from processor.io.CommStruct import CommStruct from utils.exception.ParsingException import ParsingException from utils.log.Log import Log from xml.etree.ElementTree import parse from xml.etree.ElementTree import Element, ElementTree from common.BEDSequence import BEDSequence class BedSeqCommStruct( CommStruct): BEDSEQUENCES_NUMBER = "BEDSequencesNumber" BEDSEQUENCES_MIN_SIZE = "BEDSequencesMinSize" BEDSEQUENCES_MAX_SIZE = "BEDSequencesMaxSize" BEDSEQUENCES_MEAN_SIZE = "BEDSequencesMeanSize" BEDSEQUENCES_TOTAL_SIZE = "BEDSequencesTotalSize" BED_SEQUENCES_SIZE_PATH = "BEDSequencesSizeHistogram" BED_SEQUENCES_SIZE_GRAPH_PATH = "BEDSequencesSizeHistogramGraph" # -------------------------------------------------------------------------------------- def __init__( self): CommStruct.__init__( self) self.baseSpecies = "" # dicitonnary of the BED Sequences : key = . / value = list of BEDSequence self.bedSequencesDict = {} # dictionnary of statistics parameters: key = parameter name / Value = parameter value self.paramStatistics = {} # -------------------------------------------------------------------------------------- # Add a sequence in BED format to the CommStruct def addBEDSequence(self, bed_sequence): if bed_sequence != None: key = bed_sequence.getKey() if not self.bedSequencesDict.has_key( key): self.bedSequencesDict[ key] = [] self.bedSequencesDict[ key].append( bed_sequence) # -------------------------------------------------------------------------------------- # Return a string representation of the CommStruct def toString( self): result = "BedSeqCommStruct\n" for chrom in self.bedSequencesDict.keys(): for sequence in self.bedSequencesDict[chrom]: result += "|--BED Sequence " + sequence.toString() + "\n" return result # -------------------------------------------------------------------------------------- # Read the CommStruct from the given XML file @staticmethod def fromXMLFile( input_filepath): try: return BedSeqCommStruct.getCommStructFromXML( input_filepath) except ParsingException, par_exce: Log.log( "BedSeqCommStruct.fromXMLFile : unable to get CommStruct from XML file '" + input_filepath + "'. From:\n\t--->" + str( par_exce)) return None # -------------------------------------------------------------------------------------- # Write the CommStruct to the given XML file 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( "BedSeqCommStruct.toXMLFile : Unable to write CommStruct to XML file. From:\n\t---> " + str( exce)) except ParsingException, par_exce: Log.log( "BedSeqCommStruct.toXMLFile : Unable to save CommStruct to XML file. From:\n\t---> " + str( par_exce)) # ############################# # 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( "BedSeqCommStruct.getCommStructFromXML : Unable to open/close XML file '" + commstruct_filepath, "'. From:\n\t---> " + str( io_exce)) comm_struct = BedSeqCommStruct() comm_struct.getCommStructData( root_element) for root_son in root_element: if root_son.tag.lower() == BedSeqCommStruct.BEDSEQ_TAG: bed_sequence = BedSeqCommStruct.getBEDSequence( root_son, comm_struct) base_species = bed_sequence.species elif root_son.tag.lower() == BedSeqCommStruct.STATISTICS_TAG: BedSeqCommStruct.getStatistics( root_son, comm_struct) else: raise ParsingException( "BedSeqCommStruct.getCommStructFromXML : The data contains an unauthorized element : '" + root_son.tag.lower() + "'") comm_struct.baseSpecies = base_species return comm_struct # -------------------------------------------------------------------------------------- # Retrieve the motif statistics @staticmethod def getStatistics( statistics_node, comm_struct): for son_node in statistics_node: if