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src/a/i/AIGO-0.1.0/AIGO/FunctionalAnnotation.py   AIGO(Download)
    def add(self, FA):
        logger.info("Name :\t%s" % self.name)
 
        for aspect in FA.GPtoGO:
            if not self.GPtoGO.has_key(aspect):
            self['GA']=self['GA']  | set(self.GPtoGO[a].keys())
 
        logger.info ("%d gene products are annotated" % (len(self['GA'])))
 
        self.status="Loaded"
 
        for  a in self.G.aspect:
            logger.info ("%s : %.2f annotations per set" % (a, mean([len(self.GPtoGO[a][gp]) for gp in self.GPtoGO[a]])))
    def inter(self, FA):
        logger.info("Name :\t%s" % self.name)
 
        for aspect in self.GPtoGO:
            if not FA.GPtoGO.has_key(aspect):
            self['GA']=self['GA']  | set(self.GPtoGO[a].keys())
 
        logger.info ("%d gene products are annotated" % (len(self['GA'])))
 
        self.status="Loaded"

src/a/i/AIGO-0.1.0/AIGO/go/OBO.py   AIGO(Download)
    if not force:
        try:
            logger.info("Reading serialized OBO file : %s" % picName)
            with open(picName, "rb") as f:
 
                raise IOError(fileName+" does not exist and is required ")
 
            logger.info("Reading OBO file : %s" % fileName)
 
            G = get_GOGraph(readFile(fileName, mode="r"), prefix=prefix)
            G.fileName=fileName
 
            with open(picName, "wb") as f:
                logger.info("Saving serialized OBO file")

src/a/i/AIGO-0.1.0/AIGO/ReferenceSet.py   AIGO(Download)
            logger.handleFatal(fileName+" does not exist and is required ")
 
        logger.info("Organism :\t%s" % self.organism)
 
        logger.info("%s file :\t%s " % (refType, fileName ) )

src/a/i/AIGO-0.1.0/AIGO/gui/project.py   AIGO(Download)
    def load(self, fileName):
 
        import shelve
        try:
            logger.info("File :\t%s" % fileName)
    def save(self, fileName):
        import shelve
        try:
            logger.info("File :\t%s" % fileName)
            shelf=shelve.open(fileName, protocol=-1)

src/a/i/AIGO-0.1.0/AIGO/Analyse.py   AIGO(Download)
 
        for FA in allFA:
            logger.info("\t%s" % FA.name)
 
            largestSet=dict()
 
        for FA in allFA:
            logger.info("\t%s" % FA.name)
 
            #Compute the percentage of obsolete annotations
 
        for FA in allFA:
            logger.info("\t%s" % FA.name)
 
            #Compute the percentage of obsolete annotations
 
        for FA in allFA:
            logger.info("\t%s" % FA.name)
 
            for a in FA.G.aspect:
 
        for FA in allFA:
            logger.info("\t%s" % FA.name)
 
            for a in FA.G.aspect:

src/a/i/AIGO-0.1.0/AIGO/Plot.py   AIGO(Download)
    def Multiple(self, allFA,  statistics=None, figName=None, lloc="upper right", doGrid=False):
        lLabel=[aspect.replace("_", " ") for aspect in allAspect]
 
        logger.info("\t%s" % statistics)
 
    def add(self, statistics, plotType):
        logger.info("Registering plot function %s" % statistics)
 
        if not rS.isRegistered(statistics):
            logger.handleWarning("Caution, the statistics is unknown : %s" % statistics)

src/a/i/AIGO-0.1.0/AIGO/utils/Plot.py   AIGO(Download)
def venn_NS(v,tit=None):
    logger.info(tit)
 
    idx=argsort( [len(key) for key in v.keys()])
    for key in array(v.keys())[idx]:
        logger.info("%s \t: %.2f" % (key.replace('@', '\t ^ '), v[key]))
 
    logger.info("TOTAL\t: %.2f" % (100.0-sum(v.values()) ) )

src/a/i/AIGO-0.1.0/AIGO/Compare.py   AIGO(Download)
                FA1,FA2=take(twoFAs,argsort([FA.name for FA in twoFAs]))
 
                logger.info("\tbetween %s and %s for %s" % (FA1.name, FA2.name, aspect))
 
                commonGene=self.getCommonGene(FA1, FA2, aspect)
            FA1,FA2=take(twoFAs,argsort([FA.name for FA in twoFAs]))
 
            logger.info("\tbetween %s and %s for %s" % (FA1.name, FA2.name, aspect))
 
            commonGene=self.getCommonGene(FA1, FA2, aspect)
                precision[aspect][(FA.name, GS.name)]=dict()
 
                logger.info("\t%s vs %s for %s" % (FA.name, GS.name, aspect))
 
                commonGene=self.getCommonGene(FA, GS, aspect)
                recall[aspect][(FA.name, GS.name)]=dict()
 
                logger.info("\t%s vs %s for %s" % (FA.name, GS.name, aspect))
 
                commonGene=self.getCommonGene(FA, GS, aspect)

src/a/i/AIGO-0.1.0/AIGO/Randomize.py   AIGO(Download)
        for FA in allFA:
 
            logger.info("\t%s" % (FA.name))
 
            for aspect in allAspect:
        for FA in allFA:
 
            logger.info("\t%s" % (FA.name))
 
            for aspect in allAspect:

src/a/i/AIGO-0.1.0/AIGO/Statistics.py   AIGO(Download)
    def add(self, statistics, name, unit="", types=None):
        logger.info("Registering statistics function %s" % statistics)
 
        self.all.append(statistics)
        self.name[statistics]=name

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