exonizations_ISOTOPE_part3.py

"""
@authors: Juan L. Trincado
@email: juanluis.trincado@upf.edu
exonizations_ISOTOPE.py: get significat exonizations
"""

from lib.Exonization.extract_exonized_junctions import *
from lib.Exonization.get_reads_exonizations import *
from lib.Exonization.overlap_with_repeats import *
from lib.Exonization.get_significant_exonizations import *
from lib.Exonization.generate_random_intronic_positions import *
from lib.Exonization.get_coverageBed import *
from lib.Exonization.get_coverageBed_adapter import *
from lib.Exonization.check_mutations_nearby import *
from lib.Exonization.select_fasta_candidates import *
from lib.Exonization.filter_exonizations import *
from lib.Exonization.filter_exonizations_CHESS import *
from lib.Exonization.get_peptide_sequence import *
from lib.Exonization.run_netMHC_classI_slurm_part1 import *
from lib.Exonization.run_netMHCpan_classI_slurm_part1 import *
from lib.Exonization.run_netMHC_classI_slurm_part2 import *
from lib.Exonization.run_netMHCpan_classI_slurm_part2 import *
from lib.Exonization.format_to_SPADA import *

# create logger
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)

# create console handler and set level to info
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)

# create formatter
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')

# add formatter to ch
ch.setFormatter(formatter)

# add ch to logger
logger.addHandler(ch)

description = \
"Description: Get exonization events\n\n"

parser = ArgumentParser(description=description, formatter_class=RawTextHelpFormatter,
                        add_help=True)
parser.add_argument("-HLAclass", "--HLAclass", required=True, help = "HLA genotype of the samples")
parser.add_argument("-HLAtypes", "--HLAtypes", required=True, help = "HLA alelles recognized by NetMHC")
parser.add_argument("-HLAtypespan", "--HLAtypespan", required=True, help = "HLA alelles recognized by NetMHCpan")
parser.add_argument("-netMHC", "--netMHC", required=True, help = "netMHC path")
parser.add_argument("-netMHCpan", "--netMHCpan", required=True, help = "netMHCpan path")
parser.add_argument("-o", "--output", required=True, help = "Output path")

def main(HLAclass_path, HLAtypes_path, HLAtypes_pan_path, netMHC_path, netMHC_pan_path, output_path):

    try:

        logger.info("Starting execution exonizations_ISOTOPE_part3")

        #17. Run netMHC-4.0_part2
        logger.info("Part16...")
        output_path_aux19 = output_path + "/all_exonizations_filtered_peptide_change.tab"
        run_netMHC_classI_slurm_part2(output_path_aux19, HLAclass_path,
                                      HLAtypes_path,
                                      output_path + "/exonization_fasta_files",
                                      output_path + "/exonizations_NetMHC-4.0_files",
                                      output_path + "/exonizations_NetMHC-4.0_neoantigens_type_gained.tab",
                                      output_path + "/exonizations_NetMHC-4.0_neoantigens_type_gained_all.tab",
                                      output_path + "/exonizations_NetMHC-4.0_neoantigens_type_lost.tab",
                                      output_path + "/exonizations_NetMHC-4.0_neoantigens_type_lost_all.tab",
                                      output_path + "/exonizations_NetMHC-4.0_junctions_ORF_neoantigens.tab",
                                      netMHC_path)

        #18. Run netMHCpan-4.0_part2
        logger.info("Part17...")
        run_netMHCpan_classI_slurm_part2(output_path_aux19,
                                         HLAclass_path, HLAtypes_pan_path,
                                         output_path + "/exonization_fasta_files",
                                         output_path + "/exonizations_NetMHCpan-4.0_files",
                                         output_path + "/exonizations_NetMHCpan-4.0_neoantigens_type_gained.tab",
                                         output_path + "/exonizations_NetMHCpan-4.0_neoantigens_type_gained_all.tab",
                                         output_path + "/exonizations_NetMHCpan-4.0_neoantigens_type_lost.tab",
                                         output_path + "/exonizations_NetMHCpan-4.0_neoantigens_type_lost_all.tab",
                                         output_path + "/exonizations_NetMHCpan-4.0_junctions_ORF_neoantigens.tab",
                                         netMHC_pan_path)

        # 19. Run format_to_SPADA
        #logger.info("Part18...")
        #format_to_SPADA(output_path + "/all_exonizations_ORF.tab", output_path + "/all_exonizations_ORF_sequences.tab",
        #                output_path + "/all_exonizations_Interpro.tab",
        #                output_path + "/all_exonizations_IUPred.tab", output_path + "/all_exonizations_SPADA.tab",
        #                output_path + "/all_exonizations_SPADA.fasta", output_path + "/all_exonizations_SPADA_features.tab")
        logger.info("Done.")

        exit(0)

    except Exception as error:
        logger.error('ERROR: ' + repr(error))
        logger.error("Aborting execution")
        sys.exit(1)


if __name__ == '__main__':
    args = parser.parse_args()
    main(args.HLAclass,args.HLAtypes,args.HLAtypespan,args.netMHC,args.netMHCpan,args.output)