def runProgram(Species,Array_type,mir_source,stringency,Force): global species; global array_type; global force process_microRNA_predictions = 'yes' species = Species; array_type = Array_type; force = Force import_dir = '/AltDatabase/'+species+'/'+array_type filedir = import_dir[1:]+'/' dir_list = read_directory(import_dir) #send a sub_directory to a function to identify all files in a directory probeset_seq_file='' for input_file in dir_list: #loop through each file in the directory to results if 'critical-exon-seq_updated' in input_file: probeset_seq_file = filedir+input_file elif 'critical-exon-seq' in input_file: probeset_seq_file2 = filedir+input_file if len(probeset_seq_file)==0: probeset_seq_file=probeset_seq_file2 data_type = 'critical-exons' try: splice_event_db = getParametersAndExecute(probeset_seq_file,array_type,species,data_type) except UnboundLocalError: probeset_seq_file = 'AltDatabase/'+species+'/'+array_type+'/'+array_type+'_critical-exon-seq_updated.txt' update.downloadCurrentVersion(probeset_seq_file,array_type,'txt') splice_event_db = getParametersAndExecute(probeset_seq_file,array_type,species,data_type) if process_microRNA_predictions == 'yes': print 'stringency:',stringency try: ensembl_mirna_db = ExonSeqModule.importmiRNATargetPredictionsAdvanced(species) ExonSeqModule.alignmiRNAData(array_type,mir_source,species,stringency,ensembl_mirna_db,splice_event_db) except Exception: pass
def runProgram(Species, Array_type, mir_source, stringency, Force): global species global array_type global force process_microRNA_predictions = 'yes' species = Species array_type = Array_type force = Force import_dir = '/AltDatabase/' + species + '/' + array_type filedir = import_dir[1:] + '/' dir_list = read_directory( import_dir ) #send a sub_directory to a function to identify all files in a directory probeset_seq_file = '' for input_file in dir_list: #loop through each file in the directory to results if 'critical-exon-seq_updated' in input_file: probeset_seq_file = filedir + input_file elif 'critical-exon-seq' in input_file: probeset_seq_file2 = filedir + input_file if len(probeset_seq_file) == 0: probeset_seq_file = probeset_seq_file2 data_type = 'critical-exons' try: splice_event_db = getParametersAndExecute(probeset_seq_file, array_type, species, data_type) except UnboundLocalError: probeset_seq_file = 'AltDatabase/' + species + '/' + array_type + '/' + array_type + '_critical-exon-seq_updated.txt' update.downloadCurrentVersion(probeset_seq_file, array_type, 'txt') splice_event_db = getParametersAndExecute(probeset_seq_file, array_type, species, data_type) if process_microRNA_predictions == 'yes': print 'stringency:', stringency try: ensembl_mirna_db = ExonSeqModule.importmiRNATargetPredictionsAdvanced( species) ExonSeqModule.alignmiRNAData(array_type, mir_source, species, stringency, ensembl_mirna_db, splice_event_db) except Exception: pass