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, )
