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Neoskipping_ePydoor_part1.py
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Neoskipping_ePydoor_part1.py
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"""
@authors: Juan L. Trincado
@email: juanluis.trincado@upf.edu
Neoskipping_ePydoor.py: get significant neoskipping events
"""
import os
from lib.Neoskipping.extract_neoskipping_junctions import *
from lib.Neoskipping.extract_neoskipping_junctions_Intropolis import *
from lib.Neoskipping.check_mutations_nearby import *
from lib.Neoskipping.filter_neoskipping import *
from lib.Neoskipping.filter_neoskipping_CHESS import *
from lib.Neoskipping.get_peptide_sequence import *
from lib.Neoskipping.select_fasta_candidates import *
from lib.Neoskipping.run_netMHC_classI_slurm_part1 import *
from lib.Neoskipping.run_netMHCpan_classI_slurm_part1 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")
readcounts_path = "/projects_rg/SCLC_cohorts/Smart/STAR/readCounts.tab"
transcript_expression_path = "/projects_rg/SCLC_cohorts/Smart/Salmon/iso_tpm.txt"
gtf_path = "/projects_rg/SCLC_cohorts/annotation/Homo_sapiens.GRCh37.75.formatted.only_protein_coding.gtf"
codons_gtf_path = "/projects_rg/SCLC_cohorts/annotation/Homo_sapiens.GRCh37.75.codons.gtf"
conversion_names = "/projects_rg/SCLC_cohorts/tables/Ensembl_gene_conversion.txt"
max_length = 500
threshold = 5
threshold2 = 10
repeats_path = "/projects_rg/SCLC_cohorts/cis_analysis/tables/hg19_repeats.bed"
mutations_path = "/projects_rg/babita/TCGA/mutation/mut_pipeline/juanlu_sclc/src_files/SCLC_mutations_sorted.bed.mut.out"
CHESS_SE_path = "/projects_rg/SCLC_cohorts/annotation/chess2.0_assembly_hg19_CrossMap.events_SE_strict.ioe"
tumor_specific = True
mosea = "/genomics/users/juanluis/Software/MoSEA-master/mosea.py"
fasta_genome = "/genomics/users/juanluis/Software/MoSEA-master/test_files/genome/hg19.fa"
orfs_scripts = "/genomics/users/juanluis/comprna/MxFinder/extract_orfs.py"
interpro = "/soft/EB_repo/bio/sequence/programs/noarch/interproscan/5.33-72.0/interproscan.sh"
IUPred = "/projects_rg/SCLC_cohorts/soft/IUPred2A"
HLAclass_path = "/projects_rg/SCLC_cohorts/Smart/PHLAT/PHLAT_summary_ClassI.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"
remove_temp_files = True
flag_Rudin = False
output_path = "/users/genomics/juanluis/SCLC_cohorts/Smart/epydoor/neoskipping"
# ONLY FOR MARVIN
#python2 = "Python/2.7.14-foss-2017b"
# ONLY FOR HYDRA
python2 = "Python/2.7.11"
# 1. Identify the junctions that could generate an alternative splice site
logger.info("Part1...")
dir_path = os.path.dirname(os.path.realpath(__file__))
output_path_aux = output_path + "/new_Neoskipping_junctions.tab"
extract_neoskipping_junctions(readcounts_path, gtf_path, threshold, output_path_aux)
# 2. Get the tumor specific neoskipping events
if (tumor_specific):
logger.info("Part2...")
# Get also the significant neoskipping from Rudin and Intropolis
output_Rudin_path_aux = output_path + "/new_Neoskipping_junctions_Rudin_normal_reads.tab"
readCounts_Rudin_path = "/projects_rg/SCLC_cohorts/Rudin/STAR/v1/normal_readCounts.tab"
extract_neoskipping_junctions(readCounts_Rudin_path, gtf_path, threshold, output_Rudin_path_aux)
output_Intropolis_path_aux = output_path + "/new_Neoskipping_junctions_Rudin_normal_reads.tab"
readCounts_Intropolis_path = "/projects_rg/Annotation/Intropolis/intropolis.v1.hg19.filtered.tsv"
extract_neoskipping_junctions_Intropolis(readcounts_path, readCounts_Intropolis_path, gtf_path, threshold,
output_Intropolis_path_aux)
filter_neoskipping(output_path_aux, output_Rudin_path_aux, output_Intropolis_path_aux,
output_path + "/new_Neoskipping_junctions_filtered.tab", flag_Rudin)
filter_neoskipping_CHESS(output_path + "/new_Neoskipping_junctions_filtered.tab", CHESS_SE_path,
output_path + "/new_Neoskipping_junctions_filtered2.tab")
output_path2 = output_path + "/new_Neoskipping_junctions_filtered2.tab"
else:
output_path2 = output_path + "/new_Neoskipping_junctions.tab"
# 3. Get the mutations nearby
logger.info("Part3...")
