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 loadHan(strUnicode):
urlHan = Common.pathToURL(Common.makeHanPath(strUnicode + Common.Constants.extHan), Globals.urlHan)
try: han = Genome.Han(urlHan)
except LookupError, err: raise Common.BiologicError('%s is missing one or more required elements or attributes - %s' % (urlHan, str(err)))
except OSError, err: raise Common.BiologicError('Unable to open URL %s - %s' % (urlHan, str(err)))
except urllib2.URLError, err: raise Common.BiologicError('Unable to open URL %s - %s' % (urlHan, str(err)))
return han
if option in ('-v', '--version'):
Globals.fVersion = True
if option in ('-h', '--help'):
raise Usage('')
try:
Globals.urls.validate(Common.URLs.HAN | Common.URLs.SCHEMA)
Globals.names.validate(
Globals.urls,
Common.Names.DATA | Common.Names.GENOME | Common.Names.PLAN)
except Common.BiologicError, err:
raise Usage(str(err))
if Globals.urlGlobals:
Globals.urlGlobals = Common.pathToURL(Globals.urlGlobals,
Globals.urls.urlPlan)
Common.replacePath(Globals.names.pathData)
if Globals.aryLog[2]:
if not os.path.isabs(Globals.aryLog[2]):
Globals.aryLog[2] = os.path.abspath(
os.path.join(Globals.names.pathData, Globals.aryLog[2]))
Globals.aryLog[2] = os.path.normpath(
os.path.normcase(Globals.aryLog[2]))
#==============================================================================
# Main
#==============================================================================
def main(argv=None):
Common.Globals.fQuiet = True
if option in ('-v', '--version'):
Globals.fVersion = True
if option in ('-h', '--help'):
raise Usage('')
try:
Globals.urls.validate(Common.URLs.HAN | Common.URLs.SCHEMA)
Globals.names.validate(Globals.urls, Common.Names.DATA | Common.Names.GENOME | Common.Names.PLAN)
except Common.BiologicError, err:
raise Usage(str(err))
if Globals.urlGlobals:
Globals.urlGlobals = Common.pathToURL(Globals.urlGlobals, Globals.urls.urlPlan)
Common.replacePath(Globals.names.pathData)
if Globals.aryLog[2]:
if not os.path.isabs(Globals.aryLog[2]):
Globals.aryLog[2] = os.path.abspath(os.path.join(Globals.names.pathData, Globals.aryLog[2]))
Globals.aryLog[2] = os.path.normpath(os.path.normcase(Globals.aryLog[2]))
#==============================================================================
# Main
#==============================================================================
def main(argv=None):
try:
if not os.path.exists(Globals.strArchetypePath):
try: os.makedirs(Globals.strArchetypePath)
except OSError: raise Usage('Unable to create ' + Globals.strArchetypePath)
if len(Globals.aryGenes) > 0 and not Globals.strGenePath:
raise Usage('Required gene output path was not specified')
if len(Globals.aryGenes) > 0:
Globals.strGenePath = Common.resolvePath(Globals.strGenePath)
if not os.path.exists(Globals.strGenePath):
try: os.makedirs(Globals.strGenePath)
except OSError: raise Usage('Unable to create ' + Globals.strGenePath)
if not Globals.urlHan:
raise Usage('Required Han URL was not specified')
Globals.urlHan = Common.pathToURL(Globals.urlHan, Common.Constants.schemeFile)
#------------------------------------------------------------------------------
# Function: loadHan
#
#------------------------------------------------------------------------------
def loadHan(strUnicode):
urlHan = Common.pathToURL(Common.makeHanPath(strUnicode + Common.Constants.extHan), Globals.urlHan)
try: han = Genome.Han(urlHan)
except LookupError, err: raise Common.BiologicError('%s is missing one or more required elements or attributes - %s' % (urlHan, str(err)))
except OSError, err: raise Common.BiologicError('Unable to open URL %s - %s' % (urlHan, str(err)))
except urllib2.URLError, err: raise Common.BiologicError('Unable to open URL %s - %s' % (urlHan, str(err)))
return han
#==============================================================================
# Main Routines
if len(aryArgs) > 1 and aryArgs[1]:
Globals.urlCodonTableBase = aryArgs[1]
if option in ('-a', '--author'):
Globals.strAuthor = value
if option in ('-q', '--quiet'):
Common.Globals.fQuiet = True
if option in ('-h', '--help'):
raise Usage('')
if not Globals.cmd:
raise Usage('create, validate, or translate are required')
Globals.urlGenomeBase = Common.pathToURL(Globals.urlGenomeBase,
Common.Constants.schemeFile)
if Globals.urlGenomeBase[len(Globals.urlGenomeBase) -
1] <> Common.Constants.urlSeparator:
Globals.urlGenomeBase += Common.Constants.urlSeparator
Globals.urlCodonTableBase = Common.pathToURL(Globals.urlCodonTableBase,
Common.Constants.schemeFile)
if Globals.urlCodonTableBase[len(Globals.urlCodonTableBase) -
1] <> Common.Constants.urlSeparator:
Globals.urlCodonTableBase += Common.Constants.urlSeparator
if Globals.cmd <> Constants.cmdTranslate and Globals.strGenome and Globals.strCodonTable:
raise Usage(
'%s takes either the genome or codon table as its source - not both'
% (Globals.cmd == Constants.cmdCreate and 'create' or 'validate'))
if Globals.cmd == Constants.cmdValidate and not Globals.strGenome and not Globals.strCodonTable:
if len(aryArgs) > 1 and aryArgs[1]:
Globals.urlCodonTableBase = aryArgs[1]
if option in ('-a', '--author'):
Globals.strAuthor = value
if option in ('-q', '--quiet'):
Common.Globals.fQuiet = True
if option in ('-h', '--help'):
raise Usage('')
if not Globals.cmd:
raise Usage('create, validate, or translate are required')
Globals.urlGenomeBase = Common.pathToURL(Globals.urlGenomeBase, Common.Constants.schemeFile)
if Globals.urlGenomeBase[len(Globals.urlGenomeBase)-1] <> Common.Constants.urlSeparator:
Globals.urlGenomeBase += Common.Constants.urlSeparator
Globals.urlCodonTableBase = Common.pathToURL(Globals.urlCodonTableBase, Common.Constants.schemeFile)
if Globals.urlCodonTableBase[len(Globals.urlCodonTableBase)-1] <> Common.Constants.urlSeparator:
Globals.urlCodonTableBase += Common.Constants.urlSeparator
if Globals.cmd <> Constants.cmdTranslate and Globals.strGenome and Globals.strCodonTable:
raise Usage('%s takes either the genome or codon table as its source - not both' % (Globals.cmd == Constants.cmdCreate and 'create' or 'validate'))
if Globals.cmd == Constants.cmdValidate and not Globals.strGenome and not Globals.strCodonTable:
raise Usage('validate takes either the genome or codon table as its source')
if Globals.cmd == Constants.cmdTranslate and (not Globals.strGenome or not Globals.strCodonTable):
raise Usage('translate requires both the genome to translate and the codon table to use')
if Globals.cmd <> Constants.cmdValidate:
