort?' % seq.shortName()): raise KeyboardInterrupt
os.chdir(self.info['RunPath'])
if finalrun: self.printLog('#HAQ','HAQESAC final round run for %s' % seq.shortName())
else: self.printLog('#HAQ','HAQESAC first round run for %s' % seq.shortName())
## ~ [1e] Update ScreenQry ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if not self.opt['ScreenQry'] or not finalrun: continue
qacclist = []
for qacc in rje_seq.SeqList(self.log,['seqin=%s' % infile,'autoload=T','autofilter=F']).accList():
if qacc in qryacc and qacc != acc: qacclist.append(qacc)
if qacc in qryacc and qacc not in processed: processed.append(qacc)
self.printLog('#QRY','%d other queries found in %s: [%s]' % (len(qacclist),infile,string.join(qacclist,'; ')))
self.printLog('#QRY','%d of %d queries processed' % (len(processed),self.seqNum()))
### ~ [2] MultiHAQ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not finalrun: self.printLog('#MULTI','Executing second round of multiHAQ'); self.multiHAQ(True)
except: self.errorLog('Major problem with MultiHAQ.multiHAQ',quitchoice=True)
def multiHAQ(self, secondrun=False): ### Executes main HAQESAC runs
'''Executes main HAQESAC runs.'''
try: ### ~ [0] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
finalrun = secondrun == self.opt[
'MultiHAQ'] # Whether this is the manual HAQESAC phase
qryacc = self.obj['SeqList'].accList(
) # Full list of Query accession numbers
processed = [] # List of processed sequence accession numbers
### ~ [1] Peform HAQESAC runs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
for seq in self.seqs():
## ~ [1a] Check AutoSkip ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
acc = seq.info['AccNum']
if finalrun and acc in processed and (
self.opt['AutoSkip'] or (self.i() >= 0 and rje.yesNo(
'%s already covered by previous HAQESAC. Skip?' %
seq.shortName()))):
self.printLog(
'#SKIP',
'%s already covered by previous HAQESAC: Skipped' %
seq.shortName())
continue
## ~ [1b] Check Whether to run (re-runs and low sequence number) ~~~~~~~~~~~~~~~~~~ ##
logfile = rje.makePath('%s%s.log' % (self.info['HaqDir'], acc),
wholepath=True)
infile = rje.makePath('%s%s.fas' % (self.info['HaqDir'], acc),
wholepath=True)
pkfile = rje.makePath('%s%s.pickle' %
(self.info['HaqDir'], acc),
wholepath=True)
pkzfile = rje.makePath('%s%s.pickle.gz' %
(self.info['HaqDir'], acc),
wholepath=True)
if not os.path.exists(infile):
self.printLog(
'#SKIP', '%s input file %s not found: Skipped' %
(seq.shortName(), infile))
continue
if not finalrun and not self.opt['Force'] and rje.isYounger(
pkzfile, infile) == pkzfile:
self.printLog('#SKIP',
'%s run detected: Skipped' % seq.shortName())
continue
if not finalrun and not self.opt['Force'] and rje.isYounger(
pkfile, infile) == pkfile:
self.printLog('#SKIP',
'%s run detected: Skipped' % seq.shortName())
continue
inseqx = rje_seq.SeqCount(self, infile)
if inseqx < 2:
self.printLog(
'#SKIP',
'Only one sequence found in %s: Skipped' % (infile))
continue
## ~ [1c] Pause if running in Chaser Mode and no Pickle ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
pickled = os.path.exists(pkfile) or os.path.exists(
'%s.gz' % pkfile)
tm = 0
while secondrun and self.opt['Chaser'] and not pickled:
self.progLog(
'#WAIT',
'No %s pickle. Sleeping for %d min.' % (acc, tm))
time.sleep(60 * tm)
tm += 1
pickled = os.path.exists(pkfile) or os.path.exists(
'%s.gz' % pkfile)
if not pickled:
try:
rje.choice(
'Press <ENTER> to try again, or <CTRL+C> to Quit'
)
except:
self.printLog('#PICKLE',
'No %s pickle.' % (acc, tm))
self.printLog('\r#MULTI',
'Exiting multiHAQ "Chaser" run.')
return
## ~ [1d] Run HAQESAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
runhaqesac = True
pngfile = rje.makePath('%s%s.png' % (self.info['HaqDir'], acc),
wholepath=True)
if not self.force() and rje.exists(pngfile):
self.printLog(
'#SKIP',
'Found evidence of completed run: %s (force=F). Skipping.'
% pngfile)
runhaqesac = False
ancfile = rje.makePath('%s%s.anc.fas' %
(self.info['HaqDir'], acc),
wholepath=True)
if not self.force() and rje.exists(ancfile):
self.printLog(
'#SKIP',
'Found evidence of completed run: %s (force=F). Skipping.'
