from processor.io.CommStruct import CommStruct from xml.etree.ElementTree import parse from xml.etree.ElementTree import Element, ElementTree from utils.log.Log import Log from utils.exception.ParsingException import ParsingException from common.Motif import Motif class MotifStatisticsCommStruct( CommStruct): # -------------------------------------------------------------------------------------- def __init__( self): CommStruct.__init__( self) self.motifList = [] self.motifToStatistics = {} # -------------------------------------------------------------------------------------- def addMotif( self, motif): if motif != None: self.motifList.append( motif) # -------------------------------------------------------------------------------------- def addMotifStatistics(self, motif, statistics): if motif != None and statistics != None: self.motifToStatistics[motif] = statistics # -------------------------------------------------------------------------------------- def toXMLFile( self, output_filepath): try: root_element = self.convertCommStructToElementTree() self.indent( root_element, 0) ElementTree( root_element).write( output_filepath) except IOError, exce: Log.log( "MotifStatisticsCommStruct.toXMLFile : Unable to write CommStruct to XML file. From:\n\t---> " + str( exce)) except ParsingException, par_exce: Log.log( "MotifStatisticsCommStruct.toXMLFile : Unable to save CommStruct to XML file. From:\n\t---> " + str( par_exce)) # -------------------------------------------------------------------------------------- @staticmethod def fromXMLFile( input_filepath): try: return MotifStatisticsCommStruct.getCommStructFromXML( input_filepath) except ParsingException, par_exce: Log.log( "MotifStatisticsCommStruct.fromXMLFile : Unable to get CommStruct from XML file '" + input_filepath + "'. From:\n\t---> " + str( par_exce)) return None # ############################# # METHODS TO READ THE XLM FILE # ############################# # -------------------------------------------------------------------------------------- @staticmethod def getCommStructFromXML( commstruct_filepath): file = None root_element = None try: file = open( commstruct_filepath, "r") tree = parse( file) root_element = tree.getroot() file.close() except IOError, io_exce: raise ParsingException( "MotifStatisticsCommStruct.getCommStructFromXML : Unable to open/close XML file '" + commstruct_filepath, "' : " + str( io_exce)) comm_struct = MotifStatisticsCommStruct() comm_struct.getCommStructData( root_element) for node_motif in root_element: if node_motif.tag.lower() == MotifStatisticsCommStruct.MOTIF_TAG: MotifStatisticsCommStruct.getMotif( node_motif, comm_struct) return comm_struct # -------------------------------------------------------------------------------------- # Retrieve the list of motifs of the alignment # and store it into the given SequenceAlignment @staticmethod def getMotif( node_motif, comm_struct): name = CommStruct.getAttribute( node_motif, MotifStatisticsCommStruct.MOTIF_NAME_ATT) consensus = CommStruct.getAttribute( node_motif, MotifStatisticsCommStruct.MOTIF_CONSENSUS_ATT, False) if name != None: motif = Motif( 0, 0, name, None) if consensus != None: motif.consensus = consensus comm_struct.addMotif( motif) statistics = MotifStatisticsCommStruct.getMotifStatistics( node_motif, motif) comm_struct.addMotifStatistics( motif, statistics) else: raise ParsingException( "MotifStatisticsCommStruct.getAlignmentMotifs : The motif is missing required attribute 'name'") # -------------------------------------------------------------------------------------- # Verify the param is correctly defined # if so, add a parameter to the component @staticmethod def getMotifStatistics( node_motif, motif): statistics = MotifStatistics() for node_param in node_motif: if node_param.tag.lower() == MotifStatisticsCommStruct.PARAM_TAG: param_name = MotifStatisticsCommStruct.getAttribute( node_param, MotifStatisticsCommStruct.PARAM_NAME_ATT, False) param_value = MotifStatisticsCommStruct.getAttribute( node_param, MotifStatisticsCommStruct.PARAM_VALUE_ATT, False) if param_name != None and len( param_name) > 0: if param_value != None and len( param_value) > 0: if param_name == MotifStatisticsCommStruct.CHI2_PARAM_NAME: statistics.chi2 = MotifStatisticsCommStruct.getTokenAsfloat( param_value, False) elif param_name == MotifStatisticsCommStruct.HISTOGRAM_GRAPH_PATH_PARAM_NAME: statistics.histogramGraphPath = param_value elif param_name == MotifStatisticsCommStruct.HISTOGRAM_PARAM_NAME: statistics.histogram = param_value.split( MotifStatisticsCommStruct.HISTOGRAM_ENTRY_SEPARATOR_CHAR) elif param_name == MotifStatisticsCommStruct.NULL_HISTOGRAM_PARAM_NAME: statistics.nullHistogram = param_value.split( MotifStatisticsCommStruct.HISTOGRAM_ENTRY_SEPARATOR_CHAR) else: