def buildHan(uchHan):
Common.say('Creating Han Definition file for ' + uchHan)
hcf = Genome.HCF(Common.pathToURL(Common.makeHanPath(uchHan + Common.Constants.extHCF), Globals.urlHan))
aryGroups = [ _HAN_GROUP % (str(hcfG.bounds), hcfG.length, hcfG.ptCenter.x, hcfG.ptCenter.y,
' '.join([ str(i+1) for i in hcfG.containedStrokes])) for hcfG in hcf.aryGroups ]
aryStrokes = [ _HAN_STROKE % (str(hcfS.bounds),
hcfS.length,
'\n'.join([ _HAN_POINT % (ptd.x, ptd.y, ptd.distance) for ptd in hcfS.aryPointsForward]),
'\n'.join([ _HAN_POINT % (ptd.x, ptd.y, ptd.distance) for ptd in hcfS.aryPointsReverse]) ) for hcfS in hcf.aryStrokes ]
aryOverlaps = [ _HAN_OVERLAP % (hcfO.firstStroke, hcfO.secondStroke, hcfO.fRequired and 'true' or 'false') for hcfO in hcf.aryOverlaps ]
strHan = _HAN_DEFINITION % (str(uuid.uuid4()).upper(), hcf.unicode, datetime.datetime.utcnow().isoformat(), _NAME,
str(hcf.bounds), hcf.length, hcf.minimumStrokeLength,
'\n'.join(aryGroups),
'\n'.join(aryStrokes),
aryOverlaps and ('<overlaps>%s</overlaps>' % '\n'.join(aryOverlaps)) or '')
strPath = Common.resolvePath(os.path.join(Globals.strArchetypePath, Common.makeHanPath(hcf.unicode + Common.Constants.extHan)))
strDir = os.path.dirname(strPath)
if not os.path.exists(strDir):
try: os.makedirs(os.path.dirname(strPath))
except OSError, err: raise Common.BiologicError('Unable to create %s - %s' % (strDir, str(err)))
try:
fileHan = os.open(strPath, os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileHan, strHan)
except IOError, err: raise Common.BiologicError('Unable to create %s - %s' % (strPath, str(err)))
os.close(fileHan)
Common.say('Han definition written to ' + strPath)
return
def createTable():
aryEntries = [
_CODONTABLE_ENTRY %
(codon, vector,
(_CODONTABLE_ISSTANDARD %
(Globals.codonTable.hasStandardMapping(codon) and 'true'
or 'false'))) for codon, vector in Globals.codonTable.entries()
]
strCodonTable = _CODONTABLE_DEFINITION % (
Globals.uuid, Globals.strAuthor and
(" author='%s'" % Globals.strAuthor) or '',
datetime.datetime.utcnow().isoformat(), _NAME, '\n'.join(aryEntries))
if Globals.pathOutput:
try:
fileCodonTable = os.open(Globals.pathOutput,
os.O_CREAT | os.O_TRUNC | os.O_WRONLY,
0664)
os.write(fileCodonTable, strCodonTable)
except IOError, err:
raise Common.BiologicError('Unable to create %s - %s' %
(Globals.pathOutput, str(err)))
os.close(fileCodonTable)
Common.say('Codon table written to ' + Globals.pathOutput)
def spawnStylus(fScript, dictEnv):
if (Globals.strGenomes or Globals.strPlans) and Globals.fLaunchJobs:
iJob = 0
strExecArgs = 'STYLUS_EXECARGS' in dictEnv and dictEnv[
'STYLUS_EXECARGS'] or ''
strReportArgs = 'STYLUS_RPTARGS' in dictEnv and dictEnv[
'STYLUS_RPTARGS'] or ''
aryGenomes = Globals.strGenomes and fnmatch.filter(
os.listdir(Globals.strGenomes),
Common.Constants.globNotHidden) or []
aryPlans = Globals.strPlans and fnmatch.filter(
os.listdir(Globals.strPlans),
Common.Constants.globNotHidden) or []
if aryGenomes and not aryPlans:
for fileGenome in aryGenomes:
dictEnv['STYLUS_EXECARGS'] = '%s -g %s' % (
strExecArgs, os.path.join(Globals.strGenomes, fileGenome))
dictEnv['STYLUS_RPTARGS'] = '%s -g %s' % (
strReportArgs, os.path.join(Globals.strGenomes,
fileGenome))
spawnSingle(fScript, iJob, dictEnv)
iJob += 1
elif not aryGenomes and aryPlans:
for filePlan in aryPlans:
dictEnv['STYLUS_EXECARGS'] = '%s -n ,,plan -p %s' % (
strExecArgs, os.path.join(Globals.strPlans, filePlan))
