def main(argv=None):
try:
getArguments()
if Globals.urlGenome:
Common.say('Genome : %s' % Globals.urlGenome)
if Globals.urlCodonTable:
Common.say('Codon Table: %s' % Globals.urlCodonTable)
if Globals.pathOutput:
Common.say('Output File: %s' % Globals.pathOutput)
if Globals.urlGenome:
Globals.genome = Genome.Genome(Globals.urlGenome)
if Globals.urlCodonTable:
Globals.codonTable = Genome.CodonTable(Globals.urlCodonTable)
elif Globals.urlGenome and Globals.cmd <> Constants.cmdTranslate:
Globals.codonTable = Globals.genome.codonTable
if Globals.cmd == Constants.cmdCreate:
createTable()
elif Globals.cmd == Constants.cmdValidate:
validateTable()
elif Globals.cmd == Constants.cmdTranslate:
translateGenome()
return 0
except Usage, err:
Common.sayError(err)
return 0
def main(argv=None):
try:
getArguments()
if Globals.urlGenome:
Common.say('Genome : %s' % Globals.urlGenome)
if Globals.urlCodonTable:
Common.say('Codon Table: %s' % Globals.urlCodonTable)
if Globals.pathOutput:
Common.say('Output File: %s' % Globals.pathOutput)
if Globals.urlGenome:
Globals.genome = Genome.Genome(Globals.urlGenome)
if Globals.urlCodonTable:
Globals.codonTable = Genome.CodonTable(Globals.urlCodonTable)
elif Globals.urlGenome and Globals.cmd <> Constants.cmdTranslate:
Globals.codonTable = Globals.genome.codonTable
if Globals.cmd == Constants.cmdCreate:
createTable()
elif Globals.cmd == Constants.cmdValidate:
validateTable()
elif Globals.cmd == Constants.cmdTranslate:
translateGenome()
return 0
except Usage, err:
Common.sayError(err)
return 0
def main(argv=None):
try:
getArguments()
doBackup()
except Common.BiologicError, err:
Common.sayError(str(err))
return 2
def main(argv=None):
try:
getArguments()
doBackup()
except Common.BiologicError, err:
Common.sayError(str(err))
return 2
def validateCoherence(arySegments):
# Collapse all segments into a single list and measure coherence
aryVectors = [ i for f, ary in arySegments for i in ary ]
aryCoherence = [ 0 for i in xrange(len(aryVectors)) ]
for i in xrange(2, len(aryVectors)):
if Codons.isCoherent([ aryVectors[i-2], aryVectors[i-1], aryVectors[i-0] ]):
aryCoherence[i-2] += 1
aryCoherence[i-1] += 1
aryCoherence[i-0] += 1
# Divide measured coherence into lists matching the original segments
for i in xrange(len(arySegments)):
aryCoherence[i:i] = [ aryCoherence[i:i+len(arySegments[i][1]) ] ]
aryCoherence[i+1:i+1+len(arySegments[i][1])] = []
# Check the expected coherence of each segment against that measured
for i in xrange(len(arySegments)):
fCoherent, aryVectors = arySegments[i]
if (fCoherent and aryCoherence[i].count(0)) or (not fCoherent and (aryCoherence[i].count(0) != len(aryCoherence[i]))):
if i > 0:
fC, aryV = arySegments[i-1]
Common.sayError('Coherent(%c) %d - %s' % (fC and 'T' or 'F', len(aryV), ' '.join([ Codons.Vectors.toName(id) for id in aryV ])))
Common.sayError('Coherent(%c) %d - %s' % (fCoherent and 'T' or 'F', len(aryVectors), ' '.join([ Codons.Vectors.toName(id) for id in aryVectors ])))
Common.sayError(' - %s' % ' '.join([ ' %d ' % j for j in aryCoherence[i] ]))
if i < len(arySegments)-1:
fC, aryV = arySegments[i+1]
Common.sayError('Coherent(%c) %d - %s' % (fC and 'T' or 'F', len(aryV), ' '.join([ Codons.Vectors.toName(id) for id in aryV ])))
raise Common.BiologicError('Failed to create a gene with proper coherence - segment %d should be %s but has %s vectors' % (i+1,
fCoherent and 'Coherent' or 'Incoherent',
fCoherent and 'Incoherent' or 'Coherent'))
def main(argv=None):
try:
getArguments()
if Globals.aryXgridJob:
queryXgrid()
if Globals.fRunExec:
os.environ['STYLUS_EXECARGS'] = Common.readEnvironment('$STYLUS_EXECARGS') + ' ' + ' '.join(Globals.aryArgs)
spawnStylus(_SCRIPT_EXEC, os.environ)
if Globals.fRunReport:
