def createLogos(self, input_commstruct):
db_file_path = []
for index in range(len(self.dbFiles)):
db_file_path.append(os.path.join(self.dbPath, self.dbFiles[index]))
motif_name_list = input_commstruct.motifStatistics.keys()
motif_definition = MotifUtils.getMotifsDefinitionFromTF(
motif_name_list, db_file_path)
logos_path = os.path.join(self.outPath,
FinalOutputProcessor.LOGOS_DIR_NAME)
FileUtils.createDirectory(logos_path)
for motif_name in motif_name_list:
if motif_name in motif_definition.keys():
file_name = motif_name + ".tf"
def_file_path = os.path.join(logos_path, file_name)
def_file = open(def_file_path, "w")
for line in motif_definition[motif_name]:
def_file.write(line)
def_file.flush
def_file.close()
RSATUtils.createLogoFromTF(logos_path, file_name, motif_name)
else:
Log.log(
"FinalOutputProcessor.createLogos : No definition found to create logo for motif : "
+ motif_name)
def copyWorkflowResultFileToFinalOutput(self, stats_param, stats_param_attribute, local_attribute, file_pathes):
if stats_param_attribute in stats_param.keys():
dir_path = os.path.join( self.outPath, stats_param_attribute)
file_path = stats_param[ stats_param_attribute]
FileUtils.createDirectory( dir_path)
FileUtils.copyFile( file_path, dir_path)
final_path = os.path.join( stats_param_attribute, os.path.basename( file_path))
file_pathes[ local_attribute] = final_path
def copyMotifResultFileToFinalOutput(self, motif_stats, motifStatistics_attribute, local_attribute, file_pathes):
if motif_stats.hasAttribute( motifStatistics_attribute):
if not local_attribute in file_pathes.keys():
file_pathes[ local_attribute] = {}
dir_path = os.path.join( self.outPath, motifStatistics_attribute)
file_path = motif_stats.getAttribute( motifStatistics_attribute)
FileUtils.createDirectory( dir_path)
FileUtils.copyFile( file_path, dir_path)
final_path = os.path.join( motifStatistics_attribute, os.path.basename( file_path))
file_pathes[ local_attribute][ motif_stats.motifName] = final_path
def initVariables(self, output_dir):
# Define and create the output directory parameter as the provided output_dir if non null
# or as the RSAT path + base output dir path retrieved from the manager.props
if output_dir != None:
self.config[PFConstants.BASE_OUTPUT_DIR_PARAM] = output_dir
else:
self.config[PFConstants.BASE_OUTPUT_DIR_PARAM] = os.path.join(
self.getParameter(PFConstants.RSAT_DIR_PARAM),
self.getParameter(PFConstants.BASE_OUTPUT_DIR_PARAM))
FileUtils.createDirectory(
self.config[PFConstants.BASE_OUTPUT_DIR_PARAM], 0777)
# Initialize the output directory
self.config[PFConstants.OUTPUT_DIR_PARAM] = os.path.join(
self.getParameter(PFConstants.BASE_OUTPUT_DIR_PARAM),
PFConstants.OUTPUT_DIR_NAME)
FileUtils.createDirectory(self.config[PFConstants.OUTPUT_DIR_PARAM],
0777)
# Define the path to the listening dir according situations
if self.getParameter(PFConstants.SERVER_QUEUE_DIR_PARAM) != None:
queue_path = os.path.join(
self.getParameter(PFConstants.RSAT_DIR_PARAM),
self.getParameter(PFConstants.SERVER_QUEUE_DIR_PARAM))
FileUtils.createDirectory(queue_path, 0777)
self.config[PFConstants.LISTENING_DIR_PARAM] = os.path.join(
queue_path, self.getParameter(PFConstants.LISTENING_DIR_PARAM))
else:
self.config[PFConstants.LISTENING_DIR_PARAM] = os.path.join(
self.getParameter(PFConstants.INSTALL_DIR_PARAM),
self.getParameter(PFConstants.LISTENING_DIR_PARAM))
FileUtils.createDirectory(self.config[PFConstants.LISTENING_DIR_PARAM],
0777)
# Set the path for the job queue directory
if self.getParameter(PFConstants.SERVER_QUEUE_DIR_PARAM) != None:
queue_path = os.path.join(
self.getParameter(PFConstants.RSAT_DIR_PARAM),
self.getParameter(PFConstants.SERVER_QUEUE_DIR_PARAM))
FileUtils.createDirectory(queue_path, 0777)
self.config[PFConstants.QUEUE_DIR_PARAM] = os.path.join(
queue_path, PFConstants.QUEUE_DIR_NAME)
else:
self.config[PFConstants.QUEUE_DIR_PARAM] = os.path.join(
self.getParameter(PFConstants.INSTALL_DIR_PARAM),
PFConstants.QUEUE_DIR_NAME)
FileUtils.createDirectory(self.config[PFConstants.QUEUE_DIR_PARAM])
# Set the RSAT_PATH
RSATUtils.RSAT_PATH = self.getParameter(PFConstants.RSAT_DIR_PARAM)
# Set the path to the jaspar database. This is used to create the motif logo
RSATUtils.RSAT_JASPAR_MOTIF_DATABASE = os.path.join(
RSATUtils.RSAT_PATH,
"public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf"
)