dictEnv['STYLUS_RPTARGS'] = '%s -n ,,plan -p %s' % (
strReportArgs, os.path.join(Globals.strPlans, filePlan))
spawnSingle(fScript, iJob, dictEnv)
iJob += 1
else:
for fileGenome in aryGenomes:
for filePlan in aryPlans:
dictEnv['STYLUS_EXECARGS'] = '%s -n ,,plan -g %s -p %s' % (
strExecArgs,
os.path.join(Globals.strGenomes, fileGenome),
os.path.join(Globals.strPlans, filePlan))
dictEnv['STYLUS_RPTARGS'] = '%s -n ,,plan -g %s -p %s' % (
strReportArgs,
os.path.join(Globals.strGenomes, fileGenome),
os.path.join(Globals.strPlans, filePlan))
spawnSingle(fScript, iJob, dictEnv)
iJob += 1
if not Globals.fUseXgrid:
Common.say('\tLaunched %d instances' % iJob)
else:
spawnSingle(fScript, 0, dictEnv)
def createTable():
aryEntries = [ _CODONTABLE_ENTRY % (codon, vector, (_CODONTABLE_ISSTANDARD % (Globals.codonTable.hasStandardMapping(codon) and 'true' or 'false'))) for codon, vector in Globals.codonTable.entries() ]
strCodonTable = _CODONTABLE_DEFINITION % (Globals.uuid, Globals.strAuthor and (" author='%s'" % Globals.strAuthor) or '', datetime.datetime.utcnow().isoformat(), _NAME, '\n'.join(aryEntries))
if Globals.pathOutput:
try:
fileCodonTable = os.open(Globals.pathOutput, os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileCodonTable, strCodonTable)
except IOError, err: raise Common.BiologicError('Unable to create %s - %s' % (Globals.pathOutput, str(err)))
os.close(fileCodonTable)
Common.say('Codon table written to ' + Globals.pathOutput)
else:
Common.say(strCodonTable, False, True)
return
def translateGenome():
genome = Globals.genome
oldCodonTable = genome.codonTable
newCodonTable = Globals.codonTable
bases = Codons.Constants.startCodon
for i in xrange(3, len(genome.bases), 3):
bases += newCodonTable.vectorToCodon(
oldCodonTable.codonToVector(genome.bases[i:i + 3]))
genome.bases = bases
aryEntries = [
_CODONTABLE_ENTRY %
(codon, vector,
(_CODONTABLE_ISSTANDARD %
(Globals.codonTable.hasStandardMapping(codon) and 'true'
or 'false'))) for codon, vector in Globals.codonTable.entries()
]
aryStrokes = [
_GENE_STROKE % (stroke.rgBases.baseFirst, stroke.rgBases.baseLast,
stroke.correspondsTo)
for stroke in genome.gene.aryStrokes
]
strGenome = _GENE_DEFINITION % (
Globals.uuid, Globals.strAuthor and
(" author='%s'" % Globals.strAuthor) or '',
datetime.datetime.utcnow().isoformat(), _NAME, newCodonTable.uuid,
newCodonTable.author and (" author='%s'" % newCodonTable.author)
or '', newCodonTable.creationDate, newCodonTable.creationTool,
'\n'.join(aryEntries), genome.bases, len(
genome.bases), genome.gene.xOrigin, genome.gene.yOrigin,
genome.gene.unicode, '\n'.join(aryStrokes))
if Globals.pathOutput:
try:
fileGenome = os.open(Globals.pathOutput,
os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileGenome, strGenome)
except IOError, err:
raise Common.BiologicError('Unable to create %s - %s' %
(Globals.pathOutput, str(err)))
os.close(fileGenome)
Common.say('Genome written to ' + Globals.pathOutput)
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 translateGenome():
genome = Globals.genome
oldCodonTable = genome.codonTable
newCodonTable = Globals.codonTable
bases = Codons.Constants.startCodon
for i in xrange(3,len(genome.bases),3):
bases += newCodonTable.vectorToCodon(oldCodonTable.codonToVector(genome.bases[i:i+3]))
genome.bases = bases
aryEntries = [ _CODONTABLE_ENTRY % (codon, vector, (_CODONTABLE_ISSTANDARD % (Globals.codonTable.hasStandardMapping(codon) and 'true' or 'false'))) for codon, vector in Globals.codonTable.entries() ]
