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IR_ePydoor_part3.py
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IR_ePydoor_part3.py
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"""
@authors: Juan L. Trincado
@email: juanluis.trincado@upf.edu
IR_ePydoor.py: get significat exonizations
"""
import os
from lib.IR.extract_significant_IR import *
from lib.IR.IR_associate_gene_ids import *
from lib.IR.filter_IR import *
from lib.IR.filter_IR_CHESS import *
from lib.IR.generate_random_intronic_positions import *
from lib.IR.get_coverageBed import *
from lib.IR.get_coverageBed_adapter import *
from lib.IR.get_peptide_sequence_RI import *
from lib.IR.select_fasta_candidates import *
from lib.IR.run_netMHC_classI_slurm_part1 import *
from lib.IR.run_netMHC_classI_slurm_part2 import *
from lib.IR.run_netMHCpan_classI_slurm_part1 import *
from lib.IR.run_netMHCpan_classI_slurm_part2 import *
from lib.IR.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)
def main():
try:
logger.info("Starting execution")
HLAclass_path = "/projects_rg/SCLC_cohorts/tables/PHLAT_summary_ClassI_all_samples.out"
HLAtypes_path = "/projects_rg/SCLC_cohorts/tables/NetMHC-4.0_HLA_types_accepted.tab"
HLAtypes_pan_path = "/projects_rg/SCLC_cohorts/tables/NetMHCpan-4.0_HLA_types_accepted.tab"
netMHC_path = "/projects_rg/SCLC_cohorts/soft/netMHC-4.0/netMHC"
netMHC_pan_path = "/projects_rg/SCLC_cohorts/soft/netMHCpan-4.0/netMHCpan"
output_path = "/users/genomics/juanluis/SCLC_cohorts/SCLC/epydoor/IR"
#13. Run netMHC-4.0_part2
logger.info("Part13...")
run_netMHC_classI_slurm_part2(output_path + "/IR_ORF_filtered_peptide_change.tab", HLAclass_path, HLAtypes_path,
output_path + "/IR_fasta_files",output_path + "/IR_NetMHC-4.0_files", output_path + "/IR_NetMHC-4.0_neoantigens_type_3.tab",
output_path + "/IR_NetMHC-4.0_neoantigens_type_3_all.tab", output_path + "/IR_NetMHC-4.0_neoantigens_type_2.tab",
output_path + "/IR_NetMHC-4.0_neoantigens_type_2_all.tab", output_path + "/IR_NetMHC-4.0_junctions_ORF_neoantigens.tab",
netMHC_path)
#14. Run netMHCpan-4.0_part2
logger.info("Part14...")
run_netMHCpan_classI_slurm_part2(output_path + "/IR_ORF_filtered_peptide_change.tab", HLAclass_path, HLAtypes_pan_path,
output_path + "/IR_fasta_files",output_path + "/IR_NetMHCpan-4.0_files", output_path + "/IR_NetMHCpan-4.0_neoantigens_type_3.tab",
output_path + "/IR_NetMHCpan-4.0_neoantigens_type_3_all.tab", output_path + "/IR_NetMHCpan-4.0_neoantigens_type_2.tab",
output_path + "/IR_NetMHCpan-4.0_neoantigens_type_2_all.tab", output_path + "/IR_NetMHCpan-4.0_junctions_ORF_neoantigens.tab",
netMHC_pan_path)
# 15. Run format_to_SPADA
logger.info("Part15...")
format_to_SPADA(output_path + "/IR_ORF.tab", output_path + "/IR_ORF_sequences.tab", output_path + "/IR_ORF_Interpro.tab",
output_path + "/IR_ORF_IUPred.tab", output_path + "/IR_SPADA.tab", output_path + "/IR_SPADA.fasta",
output_path + "/IR_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__':
main()