os.environ['STYLUS_RPTARGS'] = Common.readEnvironment('$STYLUS_RPTARGS') + ' ' + ' '.join(Globals.aryArgs)
spawnStylus(_SCRIPT_REPORT, os.environ)
except Common.BiologicError, err:
Common.sayError(str(err))
return 2
def main(argv=None):
try:
getArguments()
if Globals.aryXgridJob:
queryXgrid()
if Globals.fRunExec:
os.environ['STYLUS_EXECARGS'] = Common.readEnvironment(
'$STYLUS_EXECARGS') + ' ' + ' '.join(Globals.aryArgs)
spawnStylus(_SCRIPT_EXEC, os.environ)
if Globals.fRunReport:
os.environ['STYLUS_RPTARGS'] = Common.readEnvironment(
'$STYLUS_RPTARGS') + ' ' + ' '.join(Globals.aryArgs)
spawnStylus(_SCRIPT_REPORT, os.environ)
except Common.BiologicError, err:
Common.sayError(str(err))
return 2
def main(argv=None):
try:
Globals.fInteractive = True
Common.Globals.fQuiet = False
setGlobals(sys.argv[1:])
if Globals.fBuildArchetype:
Common.say('Archetypes Directory: %s' % Globals.strArchetypePath)
if len(Globals.aryGenes) > 0:
Common.say('Gene Directory : %s' % Globals.strGenePath)
Common.say('Han URL : %s' % Globals.urlHan)
if Globals.fBuildArchetype:
buildHan(Globals.uchHan)
if Globals.aryGenes:
buildGenes(Globals.uchHan, Globals.aryGenes)
return 0
except Common.BiologicError, err:
Common.sayError(err.msg)
return 2
def main(argv=None):
try:
nCompletionCode = 0
getArguments()
Common.say('Data Directory: %s' % Globals.names.pathData)
if Globals.urlGlobals:
Common.say('Globals URL : %s' % Globals.urlGlobals)
Common.say('Genome URL : %s' % Globals.names.urlGenome)
Common.say('Plan URL : %s' % Globals.names.urlPlan)
Common.say('Han URL : %s' % Globals.urls.urlHan)
Common.say('Schema URL : %s' % Globals.urls.urlSchema)
if Globals.aryLog[2] or Globals.aryLog[3] == 'silent':
os.close(_FD_STDERR)
if Globals.aryLog[3] != 'silent':
Common.redirectStderr(Globals.aryLog[2])
if Globals.fVersion:
Common.say('Version : %s' % Stylus.getVersion())
strGenome = Common.readFile(Globals.names.urlGenome)
strPlan = Common.readFile(Globals.names.urlPlan)
strGlobals = Globals.urlGlobals and Common.readFile(
Globals.urlGlobals) or ''
if Globals.aryTrace:
Stylus.setLogLevel(Globals.aryLog[0], 'trace',
Globals.aryLog[3] == 'echo', Globals.aryLog[4])
rc = Stylus.setTrace(Globals.aryTrace[0], Globals.aryTrace[1],
Globals.aryTrace[2], Globals.aryTrace[3],
Globals.aryTrace[4])
if rc:
raise StylusError(rc)
if Globals.aryLog and not Globals.aryTrace:
rc = Stylus.setLogLevel(Globals.aryLog[0], Globals.aryLog[1],
Globals.aryLog[3] == 'echo',
Globals.aryLog[4])
if rc:
raise StylusError(rc)
rc = Stylus.setScope(Globals.urls.urlHan, Globals.urls.urlSchema)
if rc:
raise StylusError(rc)
rc = Stylus.setRecordRate(Globals.aryRecord[0], Globals.aryRecord[1],
Globals.names.pathData, Globals.aryRecord[2])
if rc:
raise StylusError(rc)
if strGlobals:
rc = Stylus.setGlobals(strGlobals)
if rc:
raise StylusError(rc)
rc = Stylus.setGenome(strGenome, Globals.strAuthor)
if rc:
raise StylusError(rc)
tStart = time.clock()
rc = Stylus.executePlan(strPlan, Globals.names.nFirstPlanTrial,
Globals.names.cPlanTrialsToExecute)
tEnd = time.clock()
if Globals.aryStatistics and Globals.aryStatistics[1]:
statistics = Stylus.getStatistics()
Common.say(
'Plan executed %d trials in %f seconds' %
((statistics._iTrialCurrent - statistics._iTrialInitial),
(tEnd - tStart)))
if rc != Stylus.ST_RCSUCCESS:
if not Stylus.errorIsType(rc, Stylus.ST_INFOTYPE):
raise StylusError(rc)
else:
Common.say('Plan terminated - %s' % stylusError(rc))
nCompletionCode = 1
if Globals.aryStatistics and len(
Globals.aryStatistics
) >= 1 and Globals.aryStatistics[0] != "none":
statistics = Stylus.getStatistics()
Common.say(
'Statistics for %d trials (%d to %d)' %
((statistics._iTrialCurrent - statistics._iTrialInitial),
statistics._iTrialInitial, statistics._iTrialCurrent))