aryStrokes = [ _GENE_STROKE % (stroke.rgBases.baseFirst, stroke.rgBases.baseLast, stroke.correspondsTo) for stroke in genome.gene.aryStrokes ]
strGenome = _GENE_DEFINITION % (Globals.uuid, Globals.strAuthor and (" author='%s'" % Globals.strAuthor) or '', datetime.datetime.utcnow().isoformat(), _NAME,
newCodonTable.uuid,
newCodonTable.author and (" author='%s'" % newCodonTable.author) or '',
newCodonTable.creationDate,
newCodonTable.creationTool,
'\n'.join(aryEntries),
genome.bases,
len(genome.bases),
genome.gene.xOrigin, genome.gene.yOrigin,
genome.gene.unicode,
'\n'.join(aryStrokes))
if Globals.pathOutput:
try:
fileGenome = os.open(Globals.pathOutput, os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileGenome, strGenome)
except IOError, err: raise Common.BiologicError('Unable to create %s - %s' % (Globals.pathOutput, str(err)))
os.close(fileGenome)
Common.say('Genome written to ' + Globals.pathOutput)
else:
Common.say(strGenome, False, True)
return
def spawnStylus(fScript, dictEnv):
if (Globals.strGenomes or Globals.strPlans) and Globals.fLaunchJobs:
iJob = 0
strExecArgs = 'STYLUS_EXECARGS' in dictEnv and dictEnv['STYLUS_EXECARGS'] or ''
strReportArgs = 'STYLUS_RPTARGS' in dictEnv and dictEnv['STYLUS_RPTARGS'] or ''
aryGenomes = Globals.strGenomes and fnmatch.filter(os.listdir(Globals.strGenomes), Common.Constants.globNotHidden) or []
aryPlans = Globals.strPlans and fnmatch.filter(os.listdir(Globals.strPlans), Common.Constants.globNotHidden) or []
if aryGenomes and not aryPlans:
for fileGenome in aryGenomes:
dictEnv['STYLUS_EXECARGS'] = '%s -g %s' % (strExecArgs, os.path.join(Globals.strGenomes, fileGenome))
dictEnv['STYLUS_RPTARGS'] = '%s -g %s' % (strReportArgs, os.path.join(Globals.strGenomes, fileGenome))
spawnSingle(fScript, iJob, dictEnv)
iJob += 1
elif not aryGenomes and aryPlans:
for filePlan in aryPlans:
dictEnv['STYLUS_EXECARGS'] = '%s -n ,,plan -p %s' % (strExecArgs, os.path.join(Globals.strPlans, filePlan))
dictEnv['STYLUS_RPTARGS'] = '%s -n ,,plan -p %s' % (strReportArgs, os.path.join(Globals.strPlans, filePlan))
spawnSingle(fScript, iJob, dictEnv)
iJob += 1
else:
for fileGenome in aryGenomes:
for filePlan in aryPlans:
dictEnv['STYLUS_EXECARGS'] = '%s -n ,,plan -g %s -p %s' % (strExecArgs, os.path.join(Globals.strGenomes, fileGenome), os.path.join(Globals.strPlans, filePlan))
dictEnv['STYLUS_RPTARGS'] = '%s -n ,,plan -g %s -p %s' % (strReportArgs, os.path.join(Globals.strGenomes, fileGenome), os.path.join(Globals.strPlans, filePlan))
spawnSingle(fScript, iJob, dictEnv)
iJob += 1
if not Globals.fUseXgrid:
Common.say('\tLaunched %d instances' % iJob)
else:
spawnSingle(fScript, 0, dictEnv)
def doBackup():
Common.say('Archving folders [ %s ] in %s' %
(', '.join(Globals.aryFolders), Globals.pathSrc))
dtNow = datetime.datetime.now()
dtWeekAgo = dtNow - datetime.timedelta(days=Globals.nRemoveAge)
# Purge archives and archive directories older than one week
for item in glob.glob(os.path.join(Globals.pathDst,
Constants.strArchives)):
stat = os.stat(item)
if datetime.datetime.fromtimestamp(stat.st_mtime) < dtWeekAgo:
if os.path.isdir(item):
cc = os.system('rm -drf %s' % item)
if cc:
raise Common.BiologicError(
'Unable to remove old directory %s' % item)
else:
os.remove(item)
# Create a new archive directory
strArchive = 'Stylus_%s' % dtNow.isoformat().translate(
Constants.strTranslate)
pathArchive = os.path.abspath(os.path.join(Globals.pathDst, strArchive))
os.makedirs(pathArchive)
