本文整理汇总了Python中Constants.addPepsToAADict方法的典型用法代码示例。如果您正苦于以下问题：Python Constants.addPepsToAADict方法的具体用法？Python Constants.addPepsToAADict怎么用？Python Constants.addPepsToAADict使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Constants的用法示例。
在下文中一共展示了Constants.addPepsToAADict方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: open
# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import addPepsToAADict [as 别名]
"epsilon",
"ambiguous edges",
"num ambig edges",
]
if options.output:
outFile = open(options.output, "w")
outFile.write("\t".join([col.upper() for col in cols]) + "\n")
t1 = time.time()
print "Configuring LADS for sequencing..."
ETDPNet = PN.ProbNetwork(paramsDict["Models"]["etd"]["config"], paramsDict["Models"]["etd"]["model"])
HCDPNet = PN.ProbNetwork(paramsDict["Models"]["hcd"]["config"], paramsDict["Models"]["hcd"]["model"])
dtaList = glob.glob(options.dtadir + "/*.dta")
scanFDict = getScanFDict(dtaList)
aas = Constants.addPepsToAADict(options.minedge)
hashedAAs = Constants.hashAAsEpsilonRange(aas, epStep, maxEp)
ambigOpenPenalty = 0
ambigPenaltyFun = DNS.getAmbigEdgePenaltyFunction(options.minedge, ambigOpenPenalty, options.ambigpenalty)
ppmPenaltyFun = DNS.getPPMPenaltyFun(
options.ppmstd, hashedAAs, options.minedge, options.ppmpenalty, options.ppmsyserror, epStep
)
addEnds = DNS.getSpectrumGraphEndpointInitFunction(
np.array(Constants.NTermMods.values()),
np.array(Constants.CTermMods.values()),
paramsDict["Enzyme"]["specificity"],
)
termModHash = Constants.createTermModHashAAs(
N=copy.deepcopy(Constants.NTermMods), C=copy.deepcopy(Constants.CTermMods)示例2: open
# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import addPepsToAADict [as 别名]
with open(options.columns) as fin:
cols = pickle.load(fin)
else:
print 'Using default cols'
cols = ['light scan', 'heavy scan', 'pair configuration', 'M+H', 'score', 'seq', 'epsilon', 'ambiguous edges', 'num ambig edges']
if options.output:
outFile = open(options.output, 'w')
outFile.write('\t'.join([col.upper() for col in cols]) + '\n')
PNet = PN.ProbNetwork(options.config, options.model)
dtaList = glob.glob(options.dtadir + '/*.dta')
scanFDict = getScanFDict(dtaList)
aas = Constants.addPepsToAADict(300)
hashedAAs = Constants.hashAAsEpsilonRange(aas, epStep, maxEp)
ambigOpenPenalty = 0
ambigPenaltyFun = DNS.getAmbigEdgePenaltyFunction(options.minedge, ambigOpenPenalty, options.ambigpenalty)
ppmPenaltyFun = DNS.getPPMPenaltyFun(options.ppmstd, hashedAAs, options.minedge, options.ppmpenalty, options.ppmsyserror, epStep)
print 'Getting Clusters'
parent = os.path.abspath(os.pardir)
clusterSVMModel = svmutil.svm_load_model(parent + paramsDict['Cluster Configuration']['model'])
clusterSVMRanges = svmutil.load_ranges(parent + os.path.splitext((paramsDict['Cluster Configuration']['model']))[0] + '.range')
precMassClusters = Analytics.findSamePrecMassClusters(dtaList, ppm=options.ppmstd)
# print 'precMassClusters', precMassClusters
samePeptideClusters = Analytics.getSamePeptideClusters(precMassClusters, scanFDict, clusterSVMModel, clusterSVMRanges, ppmSTD=options.ppmstd, cutOff=float(paramsDict['Cluster Configuration']['cutoff']))
# samePeptideClusters = Analytics.getSamePeptideClusters(precMassClusters, scanFDict, clusterSVMModel, clusterSVMRanges, ppmSTD=options.ppmstd, cutOff=4)示例3: loadInit
# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import addPepsToAADict [as 别名]
def loadInit(self):
self._paramsDict = DataFile.parseParams(self._selectedInitFile.get())
with open('../Misc/symbolmap.txt', 'r') as fin:
symbolMap = pickle.load(fin)
self._seqMap = DataFile.generateSeqMap({'LADS Unit Test': 'LADS'}, symbolMap, self._paramsDict)['LADS Unit Test']
self._aas = Constants.addPepsToAADict(self._minedge)