son_node.tag.lower() == BedSeqCommStruct.PARAM_TAG: att_name = CommStruct.getAttribute( son_node, BedSeqCommStruct.PARAM_NAME_ATT) att_value = CommStruct.getAttribute( son_node, BedSeqCommStruct.PARAM_VALUE_ATT) comm_struct.paramStatistics[ att_name] = att_value else: raise ParsingException( "BedSeqCommStruct.getStatistics : The statistics contains an unauthorized element : '" + son_node.tag.lower() + "'") # -------------------------------------------------------------------------------------- # Retrieve the BED sequence information, create a BEDSequence # and store it in the CommStruct @staticmethod def getBEDSequence( node_bedseq, comm_struct): species = CommStruct.getAttribute( node_bedseq, BedSeqCommStruct.BEDSEQ_SPECIES_ATT) chrom = CommStruct.getAttribute( node_bedseq, BedSeqCommStruct.BEDSEQ_CHROM_ATT) start = CommStruct.getAttributeAsint( node_bedseq, BedSeqCommStruct.BEDSEQ_START_ATT) end = CommStruct.getAttributeAsint( node_bedseq, BedSeqCommStruct.BEDSEQ_END_ATT) score = CommStruct.getAttributeAsint( node_bedseq, BedSeqCommStruct.BEDSEQ_SCORE_ATT, False) max = CommStruct.getAttributeAsint( node_bedseq, BedSeqCommStruct.BEDSEQ_MAX_PEAK_ATT, False) id = CommStruct.getAttribute( node_bedseq, BedSeqCommStruct.BEDSEQ_ID_ATT, False) if species != None and chrom != None and start != None and end != None: bed_sequence = BEDSequence( species, chrom, start, end) if score != None: bed_sequence.score = score if max != None: bed_sequence.referenceIndex = max if id != None: bed_sequence.id = id comm_struct.addBEDSequence( bed_sequence) return bed_sequence else: raise ParsingException ( "BedSeqCommStruct.getBEDSequence : Malformed BED Sequence - unable to retrieve sequence information") # ############################# # 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( BedSeqCommStruct.DATA_TAG) self.addCommStructDataToElement( data_element) # Output the statistics data statistics_element = Element( BedSeqCommStruct.STATISTICS_TAG) data_element.append( statistics_element) for param_name in sorted( self.paramStatistics.keys()): paramstats_element = Element( BedSeqCommStruct.PARAM_TAG) statistics_element.append( paramstats_element) paramstats_element.attrib[ BedSeqCommStruct.PARAM_NAME_ATT] = param_name paramstats_element.attrib[ BedSeqCommStruct.PARAM_VALUE_ATT] = str( self.paramStatistics[ param_name]) # output the bedseq data for chrom in self.bedSequencesDict.keys(): for bedseq in self.bedSequencesDict[chrom]: bedseq_element = Element( BedSeqCommStruct.BEDSEQ_TAG) data_element.append( bedseq_element) bedseq_element.attrib[ BedSeqCommStruct.BEDSEQ_SPECIES_ATT] = bedseq.species bedseq_element.attrib[ BedSeqCommStruct.BEDSEQ_CHROM_ATT] = bedseq.chromosom bedseq_element.attrib[ BedSeqCommStruct.BEDSEQ_START_ATT] = str( bedseq.indexStart) bedseq_element.attrib[ BedSeqCommStruct.BEDSEQ_END_ATT] = str( bedseq.indexEnd) bedseq_element.attrib[ BedSeqCommStruct.BEDSEQ_SCORE_ATT] = str( bedseq.score) if bedseq.referenceIndex != 0: bedseq_element.attrib[ BedSeqCommStruct.BEDSEQ_MAX_PEAK_ATT] = str( bedseq.referenceIndex) if bedseq.id != "": bedseq_element.attrib[ BedSeqCommStruct.BEDSEQ_ID_ATT] = str( bedseq.id) return data_element # Definition of the tags and attributes names used in the XML format DATA_TAG = "data" DATA_SPECIES_ATT = "species" DATA_GENE_ATT = "gene" DATA_TF_ATT = "tf" STATISTICS_TAG = "statistics" PARAM_TAG = "param" PARAM_NAME_ATT = "name" PARAM_VALUE_ATT = "value" BEDSEQ_TAG = "bedseq" BEDSEQ_SPECIES_ATT = "species" BEDSEQ_CHROM_ATT = "chr" BEDSEQ_START_ATT = "start" BEDSEQ_END_ATT = "end" BEDSEQ_SCORE_ATT = "score" BEDSEQ_ID_ATT = "id" BEDSEQ_MAX_PEAK_ATT = "max" # eflag: FileType = Python2