def __init__(self, *args, **kwargs): AddaModuleRecord.__init__(self, *args, **kwargs) self.mFilenameSegments = self.mConfig.get("files", "output_segments", "adda.segments") self.mFilenames = (self.mFilenameSegments, ) self.covering_trees = self.mConfig.get("segments", "covering_trees", True) self.combine_repeats = self.mConfig.get("segments", "combine_repeats", True) self.normalize_matrix = self.mConfig.get('segments', 'normalize', False) self.add_local_bias = self.mConfig.get('segments', 'matrix_add_local_bias', False) self.permute_matrix = self.mConfig.get('segments', 'permute', False) if self.normalize_matrix: E.warn("matrix normalization is turned on") if self.add_local_bias: E.warn("adding local bias is turned on") if self.permute_matrix: E.warn("matrix permutation is turned on")
def __init__(self, *args, **kwargs): AddaModuleRecord.__init__(self, *args, **kwargs) self.mFilenameFit = self.mConfig.get("output", "output_fit", "adda.fit") self.mFilenameOverhang = self.mConfig.get("output", "output_fit_overhang", "adda.fit.overhang") self.mFilenameTransfer = self.mConfig.get("output", "output_fit_transfer", "adda.fit.transfer") self.mFilenameData = self.mConfig.get("output", "output_fit_data", "adda.fit.data") self.mFilenameDetails = self.mConfig.get("output", "output_fit_details", "adda.fit.details") self.mMinTransfer = float(self.mConfig.get("fit", "min_transfer")) self.mMinOverhang = float(self.mConfig.get("fit", "min_overhang")) self.mFilenameNids = self.mConfig.get("output", "output_nids", "adda.nids") self.mMaxSequenceLength = self.mConfig.get("segment", "max_sequence_length", 10000) self.min_counts = self.mConfig.get("fit", "min_counts", 10) self.mFilenames = (self.mFilenameFit, self.mFilenameTransfer, self.mFilenameOverhang) self.mOutfileDetails = None self.mOutfileData = None self.mDataIsComplete = False
def __init__(self, *args, **kwargs): AddaModuleRecord.__init__(self, *args, **kwargs) self.mFilenameRealignment = self.mConfig.get("files", "output_realignment", "adda.realign") self.mFilenames = (self.mFilenameRealignment, )
def __init__(self, *args, **kwargs ): AddaModuleRecord.__init__( self, *args, **kwargs ) self.mFilenameGraph = self.mConfig.get("files", "output_graph", "adda.graph" ) self.mFilenames = (self.mFilenameGraph, ) self.mMergeRepeats = self.mConfig.get( "graph", "merge_repeats", True ) self.mMinDomainSize = int(self.mConfig.get('adda','min_domain_size')) self.mHeaders = ("query_nid","sbjct_nid","evalue","query_start","query_end","sbjct_start", "sbjct_end")
def __init__(self, *args, **kwargs ): AddaModuleRecord.__init__( self, *args, **kwargs ) self.mFilenameProfile = self.mConfig.get( "files", "output_profiles", "adda.profiles" ) self.mScaleFactor = self.mConfig.get( "profiles", "scale_factor", 0.3 ) self.mMaxNumNeighbours = self.mConfig.get( "profiles", "max_neighbours", 1000) self.mMaxEvalue = self.mConfig.get( "profiles", "max_evalue", 0.0) self.mPrepareProfile = self.mConfig.get( "profiles", "prepare_profile", False )
def __init__(self, *args, **kwargs ): AddaModuleRecord.__init__( self, *args, **kwargs ) self.mFilenameAlignments = self.mConfig.get("files","output_align", "adda.align" ) self.mFilenameGraph = self.mConfig.get("files","output_graph", "adda.graph" ) self.mFilenameIndex = self.mConfig.get("files","output_index", "adda.graph.index" ) self.mFilenameProfiles = self.mConfig.get( "files", "output_profiles", "adda.profiles") self.mFilenameMst = self.mConfig.get( "files", "output_mst", "adda.mst" ) self.mUsePrebuiltProfiles = self.mConfig.get( "profiles", "use_prebuilt_profiles", False) self.mScaleFactor = self.mConfig.get( "profiles", "scale_factor", 0.3) self.mMaxNumNeighbours = self.mConfig.get( "profiles", "max_neighbours", 1000 ) self.mPrepareProfile = self.mConfig.get( "profiles", "prepare_profile", False ) self.mMinOverlapResidues = self.mConfig.get( "align", "min_overlap_residues", 20 ) self.mMinCoverage = self.mConfig.get( "align", "min_coverage", 0.2 ) self.mMinOverlap = self.mConfig.get( "align", "min_overlap", 0.2 ) self.mMask = self.mConfig.get( "align", "mask", False ) self.mMethodsMask = map(int, self.mConfig.get( "align", "masks", "3,4" ).split(",")) self.mUseCache = self.mConfig.get( "align", "use_cache", True ) self.mCacheSize = self.mConfig.get( "align", "cache_size", 100 ) ############################################### # options for zscore check self.mMinZScore = self.mConfig.get( "align", "min_zscore", 5.0 ) self.mNumIterationsZScore = self.mConfig.get( "align", "num_iterations_zscore", 50 ) # if score is 5 times the minimum score, do not compute zscore self.mSafetyThreshold = self.mConfig.get( "align", "safety_threshold", 5 ) ############################################### # alignment parameters self.mGop = self.mConfig.get( "align", "gop", -10.0 ) self.mGep = self.mConfig.get( "align", "gep", -1.0 ) # minimum size for using a profile for alignments self.mMinProfileSize = self.mConfig.get( "align", "min_profile_size", 0 ) # threshold parameters for significance check self.mMinAlignmentScore = self.mConfig.get( "align", "min_alignment_score", 83.0 ) self.mMinAlignmentMotifLength = self.mConfig.get( "align", "min_motif_length", 10 ) self.mFilenames = (self.mFilenameAlignments, ) self.mProfileBuilder = AddaProfiles.AddaProfiles( *args, **kwargs ) # the cache to store alignandum objects self.mCache = {}
def __init__(self, *args, **kwargs): AddaModuleRecord.__init__(self, *args, **kwargs) self.mFilenameProfile = self.mConfig.get("files", "output_profiles", "adda.profiles") self.mScaleFactor = self.mConfig.get("profiles", "scale_factor", 0.3) self.mMaxNumNeighbours = self.mConfig.get("profiles", "max_neighbours", 1000) self.mMaxEvalue = self.mConfig.get("profiles", "max_evalue", 0.0) self.mPrepareProfile = self.mConfig.get("profiles", "prepare_profile", False)
def __init__(self, *args, **kwargs ): AddaModuleRecord.__init__( self, *args, **kwargs ) self.mFilenameSegments = self.mConfig.get("files","output_segments", "adda.segments" ) self.mFilenames = (self.mFilenameSegments, ) self.covering_trees = self.mConfig.get("segments", "covering_trees", True) self.combine_repeats = self.mConfig.get( "segments", "combine_repeats", True) self.normalize_matrix = self.mConfig.get('segments','normalize', False) self.add_local_bias = self.mConfig.get('segments','matrix_add_local_bias', False ) self.permute_matrix = self.mConfig.get('segments','permute', False ) if self.normalize_matrix: E.warn( "matrix normalization is turned on" ) if self.add_local_bias: E.warn( "adding local bias is turned on" ) if self.permute_matrix: E.warn( "matrix permutation is turned on" )
def __init__(self, *args, **kwargs ): AddaModuleRecord.__init__( self, *args, **kwargs ) self.mFilenameFit = self.mConfig.get("output","fit", "adda.fit" ) self.mFilenameOverhang = self.mConfig.get( "output", "fit_overhang", "adda.fit.overhang" ) self.mFilenameTransfer = self.mConfig.get( "output", "fit_transfer", "adda.fit.transfer" ) self.mFilenameData = self.mConfig.get( "output", "fit_data", "adda.fit.data" ) self.mFilenameDetails = self.mConfig.get( "output", "fit_details", "adda.fit.details" ) self.mMinTransfer = float(self.mConfig.get( "fit", "min_transfer" )) self.mMinOverhang = float(self.mConfig.get( "fit", "min_overhang" )) self.mFilenameNids = self.mConfig.get( "output", "nids", "adda.nids" ) self.mMaxSequenceLength = self.mConfig.get( "segment", "max_sequence_length", 10000 ) self.min_counts = self.mConfig.get( "fit", "min_counts", 10 ) self.mFilenames = (self.mFilenameFit, self.mFilenameTransfer, self.mFilenameOverhang) self.mOutfileDetails = None self.mOutfileData = None self.mDataIsComplete = False
def __init__(self, *args, **kwargs ): AddaModuleRecord.__init__( self, *args, **kwargs ) self.mFilenameRealignment = self.mConfig.get("files","output_realignment", "adda.realign" ) self.mFilenames = ( self.mFilenameRealignment, )