def getPeptideFromLine(self, cols):
return pcssPeptide.PcssPeptide(
self.getValueForAttributeName("peptide_sequence", cols),
int(self.getValueForAttributeName("peptide_start", cols)),
int(self.getValueForAttributeName("peptide_end", cols)),
self.pcssRunner)
def parseFastaSequence(self, seqRecord):
"""Use user-defined rules to read protein sequence, parse peptides, and return a list of those that conform to rules"""
seqLength = len(seqRecord.seq)
pcssPeptideList = []
for i in range(0, seqLength - self.pcssRunner.getPeptideLength() + 1):
nextPeptide = str(
seqRecord.seq[i:i + self.pcssRunner.getPeptideLength()])
if (self.rules.isValidPeptide(nextPeptide)):
pcssPeptideList.append(
pcssPeptide.PcssPeptide(
nextPeptide, i,
i + self.pcssRunner.getPeptideLength() - 1,
self.pcssRunner))
return pcssPeptideList
def makePeptideFromCode(self, peptideCode, modbaseSeqId):
if (len(peptideCode.split('_')) != 3):
raise pcssErrors.PcssGlobalException(
"Peptide code %s from protein %s is not proper form of peptideStart_peptideSequence_status"
% (peptideCode, modbaseSeqId))
[peptideStart, peptideSequence, status] = peptideCode.split('_')
if (peptideSequence == self.pcssRunner.
internalConfig["keyword_peptide_sequence_mismatch"]):
return None
status = self.pcssRunner.validatePeptideCodeStatus(status, peptideCode)
peptideStart = int(peptideStart)
peptide = pcssPeptide.PcssPeptide(
peptideSequence, peptideStart,
peptideStart + len(peptideSequence) - 1, self.pcssRunner)
peptide.addStringAttribute("status", status)
return peptide
def processNormalSeqFeature(self):
self.processResultFile()
callString = self.getCallString()
self.assertEquals(callString,
self.seqData.getExpectedFullStringResult())
peptide = self.proteins[0].peptides[17]
self.assertEquals(
peptide.attributes[self.getStringFeatureName()].getValueString(),
self.seqData.stringFeatureValue)
self.assertEquals(
peptide.attributes[self.getScoreFeatureName()].getValueString(),
self.seqData.scoreFeatureValue)
self.proteins[0].setPeptide(
pcssPeptide.PcssPeptide("FAKE", 1000, 1003, self.runner))
self.processFeatureException(self.proteins[0].peptides[1000],
self.getStringFeatureName(),
self.getPeptideNotFoundCode(),
self.processResultFile)
def parseFastaSequence(self, seqRecord):
pcssPeptideList = []
firstPeptide = str(seqRecord.seq[0:1])
pcssPeptideList.append(
pcssPeptide.PcssPeptide(firstPeptide, 0, 1, self.pcssRunner))
return pcssPeptideList