def GetSpeciesGenesInfo(): speciesLabels, nSpAll, _ = util.GetSpeciesToUse( files.FileHandler.GetSpeciesIDsFN()) seqsInfo = util.GetSeqsInfo(files.FileHandler.GetSpeciesSeqsDir(), speciesLabels, nSpAll) genenumbers = list(np.diff(seqsInfo.seqStartingIndices)) genenumbers.append(seqsInfo.nSeqs - seqsInfo.seqStartingIndices[-1]) return speciesLabels, genenumbers
def __init__(self, orthofinderWorkingDir_list, speciesToUse, nSpAll, qAddSpeciesToIDs, idExtractor = util.FirstWordExtractor): self.speciesIDsEx = util.FullAccession(files.FileHandler.GetSpeciesIDsFN()) self._Spec_SeqIDs = None self._extractor = idExtractor self.seqIDsEx = None self.ogs_all = None self.iOgs4 = 0 self.speciesToUse = speciesToUse # list of ints self.seqsInfo = util.GetSeqsInfo(orthofinderWorkingDir_list, self.speciesToUse, nSpAll) self.id_to_og = None self.qAddSpeciesToIDs = qAddSpeciesToIDs
def __init__(self, orthofinderWorkingDir, speciesToUse, nSpAll, clustersFilename_pairs, idExtractor = util.FirstWordExtractor, pickleDir=None): self.workingDirOF = orthofinderWorkingDir self.seqIDsFN = orthofinderWorkingDir + "SequenceIDs.txt" self.speciesIDsFN = orthofinderWorkingDir + "SpeciesIDs.txt" self.speciesIDsEx = util.FullAccession(self.speciesIDsFN) self._Spec_SeqIDs = None self._extractor = idExtractor self.clustersFN = clustersFilename_pairs self.seqIDsEx = None self.ogs_all = None self.iOgs4 = 0 self.speciesToUse = speciesToUse self.seqsInfo = util.GetSeqsInfo(orthofinderWorkingDir, self.speciesToUse, nSpAll) self.fileInfo = util.FileInfo(workingDir = orthofinderWorkingDir, graphFilename="", separatePickleDir=pickleDir) self.id_to_og = None
def GetSpeciesGenesInfo(ogSet): speciesLabels, nSpAll = util.GetSpeciesToUse(ogSet.speciesIDsFN) seqsInfo = util.GetSeqsInfo(ogSet.workingDirOF, speciesLabels, nSpAll) genenumbers = list(np.diff(seqsInfo.seqStartingIndices)) genenumbers.append(seqsInfo.nSeqs - seqsInfo.seqStartingIndices[-1]) return speciesLabels, genenumbers