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 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]
'''
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 KeyboardInterrupt:
sys.exit()
except:
print "Problem during initial setup."
raise
def setup(self): ### Main class setup method.
'''Main class setup method.'''
try:### ~ [1] ~ Setup Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['Prog'] = None
prog = self.getStrLC('Name')
if prog in mod:
i = self.obj['ProgInfo'] = mod[prog].makeInfo()
self.printLog('#PROG','%s V%s: %s' % (i.program,i.version,i.description))
progcmd = rje.getCmdList([],info=i) + self.cmd_list + ['newlog=F']
out = rje.Out(cmd_list=progcmd)
out.printIntro(i)
#self.debug(prog); self.debug(progcmd)
if self.getBool('Help'): progcmd = mod[prog].cmdHelp(i,out,['help']+progcmd)
self.printLog('#CMD','Full %s CmdList: %s' % (i.program,rje.argString(rje.tidyArgs(progcmd,nopath=self.getStrLC('Rest') and not self.dev(),purgelist=purgelist))),screen=False)
#self.debug(prog); self.debug(progcmd)
## ~ [1a] ~ Make self.obj['Prog'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prog in ['seqlist','rje_seqlist']: self.obj['Prog'] = rje_seqlist.SeqList(self.log,progcmd)
elif prog in ['uniprot','rje_uniprot']: self.obj['Prog'] = rje_uniprot.UniProt(self.log,progcmd)
elif prog in ['taxonomy','rje_taxonomy']: self.obj['Prog'] = rje_taxonomy.Taxonomy(self.log,progcmd)
elif prog in ['tree','rje_tree']: self.obj['Prog'] = rje_tree.Tree(self.log,progcmd)
elif prog in ['xref','rje_xref']: self.obj['Prog'] = rje_xref.XRef(self.log,progcmd)
elif prog in ['seq','rje_seq']: self.obj['Prog'] = rje_seq.SeqList(self.log,progcmd)
elif prog in ['mitab','rje_mitab']: self.obj['Prog'] = rje_mitab.MITAB(self.log,progcmd)
elif prog in ['dbase','database']: self.obj['Prog'] = rje_dbase.DatabaseController(self.log,progcmd)
elif prog in ['pydocs']: self.obj['Prog'] = rje_pydocs.PyDoc(self.log,progcmd)
elif prog in ['ensembl','rje_ensembl']: self.obj['Prog'] = rje_ensembl.EnsEMBL(self.log,progcmd)
elif prog in ['genbank','rje_genbank']: self.obj['Prog'] = rje_genbank.GenBank(self.log,progcmd)
elif prog in ['extatic']: self.obj['Prog'] = extatic.ExTATIC(self.log,progcmd)
elif prog in ['revert']: self.obj['Prog'] = revert.REVERT(self.log,progcmd)
elif prog in ['fiesta']: self.obj['Prog'] = fiesta.FIESTA(self.log,progcmd)
elif prog in ['gablam']: self.obj['Prog'] = gablam.GABLAM(self.log,progcmd)
elif prog in ['gopher']: self.obj['Prog'] = gopher.Gopher(self.log,progcmd)
elif prog in ['haqesac']: self.obj['Prog'] = haqesac.HAQESAC(self.log,progcmd)
elif prog in ['multihaq']: self.obj['Prog'] = multihaq.MultiHAQ(self.log,progcmd)
elif prog in ['pingu']: self.obj['Prog'] = pingu.PINGU(self.log,progcmd)
elif prog in ['pacbio']: self.obj['Prog'] = rje_pacbio.PacBio(self.log,progcmd)
elif prog in ['rje_zen','zen']: self.obj['Prog'] = rje_zen.Zen(self.log,progcmd)
### ~ [2] ~ Failure to recognise program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not self.obj['Prog']:
self.printLog('#ERR','Program "%s" not recognised.' % self.getStr('Name'))
if self.i() < 0: return False
if rje.yesNo('Show SeqSuite help with program options?'):
extracmd = cmdHelp(cmd_list=['help'])[1:]
if extracmd:
self.cmd_list += extracmd
self._cmdList()
if prog != self.getStrLC('Name'): return self.setup()
self.setStr({'Name':rje.choice('Give program name (Blank or CTRL+C to quit)')})
if self.getStrLC('Name'): return self.setup()
else: return False
return self.obj['Prog'] # Setup successful
except KeyboardInterrupt: return False
except SystemExit: raise
except: self.errorLog('Problem during %s setup.' % self.prog()); return False # Setup failed
def setup(self,rest=False): ### Main class setup method.
