def __init__(self, inStr):
# print 'seq input', inStr
self.successfullyParsed = False
self.features = []
self.residues_nuc = '-'
self.residues_prt = '-'
self.translations = []
self.actualSeqIdNo = 0
self.actualMolType = '-'
self.actualLength = 0
self.mixedMode = False
self.isSkipCode = False
m = sequencePattern.match(inStr)
if m:
self.seqIdNo = safeStrip(m.group('seqIdNo'))
self.length = safeStrip(m.group('length'))
self.molType = safeStrip(m.group('molType'))
self.organism = safeStrip(m.group('organism'))
featureTable = safeStrip(m.group('featureTable'))
self.seqNo400 = safeStrip(m.group('seqNo400'))
if featureTable:
fiter = re.finditer(featurePattern, featureTable)
for fmatcher in fiter:
if fmatcher:
self.features.append(Feature(fmatcher))
residues = m.group('residues')
nucList = []
prtList = []
for line in residues.splitlines():
if nucPattern.match(line):
nucList.append(line)
else: #if prtPattern.match(line): TODO: add more robust code
prtList.append(line)
self.residues_nuc = ''.join(nucList)
self.residues_prt = ''.join(prtList)
self.residues_nuc = re.sub(r'[\s,\d]', '', self.residues_nuc)
self.residues_prt = re.sub(r'[\s,\d]', '', self.residues_prt)
if len(self.residues_nuc) > 0 and len(self.residues_prt) > 0:
self.mixedMode = True
if self.residues_nuc == '' and self.residues_prt == '':
self.isSkipCode = True
if self.mixedMode:
currentStart = 0
for f in self.features:
if f.key == 'CDS':
t = su.getRangeFromLocation(f.location)
currentTranslationLength = t[1] - t[0]
currentEnd = currentStart + currentTranslationLength +1
currentTranslation = self.residues_prt[currentStart:currentEnd]
currentStart = currentEnd
self.translations.append(currentTranslation)
f.translation = currentTranslation
self.__setActualMolType__()
self.__setActualLength__()
self.successfullyParsed = True #TODO: to add unittest for False
# print '='*30
else:
raise SeqlException('Parser failed for input:\n%s' % inStr)
def __init__(self, aStr):
self.successfullyParsed = False
self.features = []
self.residues_nuc = '-'
self.residues_prt = '-'
self.translations = []
self.actualSeqIdNo = 0
self.actualMolType = '-'
self.actualLength = 0
self.mixedMode = False
self.isSkipCode = False
sm = SEQUENCE_PATTERN.match(aStr)
if sm:
# print 'Sequence match found.'
self.seqIdNo_raw = sm.group('seqIdNo_raw')
self.seqIdNo = safeStrip(sm.group('seqIdNo'))
self.length_raw = sm.group('length_raw')
self.length = safeStrip(sm.group('length'))
self.molType_raw = sm.group('molType_raw')
self.molType = safeStrip(sm.group('molType'))
self.organism_raw = sm.group('organism_raw')
self.organism = safeStrip(sm.group('organism'))
featuresString = sm.group('features_raw')
# print featuresString
if featuresString:
featureMatchers = FEATURE_PATTERN.finditer(featuresString)
for fm in featureMatchers:
self.features.append(Feature(fm))
self.residues_raw = sm.group('residues_raw')
self.seqNo400 = safeStrip(sm.group('seqNo400'))
residues = sm.group('residues')
nucList = []
prtList = []
for line in residues.splitlines():
if nucPattern.match(line):
nucList.append(line)
else: #if prtPattern.match(line): TODO: add more robust code
prtList.append(line)
self.residues_nuc = ''.join(nucList)
self.residues_prt = ''.join(prtList)
self.residues_nuc = re.sub(r'[\s,\d]', '', self.residues_nuc)
self.residues_prt = re.sub(r'[\s,\d]', '', self.residues_prt)
if len(self.residues_nuc) > 0 and len(self.residues_prt) > 0:
self.mixedMode = True
# TODO: test it
if self.residues_nuc == '' and self.residues_prt == '':
self.isSkipCode = True
if self.mixedMode:
currentStart = 0
for f in self.features:
if f.key == 'CDS':
t = su.getRangeFromLocation(f.location)
currentTranslationLength = t[1] - t[0]
currentEnd = currentStart + currentTranslationLength + 1
currentTranslation = self.residues_prt[
currentStart:currentEnd]
currentStart = currentEnd
self.translations.append(currentTranslation)
f.translation = currentTranslation
self.__setActualMolType__()
self.__setActualLength__()
self.successfullyParsed = True
else:
# print 'File', self.filePath
print 'Sequence: No match for sequence pattern for input:', aStr
def __init__(self, aStr):
self.successfullyParsed = False
self.features = []
self.residues_nuc = '-'
self.residues_prt = '-'
self.translations = []
self.actualSeqIdNo = 0
self.actualMolType = '-'
self.actualLength = 0
self.mixedMode = False
self.isSkipCode = False
sm = SEQUENCE_PATTERN.match(aStr)
if sm:
# print 'Sequence match found.'
self.seqIdNo_raw = sm.group('seqIdNo_raw')
self.seqIdNo = safeStrip(sm.group('seqIdNo'))
self.length_raw = sm.group('length_raw')
self.length = safeStrip(sm.group('length'))
self.molType_raw = sm.group('molType_raw')
self.molType = safeStrip(sm.group('molType'))
self.organism_raw = sm.group('organism_raw')
self.organism = safeStrip(sm.group('organism'))
featuresString = sm.group('features_raw')
# print featuresString
if featuresString:
featureMatchers = FEATURE_PATTERN.finditer(featuresString)
for fm in featureMatchers:
self.features.append(Feature(fm))
self.residues_raw = sm.group('residues_raw')
self.seqNo400 = safeStrip(sm.group('seqNo400'))
residues = sm.group('residues')
nucList = []
prtList = []
for line in residues.splitlines():
if nucPattern.match(line):
nucList.append(line)
else: #if prtPattern.match(line): TODO: add more robust code
prtList.append(line)
self.residues_nuc = ''.join(nucList)
self.residues_prt = ''.join(prtList)
self.residues_nuc = re.sub(r'[\s,\d]', '', self.residues_nuc)
self.residues_prt = re.sub(r'[\s,\d]', '', self.residues_prt)
if len(self.residues_nuc) > 0 and len(self.residues_prt) > 0:
self.mixedMode = True
# TODO: test it
if self.residues_nuc == '' and self.residues_prt == '':
self.isSkipCode = True
if self.mixedMode:
currentStart = 0
for f in self.features:
if f.key == 'CDS':
t = su.getRangeFromLocation(f.location)
currentTranslationLength = t[1] - t[0]
currentEnd = currentStart + currentTranslationLength +1
currentTranslation = self.residues_prt[currentStart:currentEnd]
currentStart = currentEnd
self.translations.append(currentTranslation)
f.translation = currentTranslation
self.__setActualMolType__()
self.__setActualLength__()
self.successfullyParsed = True
else:
# print 'File', self.filePath
print 'Sequence: No match for sequence pattern for input:', aStr
