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")