Log.log( "MotifStatisticsCommStruct.getMotifAttributes : Unknown attribute name : " + param_name) else: raise ParsingException( "MotifStatisticsCommStruct.getMotifAttributes : Malformed parameter - unable to retrieve parameter value in motif '" + motif.name + "'") else: raise ParsingException( "MotifStatisticsCommStruct.getMotifAttributes : Malformed parameter - unable to retrieve parameter name in motif '" + motif.name + "'") return statistics # -------------------------------------------------------------------------------------- # Returns the attribute if exists and raise an exception if the attribute is required but not found @staticmethod def getAttribute( node, att_name, required = True): try: att_value = node.get( att_name) return att_value except Exception, exce: if required: raise ParsingException( "MotifStatisticsCommStruct.getAttribute : Node '" + node.tag + "' does not know the attribute :'" + att_name + "'. From:\n\t---> " + str( exce)) else: return None # -------------------------------------------------------------------------------------- # Return the value of the token as int if possible and raise an exception if the value is required but not converted @staticmethod def getTokenAsfloat( token, required=True): try: att_value = float( token) return att_value except (TypeError, ValueError), val_exce: if required: raise ParsingException( "MotifStatisticsCommStruct.getTokenAsfloat : Unable to convert the token to float :'" + token + "'. From:\n\t---> " + str( val_exce)) else: return None # ############################# # METHODS TO WRITE THE XLM FILE # ############################# # -------------------------------------------------------------------------------------- # Convert the CommStruct to an ElementTree containing all the required # suitably organized information def convertCommStructToElementTree( self): data_element = Element( MotifStatisticsCommStruct.DATA_TAG) self.addCommStructDataToElement( data_element) for motif in self.motifList: motif_element = Element( MotifStatisticsCommStruct.MOTIF_TAG) data_element.append( motif_element) motif_element.attrib[ MotifStatisticsCommStruct.MOTIF_NAME_ATT] = motif.name if motif.consensus != None and len( motif.consensus) > 0: motif_element.attrib[ MotifStatisticsCommStruct.MOTIF_NAME_ATT] = motif.consensus # Add the statistics motif_stats = self.motifToStatistics[ motif] if motif_stats.chi2 != None: param_chi2_element = Element( MotifStatisticsCommStruct.PARAM_TAG) motif_element.append( param_chi2_element) param_chi2_element.attrib[ MotifStatisticsCommStruct.PARAM_NAME_ATT] = MotifStatisticsCommStruct.CHI2_PARAM_NAME param_chi2_element.attrib[ MotifStatisticsCommStruct.PARAM_VALUE_ATT] = str( motif_stats.chi2) if motif_stats.histogramGraphPath != None: param_histopath_element = Element( MotifStatisticsCommStruct.PARAM_TAG) motif_element.append( param_histopath_element) param_histopath_element.attrib[ MotifStatisticsCommStruct.PARAM_NAME_ATT] = MotifStatisticsCommStruct.HISTOGRAM_GRAPH_PATH_PARAM_NAME param_histopath_element.attrib[ MotifStatisticsCommStruct.PARAM_VALUE_ATT] = str( motif_stats.histogramGraphPath) if motif_stats.histogram != None: line = "" for token in motif_stats.histogram: line += token + MotifStatisticsCommStruct.HISTOGRAM_ENTRY_SEPARATOR_CHAR line = line[:-1] param_histo_element = Element( MotifStatisticsCommStruct.PARAM_TAG) motif_element.append( param_histo_element) param_histo_element.attrib[ MotifStatisticsCommStruct.PARAM_NAME_ATT] = MotifStatisticsCommStruct.HISTOGRAM_PARAM_NAME param_histo_element.attrib[ MotifStatisticsCommStruct.PARAM_VALUE_ATT] = line if motif_stats.nullHistogram != None: line = "" for token in motif_stats.nullHistogram: line += token + MotifStatisticsCommStruct.HISTOGRAM_ENTRY_SEPARATOR_CHAR line = line[:-1] param_nullhisto_element = Element( MotifStatisticsCommStruct.PARAM_TAG) motif_element.append( param_nullhisto_element) param_nullhisto_element.attrib[ MotifStatisticsCommStruct.PARAM_NAME_ATT] = MotifStatisticsCommStruct.NULL_HISTOGRAM_PARAM_NAME param_nullhisto_element.attrib[ MotifStatisticsCommStruct.PARAM_VALUE_ATT] = line return data_element # -------------------------------------------------------------------------------------- # Definition of the tags and attributes names used in the XML format DATA_TAG = "data" MOTIF_TAG = "motif" MOTIF_NAME_ATT = "name" MOTIF_CONSENSUS_ATT = "consensus" PARAM_TAG = "param" PARAM_NAME_ATT = "name" PARAM_VALUE_ATT = "value" CHI2_PARAM_NAME = "Chi2" HISTOGRAM_PARAM_NAME = "Histogram" NULL_HISTOGRAM_PARAM_NAME = "NullHistogram" HISTOGRAM_GRAPH_PATH_PARAM_NAME = "HistogramGraphPath" HISTOGRAM_ENTRY_SEPARATOR_CHAR = ";" HISTOGRAM_VALUE_SEPARATOR_CHAR = ":" class MotifStatistics: def __init__(self): self.chi2 = None self.histogram = None self.histogramGraphPath = None self.nullHistogram = None