check_mutations_nearby(output_path2, mutations_path, 200, output_path + "/new_Neoskipping_junctions_mut.tab")
# 4. Get the gene ids
logger.info("Part4...")
command1 = "module load R; Rscript " + dir_path + "/lib/Neoskipping/get_Gene_ids_BiomaRt.R " + output_path + "/new_Neoskipping_junctions_mut.tab " + output_path + "/new_Neoskipping_junctions_mut2.tab"
os.system(command1)
# 5. Get the peptide sequences
logger.info("Part5...")
output_path_peptide = output_path + "/neoskipping_peptide_sequence.fa"
output_path_dna = output_path + "/neoskipping_fasta_sequence.fa"
output_path_aux14 = output_path + "/all_neoskipping_ORF.tab"
output_path_aux15 = output_path + "/all_neoskipping_ORF_sequences.tab"
output_path_aux16 = output_path + "/all_neoskipping_Interpro.tab"
output_path_aux17 = output_path + "/all_neoskipping_IUPred.tab"
get_peptide_sequence(output_path + "/new_Neoskipping_junctions_mut2.tab", transcript_expression_path, gtf_path,
codons_gtf_path,
output_path_peptide, output_path_dna, output_path_aux14,
output_path_aux15, output_path_aux16, output_path_aux17, mosea, fasta_genome, orfs_scripts,
interpro, IUPred, remove_temp_files, python2)
# 6. Filter the cases for running netMHC
logger.info("Part6...")
output_path_aux18 = output_path + "/all_neoskipping_filtered.tab"
command2 = "module load R; Rscript " + dir_path + "/lib/Neoskipping/filter_results.R " + output_path_aux14 + " " + output_path_aux18 + " " + output_path + "/all_neoskipping_filtered_peptide_change.tab"
os.system(command2)
# 7. Select the fasta candidates for being run to the epitope analysis
logger.info("Part7...")
output_path_aux20 = output_path + "/neoskipping_peptide_sequence.fa"
output_path_aux21 = output_path + "/neoskipping_peptide_sequence_filtered.fa"
# Create the folder, if it doesn't exists
if not os.path.exists(output_path + "/neoskipping_fasta_files"):
os.makedirs(output_path + "/neoskipping_fasta_files")
select_fasta_candidates(output_path + "/all_neoskipping_filtered_peptide_change.tab", output_path_aux20,
output_path_aux21, output_path + "/neoskipping_fasta_files")
# 8. Run netMHC-4.0_part1
logger.info("Part8...")
if not os.path.exists(output_path + "/neoskipping_NetMHC-4.0_files"):
os.makedirs(output_path + "/neoskipping_NetMHC-4.0_files")
run_netMHC_classI_slurm_part1(output_path + "/all_neoskipping_filtered_peptide_change.tab", HLAclass_path, HLAtypes_path,
output_path + "/neoskipping_fasta_files",output_path + "/neoskipping_NetMHC-4.0_files", output_path + "/neoskipping_NetMHC-4.0_neoantigens_type_3.tab",
output_path + "/neoskipping_NetMHC-4.0_neoantigens_type_3_all.tab", output_path + "/neoskipping_NetMHC-4.0_neoantigens_type_2.tab",
output_path + "/neoskipping_NetMHC-4.0_neoantigens_type_2_all.tab", output_path + "/neoskipping_NetMHC-4.0_junctions_ORF_neoantigens.tab",
netMHC_path)
# 9. Run netMHCpan-4.0_part1
logger.info("Part9...")
if not os.path.exists(output_path + "/neoskipping_NetMHCpan-4.0_files"):
os.makedirs(output_path + "/neoskipping_NetMHCpan-4.0_files")
run_netMHCpan_classI_slurm_part1(output_path + "/all_neoskipping_filtered_peptide_change.tab", HLAclass_path, HLAtypes_pan_path,
output_path + "/neoskipping_fasta_files",output_path + "/neoskipping_NetMHCpan-4.0_files", output_path + "/neoskipping_NetMHCpan-4.0_neoantigens_type_3.tab",
output_path + "/neoskipping_NetMHCpan-4.0_neoantigens_type_3_all.tab", output_path + "/neoskipping_NetMHCpan-4.0_neoantigens_type_2.tab",
output_path + "/neoskipping_NetMHCpan-4.0_neoantigens_type_2_all.tab", output_path + "/neoskipping_NetMHCpan-4.0_junctions_ORF_neoantigens.tab",
netMHC_pan_path)
logger.info("Wait until all jobs have finished. Then, go on with part2")
exit(0)
except Exception as error:
logger.error('ERROR: ' + repr(error))
logger.error("Aborting execution")
sys.exit(1)
if __name__ == '__main__':
main()