if Globals.aryStatistics[0] == "summary":
Common.say(
' Fitness: %0.15f - rollbacks(%d) silent(%d) changes(%d) inserted(%d) deleted(%d)'
%
(statistics._nFitness, statistics._cTotalRollbacks,
statistics._cSilent, statistics._cbBasesChanged,
statistics._cbBasesInserted, statistics._cbBasesDeleted))
else:
Common.say(
' Fitness: current(%0.15f) max(%0.15f in trial %d) min(%0.15f in trial %d)'
% (statistics._nFitness, statistics._tfMax._nValue,
statistics._tfMax._iTrial, statistics._tfMin._nValue,
statistics._tfMin._iTrial))
Common.say(
' Score: current(%0.15f) max(%0.15f in trial %d) min(%0.15f in trial %d)'
% (statistics._nScore, statistics._tsMax._nValue,
statistics._tsMax._iTrial, statistics._tsMin._nValue,
statistics._tsMin._iTrial))
Common.say(
' Size: current(%d) max(%d in trial %d) min(%d in trial %d)'
% (statistics._cbBases, statistics._tzMax._cbBases,
statistics._tzMax._iTrial, statistics._tzMin._cbBases,
statistics._tzMin._iTrial))
Common.say(
' Rollbacks: total(%d) current(%d) max(%d in trial %d) min(%d in trial %d)'
%
(statistics._cTotalRollbacks, statistics._cRollbacks,
statistics._trMax._cRollbacks, statistics._trMax._iTrial,
statistics._trMin._cRollbacks, statistics._trMin._iTrial))
Common.say(
' Mutations: silent(%d) attempts(%d) accepted(%d) changed(%d) inserted(%d) deleted(%d)'
%
(statistics._cSilent, statistics._cAttempted,
statistics._cAccepted, statistics._cbBasesChanged,
statistics._cbBasesInserted, statistics._cbBasesDeleted))
if statistics._atChanged._cAttempted:
Common.say(
' Changed: attempted(%d) accepted(%d) bases-affected(%d)'
% (statistics._atChanged._cAttempted,
statistics._atChanged._cAccepted,
statistics._atChanged._cbBases))
if statistics._atCopied._cAttempted:
Common.say(
' Copied: attempted(%d) accepted(%d) bases-affected(%d)'
% (statistics._atCopied._cAttempted,
statistics._atCopied._cAccepted,
statistics._atCopied._cbBases))
if statistics._atDeleted._cAttempted:
Common.say(
' Deleted: attempted(%d) accepted(%d) bases-affected(%d)'
% (statistics._atDeleted._cAttempted,
statistics._atDeleted._cAccepted,
statistics._atDeleted._cbBases))
if statistics._atInserted._cAttempted:
Common.say(
' Inserted: attempted(%d) accepted(%d) bases-affected(%d)'
% (statistics._atInserted._cAttempted,
statistics._atInserted._cAccepted,
statistics._atInserted._cbBases))
if statistics._atTransposed._cAttempted:
Common.say(
' Transposed: attempted(%d) accepted(%d) bases-affected(%d)'
% (statistics._atTransposed._cAttempted,
statistics._atTransposed._cAccepted,
statistics._atTransposed._cbBases))
return nCompletionCode
except Usage, err:
Common.sayError(err)
return 0
' Deleted: attempted(%d) accepted(%d) bases-affected(%d)'
% (statistics._atDeleted._cAttempted,
statistics._atDeleted._cAccepted,
statistics._atDeleted._cbBases))
if statistics._atInserted._cAttempted:
Common.say(
' Inserted: attempted(%d) accepted(%d) bases-affected(%d)'
% (statistics._atInserted._cAttempted,
statistics._atInserted._cAccepted,
statistics._atInserted._cbBases))
if statistics._atTransposed._cAttempted:
Common.say(
' Transposed: attempted(%d) accepted(%d) bases-affected(%d)'
% (statistics._atTransposed._cAttempted,
statistics._atTransposed._cAccepted,
statistics._atTransposed._cbBases))
return nCompletionCode
except Usage, err:
Common.sayError(err)
return 0
except Common.BiologicError, err:
Common.sayError(str(err))
return 2
if __name__ == "__main__":
sys.exit(main())
def main(argv=None):
try:
nCompletionCode = 0
getArguments()
Common.say('Data Directory: %s' % Globals.names.pathData)
if Globals.urlGlobals:
Common.say('Globals URL : %s' % Globals.urlGlobals)
Common.say('Genome URL : %s' % Globals.names.urlGenome)
Common.say('Plan URL : %s' % Globals.names.urlPlan)
