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IR_ePydoor_part2.py
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IR_ePydoor_part2.py
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"""
@authors: Juan L. Trincado
@email: [email protected]
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 *
# 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 IR_epydoor_part2")
transcript_expression_path = "/projects_rg/SCLC_cohorts/George/tables/iso_tpm_George_Peifer_Rudin_Yokota.tab"
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"
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/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"
remove_temp_files = True
tumor_specific = True
name_user = "juanluis"
output_path = "/users/genomics/juanluis/SCLC_cohorts/SCLC/epydoor/IR"
# ONLY FOR MARVIN
#python2 = "Python/2.7.14-foss-2017b"
# ONLY FOR HYDRA
python2 = "Python/2.7.11"
# 6. Create the folder, if it doesn't exists
logger.info("Part6...")
if not os.path.exists(output_path + "/coverageBed"):
os.makedirs(output_path + "/coverageBed")
# Move all the coverage.sorted files to the created directory
command1="mv "+output_path+"/*coverage_sorted "+output_path + "/coverageBed/"
os.system(command1)
# 7.1. Get the coverage for each exonization
logger.info("Part7.1...")
if(tumor_specific):
output_path_filtered2 = output_path + "/IR_expressed_genes_filtered2.tab"
else:
output_path_filtered2 = output_path + "/IR_expressed_genes.tab"
get_coverageBed_adapter(output_path_filtered2, output_path + "/random_introns.bed",output_path + "/coverageBed", output_path, name_user)
# 7.2. Assemble all pieces into one single file
logger.info("Part7.2...")
command2="awk 'FNR==1 && NR!=1{next;}{print}' "+output_path+"/get_coverageBed_*.tab > "+output_path+"/IR_coverage.tab"
os.system(command2)
# 7.3. Get the introns with a significant p_value
logger.info("Part7.3...")
command3="head -n1 "+output_path+"/IR_coverage.tab > "+output_path+"/IR_significant_introns.tab; " \
"awk '{ if ($7 <= 0.05) print }' "+output_path+"/IR_coverage.tab >> "+output_path+"/IR_significant_introns.tab"
os.system(command3)
# 8. Get the peptide sequence associated
logger.info("Part8...")
get_peptide_sequence(output_path + "/IR_significant_introns.tab", transcript_expression_path, gtf_path, codons_gtf_path,
output_path + "/IR_peptide_sequence.fa", output_path + "/IR_fasta_sequence.fa",
output_path + "/IR_ORF.tab", output_path + "/IR_ORF_sequences.tab", output_path + "/IR_Interpro.tab",
output_path + "/IR_IUPred.tab", mosea, fasta_genome, orfs_scripts, interpro,IUPred, remove_temp_files,
python2)
# 9. Filter the significant results
logger.info("Part9...")
dir_path = os.path.dirname(os.path.realpath(__file__))
command4="module load R; Rscript "+dir_path+"/lib/IR/filter_results.R "+output_path + "/IR_ORF.tab"+" "+ \
output_path + "/IR_ORF_filtered.tab" +" "+output_path + "/IR_ORF_filtered_peptide_change.tab"
os.system(command4)
# 10. Select the fasta candidates for being run to the epitope analysis
logger.info("Part10...")
#Create the folder, if it doesn't exists
if not os.path.exists(output_path + "/IR_fasta_files"):
os.makedirs(output_path + "/IR_fasta_files")
select_fasta_candidates(output_path + "/IR_ORF_filtered_peptide_change.tab", output_path + "/IR_peptide_sequence.fa", output_path + "/IR_peptide_sequence_filtered.fa", output_path + "/IR_fasta_files")
#11. Run netMHC-4.0_part1
logger.info("Part11...")
if not os.path.exists(output_path + "/IR_NetMHC-4.0_files"):
os.makedirs(output_path + "/IR_NetMHC-4.0_files")
run_netMHC_classI_slurm_part1(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)
#12. Run netMHCpan-4.0_part1
logger.info("Part12...")
if not os.path.exists(output_path + "/IR_NetMHCpan-4.0_files"):
os.makedirs(output_path + "/IR_NetMHCpan-4.0_files")
run_netMHCpan_classI_slurm_part1(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)
logger.info("Wait until all jobs have finished. Then, go on with part3")
exit(0)
except Exception as error:
logger.error('ERROR: ' + repr(error))
logger.error("Aborting execution")
sys.exit(1)
if __name__ == '__main__':
main()