# Populate the archive directory
for folder in Globals.aryFolders:
pathSrc = os.path.abspath(os.path.join(Globals.pathSrc, folder))
pathDst = os.path.abspath(os.path.join(pathArchive, folder))
cc = os.system('ditto %s %s' % (pathSrc, pathDst))
if cc:
raise Common.BiologicError(
'Unable to copy folder %s to archive directory %s - error code(%d)'
% (folder, pathArchive, cc))
Common.say('...copied %s' % folder)
# Create the archive
fileArchive = os.path.abspath(
os.path.join(Globals.pathDst, strArchive + Constants.extArchive))
cc = os.system('ditto -c -z %s %s' % (pathArchive, fileArchive))
if cc:
raise Common.BiologicError(
'Unable to create archive %s - error code(%d)' % (fileArchive, cc))
Common.say('...created archive %s' % pathArchive)
# Remove the archive directory
cc = os.system('rm -drf %s' % pathArchive)
if cc:
raise Common.BiologicError('Unable to temporary archive directory %s' %
fileArchive)
def doBackup():
Common.say('Archving folders [ %s ] in %s' % (', '.join(Globals.aryFolders), Globals.pathSrc))
dtNow = datetime.datetime.now()
dtWeekAgo = dtNow - datetime.timedelta(days=Globals.nRemoveAge)
# Purge archives and archive directories older than one week
for item in glob.glob(os.path.join(Globals.pathDst, Constants.strArchives)):
stat = os.stat(item)
if datetime.datetime.fromtimestamp(stat.st_mtime) < dtWeekAgo:
if os.path.isdir(item):
cc = os.system('rm -drf %s' % item)
if cc:
raise Common.BiologicError('Unable to remove old directory %s' % item)
else:
os.remove(item)
# Create a new archive directory
strArchive = 'Stylus_%s' % dtNow.isoformat().translate(Constants.strTranslate)
pathArchive = os.path.abspath(os.path.join(Globals.pathDst, strArchive))
os.makedirs(pathArchive)
# Populate the archive directory
for folder in Globals.aryFolders:
pathSrc = os.path.abspath(os.path.join(Globals.pathSrc, folder))
pathDst = os.path.abspath(os.path.join(pathArchive, folder))
cc = os.system('ditto %s %s' % (pathSrc, pathDst))
if cc:
raise Common.BiologicError('Unable to copy folder %s to archive directory %s - error code(%d)' % (folder, pathArchive, cc))
Common.say('...copied %s' % folder)
# Create the archive
fileArchive = os.path.abspath(os.path.join(Globals.pathDst, strArchive + Constants.extArchive))
cc = os.system('ditto -c -z %s %s' % (pathArchive, fileArchive))
if cc:
raise Common.BiologicError('Unable to create archive %s - error code(%d)' % (fileArchive, cc))
Common.say('...created archive %s' % pathArchive)
# Remove the archive directory
cc = os.system('rm -drf %s' % pathArchive)
if cc:
raise Common.BiologicError('Unable to temporary archive directory %s' % fileArchive)
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
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
def buildGenes(uchHan, aryGenes):
Common.say('Creating %d gene(s)' % len(aryGenes))
han = loadHan(uchHan)
strAuthor = Globals.strAuthor and (" author='%s'" % Globals.strAuthor) or ''
aryGeneNames = []
for specification in aryGenes:
Common.say('Creating gene from specification ' + specification)
gs = GeneSpecification(specification != Constants.strDefault and specification or '', han)
gsName = gs.toName(han.unicode) + Common.Constants.extGene
gsPoints = gs.getPoints()
Common.say('Gene to be named ' + gsName)
ptCurrent = Genome.Point(pt=gsPoints[0][1][0])
arySegments = []
# Convert each set of points into a list of vectors
for iSegment in xrange(len(gsPoints)):
fCoherent, aryPoints = gsPoints[iSegment]