# Set the path to the Jaspar TF details files. Those files contains information on TF like family, class...
MotifUtils.JASPAR_FLAT_DB_PATH = os.path.join(
self.getParameter(PFConstants.INSTALL_DIR_PARAM),
"resources/jaspar/motif")
def execute(self, input_commstructs):
if input_commstructs == None or len(input_commstructs) == 0:
raise ExecutionException(
"FinalOutputProcessor.execute : No inputs")
input_commstruct = input_commstructs[0]
# Get all the pipeline parameters
parameter_dic = self.collectAllParameters()
# Retrieve the processor parameters
self.dbPath = self.getParameter(
FinalOutputProcessor.MOTIF_DATABASE_PATH_PARAM)
# Retrieve the list of motif database files to use and count motifs in the list
database_file_line = self.getParameter(
FinalOutputProcessor.MOTIF_DATABASE_FILE_LIST_PARAM)
if database_file_line != None and not database_file_line.isspace():
file_list = database_file_line.split()
self.dbFiles = []
count_motif_in_db = 0
for file_path in file_list:
current_path = os.path.join(self.dbPath, file_path)
current_size = MotifUtils.getMotifsNumberFromTransfac(
current_path)
if current_size != None:
count_motif_in_db = count_motif_in_db + current_size
self.dbFiles.append(current_path)
parameter_dic[
FinalOutputProcessor.PARAM_MotifDatabaseFileListSize] = str(
count_motif_in_db)
else:
raise ExecutionException(
"FinalOutputProcessor.getMethodParameters : No motif database file specified in parameter '"
+ FinalOutputProcessor.MOTIF_DATABASE_FILE_LIST_PARAM + "'")
# Add the custom motif database files if any
custom_database_file_line = self.getParameter(
FinalOutputProcessor.CUSTOM_MOTIF_DATABASE_FILE_PARAM, False)
if custom_database_file_line != None and not custom_database_file_line.isspace(
):
self.dbFiles.append(custom_database_file_line)
# Retrieve the ID and the name of the reference motif
motif_name = parameter_dic[FinalOutputProcessor.PARAM_ReferenceMotif]
for current_database in self.dbFiles:
motif_ID = MotifUtils.getMotifIDFromTransfac(
motif_name, current_database)
if motif_ID != None:
break
parameter_dic[FinalOutputProcessor.PARAM_ReferenceMotifID] = motif_ID
# Retrieve the Hypergeometric e/p-value threshold
limit_value = self.getParameter(
FinalOutputProcessor.DISPLAY_LIMIT_VALUE, False)
if limit_value == None:
limit_value = 1.0
# Prepare the processor output dir
self.outPath = os.path.join(self.component.outputDir,
self.component.getComponentPrefix())
shutil.rmtree(self.outPath, True)
FileUtils.createDirectory(self.outPath, 0777)
# Copy motif graph and stats files
analysis = self.AnalyseMotifStats(input_commstruct)
# Create motif logos
self.createLogos(input_commstruct)
# Copy input BED and custom motif files
input_bed_file_destination_path = os.path.join(
self.outPath, FinalOutputProcessor.PARAM_BEDFile)
FileUtils.createDirectory(input_bed_file_destination_path)
FileUtils.copyFile(parameter_dic[FinalOutputProcessor.PARAM_BEDFile],
input_bed_file_destination_path)
parameter_dic[FinalOutputProcessor.PARAM_BEDFile] = os.path.join(
input_bed_file_destination_path,
os.path.basename(
parameter_dic[FinalOutputProcessor.PARAM_BEDFile]))
# Copy the custom motif file (if any) to output location and count motifs in this db
if FinalOutputProcessor.PARAM_CustomMotifDatabaseFile in parameter_dic.keys(
) and parameter_dic[
FinalOutputProcessor.PARAM_CustomMotifDatabaseFile] != None:
custom_db_file_destination_path = os.path.join(
self.outPath,
FinalOutputProcessor.PARAM_CustomMotifDatabaseFile)
FileUtils.createDirectory(custom_db_file_destination_path)
FileUtils.copyFile(
parameter_dic[
FinalOutputProcessor.PARAM_CustomMotifDatabaseFile],
custom_db_file_destination_path)
parameter_dic[
FinalOutputProcessor.
PARAM_CustomMotifDatabaseFile] = os.path.join(
custom_db_file_destination_path,
os.path.basename(parameter_dic[
FinalOutputProcessor.PARAM_CustomMotifDatabaseFile]))
count_custom_motif = MotifUtils.getMotifsNumberFromTransfac(
parameter_dic[
FinalOutputProcessor.PARAM_CustomMotifDatabaseFile])
if (count_custom_motif != None):
parameter_dic[FinalOutputProcessor.
PARAM_CustomMotifDatabaseFileSize] = str(
count_custom_motif)
else:
parameter_dic[FinalOutputProcessor.
PARAM_CustomMotifDatabaseFileSize] = "0"
# Output Results
self.outputClassification(input_commstruct, analysis, limit_value,
parameter_dic)
# Copy other information
FileUtils.copyFile(
os.path.join(self.component.outputDir,
Constants.PROGRESSION_XSL_FILE), self.outPath)
FileUtils.copyFile(
os.path.join(self.component.outputDir,
Constants.PROGRESSION_XML_FILE), self.outPath)
# Zip the complete result
self.zipdir(self.outPath)