Common.say('Han URL : %s' % Globals.urls.urlHan)
Common.say('Schema URL : %s' % Globals.urls.urlSchema)
if Globals.aryLog[2] or Globals.aryLog[3] == 'silent':
os.close(_FD_STDERR)
if Globals.aryLog[3] != 'silent':
Common.redirectStderr(Globals.aryLog[2])
if Globals.fVersion:
Common.say('Version : %s' % Stylus.getVersion())
strGenome = Common.readFile(Globals.names.urlGenome)
strPlan = Common.readFile(Globals.names.urlPlan)
strGlobals = Globals.urlGlobals and Common.readFile(Globals.urlGlobals) or ''
if Globals.aryTrace:
Stylus.setLogLevel(Globals.aryLog[0], 'trace', Globals.aryLog[3] == 'echo', Globals.aryLog[4])
rc = Stylus.setTrace(Globals.aryTrace[0], Globals.aryTrace[1], Globals.aryTrace[2], Globals.aryTrace[3], Globals.aryTrace[4])
if rc:
raise StylusError(rc)
if Globals.aryLog and not Globals.aryTrace:
rc = Stylus.setLogLevel(Globals.aryLog[0], Globals.aryLog[1], Globals.aryLog[3] == 'echo', Globals.aryLog[4])
if rc:
raise StylusError(rc)
rc = Stylus.setScope(Globals.urls.urlHan, Globals.urls.urlSchema)
if rc:
raise StylusError(rc)
rc = Stylus.setRecordRate(Globals.aryRecord[0], Globals.aryRecord[1], Globals.names.pathData, Globals.aryRecord[2])
if rc:
raise StylusError(rc)
if strGlobals:
rc = Stylus.setGlobals(strGlobals)
if rc:
raise StylusError(rc)
rc = Stylus.setGenome(strGenome, Globals.strAuthor)
if rc:
raise StylusError(rc)
tStart = time.clock()
rc = Stylus.executePlan(strPlan, Globals.names.nFirstPlanTrial, Globals.names.cPlanTrialsToExecute)
tEnd = time.clock()
if Globals.aryStatistics and Globals.aryStatistics[1]:
statistics = Stylus.getStatistics()
Common.say('Plan executed %d trials in %f seconds' % ((statistics._iTrialCurrent-statistics._iTrialInitial), (tEnd - tStart)))
if rc != Stylus.ST_RCSUCCESS:
if not Stylus.errorIsType(rc, Stylus.ST_INFOTYPE):
raise StylusError(rc)
else:
Common.say('Plan terminated - %s' % stylusError(rc))
nCompletionCode = 1
if Globals.aryStatistics and len(Globals.aryStatistics) >= 1 and Globals.aryStatistics[0] != "none":
statistics = Stylus.getStatistics()
Common.say('Statistics for %d trials (%d to %d)' % ((statistics._iTrialCurrent-statistics._iTrialInitial), statistics._iTrialInitial, statistics._iTrialCurrent))
if Globals.aryStatistics[0] == "summary":
Common.say(' Fitness: %0.15f - rollbacks(%d) silent(%d) changes(%d) inserted(%d) deleted(%d)' %
(statistics._nFitness, statistics._cTotalRollbacks, statistics._cSilent, statistics._cbBasesChanged, statistics._cbBasesInserted, statistics._cbBasesDeleted))
else:
Common.say(' Fitness: current(%0.15f) max(%0.15f in trial %d) min(%0.15f in trial %d)' %
(statistics._nFitness, statistics._tfMax._nValue, statistics._tfMax._iTrial, statistics._tfMin._nValue, statistics._tfMin._iTrial))
Common.say(' Score: current(%0.15f) max(%0.15f in trial %d) min(%0.15f in trial %d)' %
(statistics._nScore, statistics._tsMax._nValue, statistics._tsMax._iTrial, statistics._tsMin._nValue, statistics._tsMin._iTrial))
Common.say(' Size: current(%d) max(%d in trial %d) min(%d in trial %d)' %
(statistics._cbBases, statistics._tzMax._cbBases, statistics._tzMax._iTrial, statistics._tzMin._cbBases, statistics._tzMin._iTrial))
Common.say(' Rollbacks: total(%d) current(%d) max(%d in trial %d) min(%d in trial %d)' %
(statistics._cTotalRollbacks, statistics._cRollbacks, statistics._trMax._cRollbacks, statistics._trMax._iTrial, statistics._trMin._cRollbacks, statistics._trMin._iTrial))
Common.say(' Mutations: silent(%d) attempts(%d) accepted(%d) changed(%d) inserted(%d) deleted(%d)' %
(statistics._cSilent, statistics._cAttempted, statistics._cAccepted, statistics._cbBasesChanged, statistics._cbBasesInserted, statistics._cbBasesDeleted))
if statistics._atChanged._cAttempted:
