def trim(runobj): # def is in utils.py # open_zipped_directory(runobj.run_date, runobj.output_dir) # (re) create the trim status file runobj.trim_status_file_h = open(runobj.trim_status_file_name, "w") idx_keys = get_keys(runobj) # do the trim work mytrim = TrimRun(runobj, idx_keys) # pass True to write out the straight fasta file of all trimmed non-deleted seqs # Remember: this is before chimera checking # trim_codes should alwas be a tuple with 3 elements! if runobj.vamps_user_upload: trim_codes = mytrim.trimrun_vamps(True) else: if runobj.platform == 'illumina': trim_codes = mytrim.filter_illumina() # trim_codes = mytrim.trim_illumina(file_list = trim_codes[2]) elif runobj.platform == '454': trim_codes = mytrim.trimrun_454(True) elif runobj.platform == 'ion-torrent': trim_codes = mytrim.trimrun_ion_torrent(True) else: trim_codes = ('ERROR', 'No Platform Found', '') trim_results_dict = {} if trim_codes[0] == 'SUCCESS': # setup to write the status new_lane_keys = trim_codes[2] trimmed_seq_count = trim_codes[1] if trimmed_seq_count == 0 or trimmed_seq_count == '0': trim_results_dict['status'] = "ERROR" logger.debug("Trimming finished: ERROR: no seqs passed trim") else: trim_results_dict['status'] = "success" logger.debug("Trimming finished successfully") trim_results_dict['new_lane_keys'] = new_lane_keys trim_results_dict['trimmed_seq_count'] = trimmed_seq_count # write the data files mytrim.write_data_files(new_lane_keys) runobj.trim_status_file_h.write(json.dumps(trim_results_dict) + "\n") runobj.trim_status_file_h.close() runobj.run_status_file_h.write(json.dumps(trim_results_dict) + "\n") runobj.run_status_file_h.close() else: logger.debug("Trimming finished ERROR") trim_results_dict['status'] = "ERROR" trim_results_dict['code1'] = trim_codes[1] trim_results_dict['code2'] = trim_codes[2] runobj.trim_status_file_h.write(json.dumps(trim_results_dict) + "\n") runobj.trim_status_file_h.close() runobj.run_status_file_h.write(json.dumps(trim_results_dict) + "\n") runobj.run_status_file_h.close() sys.exit("Trim Error")
def trim(runobj): # def is in utils.py #open_zipped_directory(runobj.run_date, runobj.output_dir) # (re) create the trim status file runobj.trim_status_file_h = open(runobj.trim_status_file_name, "w") idx_keys = get_keys(runobj) # do the trim work mytrim = TrimRun(runobj, idx_keys) # pass True to write out the straight fasta file of all trimmed non-deleted seqs # Remember: this is before chimera checking # trim_codes should alwas be a tuple with 3 elements! if runobj.vamps_user_upload: trim_codes = mytrim.trimrun_vamps(True) else: if runobj.platform == 'illumina': trim_codes = mytrim.filter_illumina() # trim_codes = mytrim.trim_illumina(file_list = trim_codes[2]) elif runobj.platform == '454': trim_codes = mytrim.trimrun_454(True) elif runobj.platform == 'ion-torrent': trim_codes = mytrim.trimrun_ion_torrent(True) else: trim_codes = ('ERROR','No Platform Found','') trim_results_dict = {} if trim_codes[0] == 'SUCCESS': # setup to write the status new_lane_keys = trim_codes[2] trimmed_seq_count = trim_codes[1] if trimmed_seq_count == 0 or trimmed_seq_count == '0': trim_results_dict['status'] = "ERROR" logger.debug("Trimming finished: ERROR: no seqs passed trim") else: trim_results_dict['status'] = "success" logger.debug("Trimming finished successfully") trim_results_dict['new_lane_keys'] = new_lane_keys trim_results_dict['trimmed_seq_count'] = trimmed_seq_count # write the data files mytrim.write_data_files(new_lane_keys) runobj.trim_status_file_h.write(json.dumps(trim_results_dict)+"\n") runobj.trim_status_file_h.close() runobj.run_status_file_h.write(json.dumps(trim_results_dict)+"\n") runobj.run_status_file_h.close() else: logger.debug("Trimming finished ERROR") trim_results_dict['status'] = "ERROR" trim_results_dict['code1'] = trim_codes[1] trim_results_dict['code2'] = trim_codes[2] runobj.trim_status_file_h.write(json.dumps(trim_results_dict)+"\n") runobj.trim_status_file_h.close() runobj.run_status_file_h.write(json.dumps(trim_results_dict)+"\n") runobj.run_status_file_h.close() sys.exit("Trim Error")
def trim(runobj): # def is in utils.py # open_zipped_directory(runobj.run_date, runobj.output_dir) # (re) create the trim status file runobj.trim_status_file_h = open(runobj.trim_status_file_name, "w") # do the trim work mytrim = TrimRun(runobj) # pass True to write out the straight fasta file of all trimmed non-deleted seqs # Remember: this is before chimera checking if runobj.platform == "illumina": trim_codes = mytrim.trimrun_illumina(True) elif runobj.platform == "454": trim_codes = mytrim.trimrun_454(True) elif runobj.platform == "ion-torrent": trim_codes = mytrim.trimrun_ion_torrent(True) else: trim_codes = ["ERROR", "No Platform Found"] trim_results_dict = {} if trim_codes[0] == "SUCCESS": # setup to write the status new_lane_keys = trim_codes[2] trim_results_dict["status"] = "success" trim_results_dict["new_lane_keys"] = new_lane_keys logger.debug("Trimming finished successfully") # write the data files mytrim.write_data_files(new_lane_keys) runobj.trim_status_file_h.write(json.dumps(trim_results_dict)) runobj.trim_status_file_h.close() runobj.run_status_file_h.write(json.dumps(trim_results_dict) + "\n") runobj.run_status_file_h.close() else: logger.debug("Trimming finished ERROR") trim_results_dict["status"] = "error" trim_results_dict["code1"] = trim_codes[1] trim_results_dict["code2"] = trim_codes[2] runobj.trim_status_file_h.write(json.dumps(trim_results_dict)) runobj.trim_status_file_h.close() runobj.run_status_file_h.write(json.dumps(trim_results_dict) + "\n") runobj.run_status_file_h.close() sys.exit("Trim Error")