import os, shutil, commands from processor.Processor import Processor from processor.io.BedSeqAlignmentStatsCommStruct import BedSeqAlignmentStatsCommStruct from utils.log.Log import Log from utils.MotifUtils import MotifUtils from utils.Constants import Constants from utils.exception.ExecutionException import ExecutionException from manager.ProgressionManager import ProgressionManager from common.Motif import Motif class CompareIdentifiedMotifsProcessor( Processor): MOTIF_LIST_PARAM = "MotifList" MOTIF_DATABASE_FILE_PARAM = "MotifDatabaseFile" MOTIF_DATABASE_FORMAT_PARAM = "MotifDatabaseFormat" # --------------------------------------------------------------------------------------------- def __init__( self): Processor.__init__( self) # --------------------------------------------------------------------------------------------- # Returns the name of the CommStruct class used as input # (None if no input CommStruct) @staticmethod def getInputCommStructClass(): return ( BedSeqAlignmentStatsCommStruct, ) # --------------------------------------------------------------------------------------------- # Returns the name of the CommStruct class used as output # (None if no output CommStruct) @staticmethod def getOutputCommStructClass(): return ( BedSeqAlignmentStatsCommStruct, ) # -------------------------------------------------------------------------------------- # Returns a name that will be used as display name in the user friendly outputs @staticmethod def getDisplayName(): return "Comparison of identified motifs" #------------------------------------------------------------------------------------ # Returns a list of parameters names that are required parameters for the corresponding processor @staticmethod def getRequiredParameters(): return ( CompareIdentifiedMotifsProcessor.MOTIF_DATABASE_FILE_PARAM, CompareIdentifiedMotifsProcessor.MOTIF_DATABASE_FORMAT_PARAM, CompareIdentifiedMotifsProcessor.MOTIF_LIST_PARAM) # --------------------------------------------------------------------------------------------- # Execute the processor def execute( self, input_commstructs): if input_commstructs == None or len( input_commstructs) == 0: raise ExecutionException( "CompareIdentifiedMotifsProcessor.execute : No inputs") input_commstruct = input_commstructs[0] # Retrieve the processor parameters database_file = self.getParameter( CompareIdentifiedMotifsProcessor.MOTIF_DATABASE_FILE_PARAM) database_format = self.getParameter( CompareIdentifiedMotifsProcessor.MOTIF_DATABASE_FORMAT_PARAM) motif_list_line = self.getParameter( CompareIdentifiedMotifsProcessor.MOTIF_LIST_PARAM) motif_name_list = motif_list_line.split() # Retrieve the PWM of the reference motifs reference_motif_list = self.getMotifMatrices( motif_name_list, database_file, database_format) # Retrieve the list of identified motifs identified_motifs = self.getIdentifiedMotifs( input_commstruct) # Compare motifs self.compareMotifs( reference_motif_list, identified_motifs) return input_commstruct # --------------------------------------------------------------------------------------------- # Retrieve the definition of given motifs in given database file def getMotifMatrices( self, motif_name_list, database_file_path, database_format): motif_list = [] for name in motif_name_list: motif_list.append( Motif( 0, 0, name, None)) if database_format == "transfac" or database_format == "tf": MotifUtils.getMotifsPWMFromJasparTF( motif_list, database_file_path) elif database_format == "meme": MotifUtils.getMotifsPWMFromMeme( motif_list, database_file_path) else: raise ExecutionException( "CompareIdentifiedMotifsProcessor.getMotifMatrices : Unknown database format : " + database_format) return motif_list # --------------------------------------------------------------------------------------------- # Retrieve the list of identified motifs avoiding repetition def getIdentifiedMotifs(self, input_commstruct): identified_motifs = {} for bedseq in input_commstruct.bedToMA.keys(): for msa in input_commstruct.bedToMA[ bedseq]: for motif in msa.motifs: if not motif.name in identified_motifs.keys(): identified_motifs[ motif.name] = [] identified_motifs[ motif.name].append( motif) else: exists = False for other_motif in identified_motifs[ motif.name]: if motif.pwm.equals( other_motif.pwm): exists = True if not exists: identified_motifs[ motif.name].append( motif) return identified_motifs # --------------------------------------------------------------------------------------------- # Retrieve the list of identified motifs avoiding repetition def compareMotifs(self, reference_motifs, identified_motifs): # Retrieve required parameters RSAT_PATH = self.component.getParameter( Constants.RSAT_DIR_PARAM) #Prepare outputdir dir_path = os.path.join( self.component.outputDir, self.component.getComponentPrefix()) shutil.rmtree( dir_path, True) os.mkdir( dir_path) old_working_dir = os.getcwd() os.chdir( dir_path) # Establish the progression total_length = len( reference_motifs) * len( identified_motifs.keys()) ProgressionManager.setTaskProgression( "Comparing motifs", self.component, 0.0) progress = 0 for reference_motif in reference_motifs: ref_file_info = self.outputMotifToTransfacFile( reference_motif, dir_path) for identified_motif_name in identified_motifs.keys(): progress += 1 if reference_motif.name != identified_motif_name: count = 0 identified_motif_list = identified_motifs[ identified_motif_name] for identified_motif in identified_motif_list: count += 1 ident_file_info = self.outputMotifToTransfacFile( identified_motif, dir_path) # Compose the compare-matrices command line with all required options cmd = os.path.join( RSAT_PATH , "perl-scripts/compare-matrices") cmd += " -file1 " + ref_file_info[1] + " -format1 tf" cmd += " -file2 " + ident_file_info[1] + " -format2 tf" cmd += " -mode matches" cmd += " -return all" if len( identified_motif_list) > 1: cmd += " -o " + reference_motif.name + "_" + identified_motif_name + "_" + count count += 1 else: cmd += " -o " + reference_motif.name + "_" + identified_motif_name # Execute the command cmd_result = commands.getstatusoutput( cmd) if cmd_result[0] != 0: Log.log( "CompareIdentifiedMotifsProcessor.compareMotifs : status returned is :" + str( cmd_result[0]) + " for command '" + cmd + "'" ) Log.log( "CompareIdentifiedMotifsProcessor.compareMotifs : command output is = \n" + str( cmd_result[1])) continue if progress%10 == 0: ProgressionManager.setTaskProgression( "Identifying motifs", self.component, progress / float( total_length)) # returns to initial working dir os.chdir( old_working_dir) # --------------------------------------------------------------------------------------------- # Output the motif to file and prepare the output directory def outputMotifToTransfacFile(self, motif, dir_path): try: file_path = os.path.join( dir_path, motif.name + ".tf") file = open( file_path, "w") file.write( "AC\t" + motif.name + "\n") file.write( "XX\n") file.write( "ID\t" + motif.name + "\n") file.write( "XX\n") file.write( motif.pwm.convertToTransfac()) file.write( "XX\n") file.write("//\n") file.flush() file.close() return (dir_path, file_path) except IOError, io_exce: raise ExecutionException( "CompareIdentifiedMotifsProcessor.outputMotifListToTransfacFile : Unable to save motifs to tab file : '" + file_path + "'. From:\n\t---> " +str( io_exce))