% ancfile)
runhaqesac = False
#if not finalrun or self.opt['Force'] or rje.isYounger(logfile,nsfile) != logfile:
if runhaqesac:
haqcmd = [
'ini=haqesac.ini',
'seqin=%s.fas' % acc,
'query=%s' % acc,
'basefile=%s' % acc, 'newlog=F'
]
self.printLog(
'#HAQ',
'Running HAQESAC for %s - will have own log etc.' %
seq.shortName(),
log=False)
os.chdir(self.info['HaqDir'])
info = haqesac.makeInfo()
haqcmd = rje.getCmdList(haqcmd, info=info)
out = rje.Out(
cmd_list=haqcmd
) # Sets up Out object for controlling output to screen
out.printIntro(
info
) # Prints intro text using details from Info object
haqlog = rje.setLog(
info, out, haqcmd
) # Sets up Log object for controlling log file output
try:
haqesac.HAQESAC(log=haqlog,
cmd_list=haqcmd).run(setobjects=True)
except:
os.chdir(self.info['RunPath'])
if self.i() >= 0 and rje.yesNo(
'Problem with %s HAQESAC run. Abort?' %
seq.shortName()):
raise KeyboardInterrupt
os.chdir(self.info['RunPath'])
if finalrun:
self.printLog(
'#HAQ',
'HAQESAC final round run for %s' % seq.shortName())
else:
self.printLog(
'#HAQ',
'HAQESAC first round run for %s' % seq.shortName())
## ~ [1e] Update ScreenQry ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if not self.opt['ScreenQry'] or not finalrun: continue
qacclist = []
for qacc in rje_seq.SeqList(
self.log,
['seqin=%s' % infile, 'autoload=T', 'autofilter=F'
]).accList():
if qacc in qryacc and qacc != acc: qacclist.append(qacc)
if qacc in qryacc and qacc not in processed:
processed.append(qacc)
self.printLog(
'#QRY', '%d other queries found in %s: [%s]' %
(len(qacclist), infile, string.join(qacclist, '; ')))
self.printLog(
'#QRY', '%d of %d queries processed' %
(len(processed), self.seqNum()))
### ~ [2] MultiHAQ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not finalrun:
self.printLog('#MULTI', 'Executing second round of multiHAQ')
self.multiHAQ(True)
except:
self.errorLog('Major problem with MultiHAQ.multiHAQ',
quitchoice=True)
def batchRun(self, returnobj=False): ### Execute batch mode runs
'''Execute batch mode runs.'''
try: ### ~ [0] Setup ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
barg = self.getStrLC('BatchArg')
if not barg:
raise ValueError(
'Cannot use batchrun=FILELIST if batcharg=None.')
batchfiles = self.list['BatchRun'][0:]
self.list['BatchRun'] = [] # Avoid recursive running!
blog = self.getStr('BatchLog')
if not blog.startswith('.'): blog = '.%s' % blog
if not blog.endswith('.log'): blog = '%s.log' % blog
rawcmd = self.cmd_list[0:]
rawlog = self.log
batchobj = []
### ~ [1] Batch Run ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
bx = 0
for bfile in batchfiles:
bx += 1
self.printLog(
'#BATCH', 'Batch running %s of %s: %s=%s' %
(rje.iStr(bx), rje.iLen(batchfiles), barg, bfile))
## Setup parameters
bbase = rje.baseFile(bfile, strip_path=True)
bcmd = ['%s=%s' % (barg, bfile)]
if self.getBool('BatchBase'):
if blog == '.log': bcmd += ['basefile=%s' % bbase]
else:
bcmd += ['basefile=%s%s' % (bbase, rje.baseFile(blog))]
elif self.getStrLC('BatchLog'):
bcmd += ['log=%s%s' % (bbase, blog)]
else:
bcmd += ['newlog=F']
#self.debug(bcmd)
## Setup Seqsuite object
self.cmd_list = rawcmd + bcmd
self.log = rje.setLog(
self.log.obj['Info'], self, self.cmd_list
) # Sets up Log object for controlling log file output
## Run
batchobj.append(self.run())
## Finish and Tidy
self.log = rawlog
runobj = batchobj[-1]
if runobj:
if not returnobj: batchobj[-1] = True
info = runobj.log.obj['Info']
self.printLog(
'#RUN',
'%s V%s run finished.' % (info.program, info.version))
else:
self.warnLog('Batch run failed (%s=%s).' % (barg, bfile))
### ~ [2] Finish and Return ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
failx = batchobj.count(False)
self.printLog(
'#BATCH', '%s batch runs complete: %s failed.' %
(rje.iLen(batchfiles), rje.iStr(failx)))
self.list['BatchRun'] = batchfiles
return batchobj
except:
self.errorLog('%s.batchRun error' % self)
return False
