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/A5_A3"
#17. Run netMHC-4.0_part2
logger.info("Part13...")
run_netMHC_classI_slurm_part2(
output_path + "/A5_A3_ORF_filtered_peptide_change.tab",
HLAclass_path, HLAtypes_path, output_path + "/A5_A3_fasta_files",
output_path + "/A5_A3_NetMHC-4.0_files",
output_path + "/A5_A3_NetMHC-4.0_neoantigens_type_3.tab",
output_path + "/A5_A3_NetMHC-4.0_neoantigens_type_3_all.tab",
output_path + "/A5_A3_NetMHC-4.0_neoantigens_type_2.tab",
output_path + "/A5_A3_NetMHC-4.0_neoantigens_type_2_all.tab",
output_path + "/A5_A3_NetMHC-4.0_junctions_ORF_neoantigens.tab",
netMHC_path)
#18. Run netMHCpan-4.0_part2
logger.info("Part14...")
run_netMHCpan_classI_slurm_part2(
output_path + "/A5_A3_ORF_filtered_peptide_change.tab",
HLAclass_path, HLAtypes_pan_path,
output_path + "/A5_A3_fasta_files",
output_path + "/A5_A3_NetMHCpan-4.0_files",
output_path + "/A5_A3_NetMHCpan-4.0_neoantigens_type_3.tab",
output_path + "/A5_A3_NetMHCpan-4.0_neoantigens_type_3_all.tab",
output_path + "/A5_A3_NetMHCpan-4.0_neoantigens_type_2.tab",
output_path + "/A5_A3_NetMHCpan-4.0_neoantigens_type_2_all.tab",
output_path + "/A5_A3_NetMHCpan-4.0_junctions_ORF_neoantigens.tab",
netMHC_pan_path)
# 19. Run format_to_SPADA
logger.info("Part18...")
format_to_SPADA(output_path + "/A5_A3_ORF.tab",
output_path + "/A5_A3_ORF_sequences.tab",
output_path + "/A5_A3_Interpro.tab",
output_path + "/A5_A3_IUPred.tab",
output_path + "/A5_A3_SPADA.tab",
output_path + "/A5_A3_SPADA.fasta",
output_path + "/A5_A3_SPADA_features.tab")
logger.info("Done.")
exit(0)
except Exception as error:
logger.error('ERROR: ' + repr(error))
logger.error("Aborting execution")
sys.exit(1)
def main(HLAclass_path, HLAtypes_path, HLAtypes_pan_path, netMHC_path,
netMHC_pan_path, output_path):
try:
logger.info("Starting execution A5_A3_ISOTOPE_part2")
#17. Run netMHC-4.0_part2
logger.info("Part13...")
run_netMHC_classI_slurm_part2(
output_path + "/A5_A3_ORF_filtered_peptide_change.tab",
HLAclass_path, HLAtypes_path, output_path + "/A5_A3_fasta_files",
output_path + "/A5_A3_NetMHC-4.0_files",
output_path + "/A5_A3_NetMHC-4.0_neoantigens_type_gained.tab",
output_path + "/A5_A3_NetMHC-4.0_neoantigens_type_gained_all.tab",
output_path + "/A5_A3_NetMHC-4.0_neoantigens_type_lost.tab",
output_path + "/A5_A3_NetMHC-4.0_neoantigens_type_lost_all.tab",
output_path + "/A5_A3_NetMHC-4.0_junctions_ORF_neoantigens.tab",
netMHC_path)
#18. Run netMHCpan-4.0_part2
logger.info("Part14...")
run_netMHCpan_classI_slurm_part2(
output_path + "/A5_A3_ORF_filtered_peptide_change.tab",
HLAclass_path, HLAtypes_pan_path, output_path +
"/A5_A3_fasta_files", output_path + "/A5_A3_NetMHCpan-4.0_files",
output_path + "/A5_A3_NetMHCpan-4.0_neoantigens_type_gained.tab",
output_path +
"/A5_A3_NetMHCpan-4.0_neoantigens_type_gained_all.tab",
output_path + "/A5_A3_NetMHCpan-4.0_neoantigens_type_lost.tab",
output_path + "/A5_A3_NetMHCpan-4.0_neoantigens_type_lost_all.tab",
output_path + "/A5_A3_NetMHCpan-4.0_junctions_ORF_neoantigens.tab",
netMHC_pan_path)
# # 19. Run format_to_SPADA
# logger.info("Part18...")
# format_to_SPADA(output_path + "/A5_A3_ORF.tab", output_path + "/A5_A3_ORF_sequences.tab",
# output_path + "/A5_A3_Interpro.tab",
# output_path + "/A5_A3_IUPred.tab", output_path + "/A5_A3_SPADA.tab",
# output_path + "/A5_A3_SPADA.fasta", output_path + "/A5_A3_SPADA_features.tab")
logger.info("Done.")
exit(0)
except Exception as error:
logger.error('ERROR: ' + repr(error))
logger.error("Aborting execution")
sys.exit(1)