'''Main class setup method.'''
try:### ~ [1] ~ Setup Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['Prog'] = None
prog = self.getStrLC('Name')
if prog in mod:
i = self.obj['ProgInfo'] = mod[prog].makeInfo()
self.printLog('#PROG','%s V%s: %s' % (i.program,i.version,i.description))
progcmd = rje.getCmdList([],info=i) + self.cmd_list + ['newlog=F']
out = rje.Out(cmd_list=progcmd)
out.printIntro(i)
if self.getBool('Help'): progcmd = mod[prog].cmdHelp(i,out,['help']+progcmd)
purgelist = seqsuite.purgelist
self.printLog('#CMD','Full %s CmdList: %s' % (i.program,rje.argString(rje.tidyArgs(progcmd,nopath=self.getStrLC('Rest') and not self.dev(),purgelist=purgelist))),screen=False)
#self.debug(prog)
## ~ [1a] ~ Make self.obj['Prog'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prog in ['slimcore','rje_slimcore','core']: self.obj['Prog'] = rje_slimcore.SLiMCore(self.log,progcmd)
elif prog in ['rlc','iuscore']: self.obj['Prog'] = rje_slimcore.SLiMCore(self.log,progcmd+['prog=%s' % prog])
elif prog in ['slimlist','rje_slimlist']: self.obj['Prog'] = rje_slimlist.SLiMList(self.log,progcmd)
elif prog in ['slimfinder']: self.obj['Prog'] = slimfinder.SLiMFinder(self.log,progcmd)
elif prog in ['qslimfinder']: self.obj['Prog'] = qslimfinder.QSLiMFinder(self.log,progcmd)
elif prog in ['slimprob']: self.obj['Prog'] = slimprob.SLiMProb(self.log,progcmd)
elif prog in ['slimmaker']: self.obj['Prog'] = slimmaker.SLiMMaker(self.log,progcmd)
elif prog in ['slimfarmer','farm']: self.obj['Prog'] = slimfarmer.SLiMFarmer(self.log,progcmd)
elif prog in ['slimbench']: self.obj['Prog'] = slimbench.SLiMBench(self.log,progcmd)
elif prog in ['comparimotif']: self.obj['Prog'] = comparimotif.CompariMotif(self.log,progcmd)
elif prog in ['peptcluster']: self.obj['Prog'] = peptcluster.PeptCluster(self.log,progcmd)
elif prog in ['peptalign']: self.obj['Prog'] = peptcluster.PeptCluster(self.log,['peptalign=T']+progcmd+['peptdis=None'])
self.obj['Prog'].dict['Output']['help'] = mod[prog].__doc__
elif prog in seqsuite.mod:
seqsuiteobj = seqsuite.SeqSuite(self.log,self.cmd_list)
self.obj['Prog'] = seqsuiteobj.setup()
self.obj['ProgInfo'] = seqsuiteobj.obj['ProgInfo']
self.obj['Prog'].dict['Output']['help'] = seqsuite.mod[prog].__doc__
### ~ [2] ~ Failure to recognise program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not self.obj['Prog']:
if self.getStrLC('Name') != 'help':
if not rest: self.printLog('#ERR','Program "%s" not recognised.' % self.getStr('Name'))
if self.i() < 0 or rest: return False
#!# Try SeqSuite? #!#
if self.getStrLC('Name') == 'help' or rje.yesNo('Show SLiMSuite help with program options?'):
extracmd = cmdHelp(cmd_list=['help'])[1:]
if extracmd:
self.cmd_list += extracmd
self._cmdList()
if prog != self.getStrLC('Name'): return self.setup()
self.setStr({'Name':rje.choice('Give program name (Blank or CTRL+C to quit)')})
if self.getStrLC('Name'): return self.setup()
else: return False
return self.obj['Prog'] # Setup successful
except KeyboardInterrupt: return False
except SystemExit: raise
except: self.errorLog('Problem during %s setup.' % self.prog()); return False # Setup failed
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 setup(self): ### Main class setup method.