# Build the segment starting from the current location
# - Ensure incoherent segments always begin at the current location
# (This causes moves to absorb the tracing error, effectively trading placement error for stroke fit error.)
if not fCoherent:
aryPoints[0].x = ptCurrent.x
aryPoints[0].y = ptCurrent.y
ptCurrent, aryVectors = buildSegment(ptCurrent, fCoherent, aryPoints)
if not fCoherent:
# If the segment contains too few vectors, pad it with an incoherent sequence
# - If there are no vectors, use No/So/Ea/We - binding code will ensure proper coherence at the endpoints
# - Otherwise, use the four points of the direction "compass" that are guaranteed incoherent with the last vector
if len(aryVectors) < 3:
iDirection = len(aryVectors) and Codons.Directions.add(Codons.Vectors.toDirection(aryVectors[-1]), 3) or Codons.Directions.North
aryVectors.append(Codons.Vectors.create(iDirection))
aryVectors.append(Codons.Vectors.create(Codons.Directions.toOpposite(iDirection)))
iDirection = Codons.Directions.add(iDirection, 2)
aryVectors.append(Codons.Vectors.create(iDirection))
aryVectors.append(Codons.Vectors.create(Codons.Directions.toOpposite(iDirection)))
# Inject vectors to force incoherency for incoherent segments
# - Essentially, add a vector pair to every two that forces incoherency
# - Walking the list must take into account injected vector pairs
else:
iVector = 0
while iVector < len(aryVectors):
if Codons.isCoherent([aryVectors[iVector-2], aryVectors[iVector-1], aryVectors[iVector+0]]):
idVector = aryVectors[iVector]
aryVectors.insert(iVector+0, Codons.Vectors.toOpposite(idVector))
aryVectors.insert(iVector+1, idVector)
iVector += 1
# Ensure the vectors "bind" without affecting the coherence of an adjoining segment
if iSegment:
fCoherencePrev, aryVectorsPrev = arySegments[-1]
if Codons.isCoherent([ aryVectorsPrev[-2], aryVectorsPrev[-1], aryVectors[0] ]) or Codons.isCoherent([ aryVectorsPrev[-1], aryVectors[0], aryVectors[1] ]):
if not fCoherencePrev:
aryVectorsPrev += [ Codons.Vectors.toOpposite(aryVectorsPrev[-1]), aryVectorsPrev[-1], aryVectors[0], Codons.Vectors.toOpposite(aryVectors[0]) ]
else:
aryVectors[:0] = [ Codons.Vectors.toOpposite(aryVectorsPrev[-1]), aryVectorsPrev[-1], aryVectors[0], Codons.Vectors.toOpposite(aryVectors[0]) ]
arySegments.append((fCoherent, aryVectors))
validateCoherence(arySegments)
aryCodons = [ Codons.Vectors.toVector(idVector).codon for fCoherent, aryVectors in arySegments for idVector in aryVectors ]
aryCodons[:0] = [ 'ATG' ]
aryCodons.append(Codons.Vectors.toVector(Codons.Vectors.create(Codons.Directions.Stop, Codons.Constants.iVectorShort)).codon)
aryStrokes = []
iStroke = 0
iBase = 4
for fCoherent, aryVectors in arySegments:
if fCoherent:
aryStrokes.append(_GENE_STROKE % (iBase, iBase+(len(aryVectors)*3-1), gs.mapStrokeToHan(iStroke)+1))
iStroke += 1
iBase += len(aryVectors) * 3
strGene = _GENE_DEFINITION % (str(uuid.uuid4()).upper(), strAuthor, datetime.datetime.utcnow().isoformat(), _NAME, str(gs),
''.join(aryCodons), len(aryCodons)*3,
gsPoints[0][1][0].x, gsPoints[0][1][0].y,
han.unicode,
'\n'.join(aryStrokes))
strPath = Common.resolvePath(os.path.join(Globals.strGenePath, Common.makeHanPath(gsName)))
strDir = os.path.dirname(strPath)
if not os.path.exists(strDir):
try: os.makedirs(os.path.dirname(strPath))
except OSError, err: raise Common.BiologicError('Unable to create %s - %s' % (strDir, str(err)))
try:
fileGene = os.open(strPath, os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileGene, strGene)
except IOError, err: raise Common.BiologicError('Unable to create %s - %s' % (strPath, str(err)))
os.close(fileGene)
Common.say('\tWrote %s - %d codons, %d bases' % (strPath, len(aryCodons), len(aryCodons)*3))
aryGeneNames.append(gsName)
return aryGeneNames
def validateTable():
Globals.codonTable.validate()
Common.say('%s successfully validated' % (Globals.urlCodonTable and Globals.urlCodonTable or Globals.urlGenome))
return
if Globals.pathOutput:
try:
fileCodonTable = os.open(Globals.pathOutput,
os.O_CREAT | os.O_TRUNC | os.O_WRONLY,
0664)
os.write(fileCodonTable, strCodonTable)
except IOError, err:
raise Common.BiologicError('Unable to create %s - %s' %
(Globals.pathOutput, str(err)))
os.close(fileCodonTable)
Common.say('Codon table written to ' + Globals.pathOutput)
else:
Common.say(strCodonTable, False, True)
return
#------------------------------------------------------------------------------
# Function: validateTable
#
#------------------------------------------------------------------------------
def validateTable():
Globals.codonTable.validate()
Common.say(
'%s successfully validated' %
(Globals.urlCodonTable and Globals.urlCodonTable or Globals.urlGenome))
return
def validateTable():
Globals.codonTable.validate()
Common.say(
'%s successfully validated' %
(Globals.urlCodonTable and Globals.urlCodonTable or Globals.urlGenome))
return