Common.say(' Changed: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atChanged._cAttempted, statistics._atChanged._cAccepted, statistics._atChanged._cbBases))
if statistics._atCopied._cAttempted:
Common.say(' Copied: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atCopied._cAttempted, statistics._atCopied._cAccepted, statistics._atCopied._cbBases))
if statistics._atDeleted._cAttempted:
Common.say(' Deleted: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atDeleted._cAttempted, statistics._atDeleted._cAccepted, statistics._atDeleted._cbBases))
if statistics._atInserted._cAttempted:
Common.say(' Inserted: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atInserted._cAttempted, statistics._atInserted._cAccepted, statistics._atInserted._cbBases))
if statistics._atTransposed._cAttempted:
Common.say(' Transposed: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atTransposed._cAttempted, statistics._atTransposed._cAccepted, statistics._atTransposed._cbBases))
return nCompletionCode
except Usage, err:
Common.sayError(err)
return 0
Common.say(' Mutations: silent(%d) attempts(%d) accepted(%d) changed(%d) inserted(%d) deleted(%d)' %
(statistics._cSilent, statistics._cAttempted, statistics._cAccepted, statistics._cbBasesChanged, statistics._cbBasesInserted, statistics._cbBasesDeleted))
if statistics._atChanged._cAttempted:
Common.say(' Changed: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atChanged._cAttempted, statistics._atChanged._cAccepted, statistics._atChanged._cbBases))
if statistics._atCopied._cAttempted:
Common.say(' Copied: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atCopied._cAttempted, statistics._atCopied._cAccepted, statistics._atCopied._cbBases))
if statistics._atDeleted._cAttempted:
Common.say(' Deleted: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atDeleted._cAttempted, statistics._atDeleted._cAccepted, statistics._atDeleted._cbBases))
if statistics._atInserted._cAttempted:
Common.say(' Inserted: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atInserted._cAttempted, statistics._atInserted._cAccepted, statistics._atInserted._cbBases))
if statistics._atTransposed._cAttempted:
Common.say(' Transposed: attempted(%d) accepted(%d) bases-affected(%d)' %
(statistics._atTransposed._cAttempted, statistics._atTransposed._cAccepted, statistics._atTransposed._cbBases))
return nCompletionCode
except Usage, err:
Common.sayError(err)
return 0
except Common.BiologicError, err:
Common.sayError(str(err))
return 2
if __name__ == "__main__":
sys.exit(main())
if Globals.urlGenome:
Globals.genome = Genome.Genome(Globals.urlGenome)
if Globals.urlCodonTable:
Globals.codonTable = Genome.CodonTable(Globals.urlCodonTable)
elif Globals.urlGenome and Globals.cmd <> Constants.cmdTranslate:
Globals.codonTable = Globals.genome.codonTable
if Globals.cmd == Constants.cmdCreate:
createTable()
elif Globals.cmd == Constants.cmdValidate:
validateTable()
elif Globals.cmd == Constants.cmdTranslate:
translateGenome()
return 0
except Usage, err:
Common.sayError(err)
return 0
except Common.BiologicError, err:
Common.sayError(err)
return 2
if __name__ == "__main__":
sys.exit(main())
if Globals.urlGenome:
Globals.genome = Genome.Genome(Globals.urlGenome)
if Globals.urlCodonTable:
Globals.codonTable = Genome.CodonTable(Globals.urlCodonTable)
elif Globals.urlGenome and Globals.cmd <> Constants.cmdTranslate:
Globals.codonTable = Globals.genome.codonTable
if Globals.cmd == Constants.cmdCreate:
createTable()
elif Globals.cmd == Constants.cmdValidate:
validateTable()
elif Globals.cmd == Constants.cmdTranslate:
translateGenome()
return 0
except Usage, err:
Common.sayError(err)
return 0
except Common.BiologicError, err:
Common.sayError(err)
return 2
if __name__ == "__main__":
sys.exit(main())