'''Main class setup method.'''
try: ### ~ [1] ~ Setup Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['Prog'] = None
prog = self.getStrLC('Name')
if prog in mod:
i = self.obj['ProgInfo'] = mod[prog].makeInfo()
self.printLog(
'#PROG',
'%s V%s: %s' % (i.program, i.version, i.description))
progcmd = rje.getCmdList(
[], info=i) + self.cmd_list + ['newlog=F']
out = rje.Out(cmd_list=progcmd)
out.printIntro(i)
if self.getBool('Help'):
progcmd = mod[prog].cmdHelp(i, out, ['help'] + progcmd)
purgelist = seqsuite.purgelist
self.printLog('#CMD',
'Full %s CmdList: %s' %
(i.program,
rje.argString(
rje.tidyArgs(progcmd,
nopath=self.getStrLC('Rest')
and not self.dev(),
purgelist=purgelist))),
screen=False)
#self.debug(prog)
## ~ [1a] ~ Make self.obj['Prog'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prog in ['slimcore', 'rje_slimcore']:
self.obj['Prog'] = rje_slimcore.SLiMCore(self.log, progcmd)
elif prog in ['rlc', 'disorder']:
self.obj['Prog'] = rje_slimcore.SLiMCore(
self.log, progcmd + ['prog=%s' % prog])
elif prog in ['slimlist', 'rje_slimlist']:
self.obj['Prog'] = rje_slimlist.SLiMList(self.log, progcmd)
elif prog in ['slimfinder']:
self.obj['Prog'] = slimfinder.SLiMFinder(self.log, progcmd)
elif prog in ['qslimfinder']:
self.obj['Prog'] = qslimfinder.QSLiMFinder(
self.log, progcmd)
elif prog in ['slimprob']:
self.obj['Prog'] = slimprob.SLiMProb(self.log, progcmd)
elif prog in ['slimmaker']:
self.obj['Prog'] = slimmaker.SLiMMaker(self.log, progcmd)
elif prog in ['slimfarmer', 'farm']:
self.obj['Prog'] = slimfarmer.SLiMFarmer(self.log, progcmd)
elif prog in ['slimbench']:
self.obj['Prog'] = slimbench.SLiMBench(self.log, progcmd)
elif prog in ['comparimotif']:
self.obj['Prog'] = comparimotif.CompariMotif(
self.log, progcmd)
elif prog in ['peptcluster']:
self.obj['Prog'] = peptcluster.PeptCluster(
self.log, progcmd)
elif prog in ['peptalign']:
self.obj['Prog'] = peptcluster.PeptCluster(
self.log, ['peptalign=T'] + progcmd)
self.obj['Prog'].dict['Output']['help'] = mod[prog].__doc__
elif prog in seqsuite.mod:
seqsuiteobj = seqsuite.SeqSuite(self.log, self.cmd_list)
self.obj['Prog'] = seqsuiteobj.setup()
self.obj['ProgInfo'] = seqsuiteobj.obj['ProgInfo']
self.obj['Prog'].dict['Output']['help'] = seqsuite.mod[
prog].__doc__
### ~ [2] ~ Failure to recognise program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not self.obj['Prog']:
self.printLog(
'#ERR',
'Program "%s" not recognised.' % self.getStr('Name'))
if self.i() < 0: return False
#!# Try SeqSuite? #!#
if rje.yesNo('Show SLiMSuite help with program options?'):
extracmd = cmdHelp(cmd_list=['help'])[1:]
if extracmd:
self.cmd_list += extracmd
self._cmdList()
if prog != self.getStrLC('Name'): return self.setup()
self.setStr({
'Name':
rje.choice('Give program name (Blank or CTRL+C to quit)')
})
if self.getStrLC('Name'): return self.setup()
else: return False
return self.obj['Prog'] # Setup successful
except KeyboardInterrupt:
return False
except SystemExit:
raise
except:
self.errorLog('Problem during %s setup.' % self.prog())
return False # Setup failed
def setup(self): ### Main class setup method.
'''Main class setup method.'''
try: ### ~ [1] ~ Setup Program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
self.obj['Prog'] = None
prog = self.getStrLC('Name')
if prog in mod:
i = self.obj['ProgInfo'] = mod[prog].makeInfo()
self.printLog(
'#PROG',
'%s V%s: %s' % (i.program, i.version, i.description))
progcmd = rje.getCmdList(
[], info=i) + self.cmd_list + ['newlog=F']
out = rje.Out(cmd_list=progcmd)
out.printIntro(i)
#self.debug(prog); self.debug(progcmd)
if self.getBool('Help'):
progcmd = mod[prog].cmdHelp(i, out, ['help'] + progcmd)
self.printLog('#CMD',
'Full %s CmdList: %s' %
(i.program,
rje.argString(
rje.tidyArgs(progcmd,
nopath=self.getStrLC('Rest')
and not self.dev(),
purgelist=purgelist))),
screen=False)
#self.debug(prog); self.debug(progcmd)
## ~ [1a] ~ Make self.obj['Prog'] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
if prog in ['seqlist', 'rje_seqlist']:
self.obj['Prog'] = rje_seqlist.SeqList(self.log, progcmd)
elif prog in ['uniprot', 'rje_uniprot']:
self.obj['Prog'] = rje_uniprot.UniProt(self.log, progcmd)
elif prog in ['taxonomy', 'rje_taxonomy']:
self.obj['Prog'] = rje_taxonomy.Taxonomy(self.log, progcmd)
elif prog in ['tree', 'rje_tree']:
self.obj['Prog'] = rje_tree.Tree(self.log, progcmd)
elif prog in ['xref', 'rje_xref']:
self.obj['Prog'] = rje_xref.XRef(self.log, progcmd)
elif prog in ['seq', 'rje_seq']:
self.obj['Prog'] = rje_seq.SeqList(self.log, progcmd)
elif prog in ['mitab', 'rje_mitab']:
self.obj['Prog'] = rje_mitab.MITAB(self.log, progcmd)
elif prog in ['dbase', 'database']:
self.obj['Prog'] = rje_dbase.DatabaseController(
self.log, progcmd)
elif prog in ['pydocs']:
self.obj['Prog'] = rje_pydocs.PyDoc(self.log, progcmd)
elif prog in ['ensembl', 'rje_ensembl']:
self.obj['Prog'] = rje_ensembl.EnsEMBL(self.log, progcmd)
elif prog in ['genbank', 'rje_genbank']:
self.obj['Prog'] = rje_genbank.GenBank(self.log, progcmd)
elif prog in ['extatic']:
self.obj['Prog'] = extatic.ExTATIC(self.log, progcmd)
elif prog in ['revert']:
self.obj['Prog'] = revert.REVERT(self.log, progcmd)
elif prog in ['fiesta']:
self.obj['Prog'] = fiesta.FIESTA(self.log, progcmd)
elif prog in ['gablam']:
self.obj['Prog'] = gablam.GABLAM(self.log, progcmd)
elif prog in ['gopher']:
self.obj['Prog'] = gopher.Gopher(self.log, progcmd)
elif prog in ['haqesac']:
self.obj['Prog'] = haqesac.HAQESAC(self.log, progcmd)
elif prog in ['multihaq']:
self.obj['Prog'] = multihaq.MultiHAQ(self.log, progcmd)
elif prog in ['pingu']:
self.obj['Prog'] = pingu.PINGU(self.log, progcmd)
elif prog in ['pacbio']:
self.obj['Prog'] = rje_pacbio.PacBio(self.log, progcmd)
elif prog in ['rje_zen', 'zen']:
self.obj['Prog'] = rje_zen.Zen(self.log, progcmd)
### ~ [2] ~ Failure to recognise program ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ###
if not self.obj['Prog']:
self.printLog(
'#ERR',
'Program "%s" not recognised.' % self.getStr('Name'))
if self.i() < 0: return False
if rje.yesNo('Show SeqSuite help with program options?'):
extracmd = cmdHelp(cmd_list=['help'])[1:]
if extracmd:
self.cmd_list += extracmd
self._cmdList()
if prog != self.getStrLC('Name'): return self.setup()
self.setStr({
'Name':
rje.choice('Give program name (Blank or CTRL+C to quit)')
})
if self.getStrLC('Name'): return self.setup()
else: return False
return self.obj['Prog'] # Setup successful
except KeyboardInterrupt:
return False
except SystemExit:
raise
except:
self.errorLog('Problem during %s setup.' % self.prog())
return False # Setup failed
