def main(readcounts_path, gtf_path, genome_path, transcript_expression_path,
HLAclass_path, HLAtypes_path, HLAtypes_pan_path, netMHC_path,
netMHC_pan_path, mosea_path, orfs_scripts, output_path, repeats_path,
threshold, max_length, tumor_specific, control_path, Intropolis_path,
mutations_path, CHESS_SE_path, flag_Rudin, remove_temp_files,
name_user):
try:
logger.info("Starting execution exonizations_ISOTOPE_part2")
# 6. Create the folder, if it doesn't exists
logger.info("Part6...")
logger.info("Moving all coverageBed files...")
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...")
dir_path = os.path.dirname(os.path.realpath(__file__))
get_coverageBed_adapter(output_path + "/exonizations_by_sample.tab",
output_path + "/random_exonizations.bed",
output_path + "/coverageBed", output_path,
name_user)
# 7.2. Assemble all pieces into one single file
command2 = "awk 'FNR==1 && NR!=1{next;}{print}' " + output_path + "/get_coverageBed_*.tab > " + output_path + "/exonizations_by_sample_coverage.tab"
os.system(command2)
# 8. Check if in the exonizations there are mutations nearby
logger.info("Part8...")
check_mutations_nearby(
output_path + "/exonizations_by_sample_coverage.tab",
mutations_path, 200,
output_path + "/exonizations_by_sample_coverage_mut.tab")
# 9. Separate between mutated and non-mutated cases
logger.info("Part9...")
command2="Rscript "+dir_path+"/lib/Exonization/separate_mutated_cases.R "+output_path + \
"/exonizations_by_sample_coverage_mut.tab"+" "+output_path + "/mutated_exonizations.tab"+" "+output_path + "/non_mutated_exonizations.tab"
# print(command2)
os.system(command2)
# 10. Get the tumor specific events
logger.info("Part10...")
if (tumor_specific):
logger.info("Get the tumor specific events...")
# Get the significant exonizations from Intropolis (control)
logger.info("Intropolis...")
output_path_aux = output_path + "/new_exonized_junctions.tab"
output_Intropolis_path_aux2 = output_path + "/new_exonized_junctions_Intropolis_reads.tab"
get_reads_exonizations(output_path_aux, Intropolis_path,
output_Intropolis_path_aux2, True)
output_Intropolis_path_aux3 = output_path + "/new_exonized_junctions_Intropolis_reads_repeatitions.tab"
overlap_with_repeats(output_Intropolis_path_aux2, repeats_path,
output_Intropolis_path_aux3)
output_Intropolis_path_aux4 = output_path + "/exonizations_by_sample_Intropolis.tab"
get_significant_exonizations(output_Intropolis_path_aux3,
threshold,
output_Intropolis_path_aux4)
if (control_path != "Missing"):
# Get the significant exonizations from normal samples
logger.info("Additional controls...")
extract_exonized_junctions(
control_path, gtf_path, genome_path, max_length,
output_path + "/exonized_junctions_control.tab",
mosea_path)
get_reads_exonizations(
output_path + "/exonized_junctions_control.tab",
control_path,
output_path + "/exonized_junctions_control_reads.tab",
False)
get_significant_exonizations(
output_path + "/exonized_junctions_control_reads.tab",
threshold,
output_path + "/exonizations_by_sample_control.tab")
#Filter exonizations
logger.info("Filtering events...")
filter_exonizations(
output_path + "/non_mutated_exonizations.tab",
output_path + "/exonizations_by_sample_control.tab",
output_path + "/exonizations_by_sample_Intropolis.tab",
output_path + "/non_mutated_exonizations_filtered.tab",
control_path)
filter_exonizations_CHESS(
output_path + "/non_mutated_exonizations_filtered.tab",
CHESS_SE_path,
output_path + "/non_mutated_exonizations_filtered2.tab")
else:
#Filter exonizations
logger.info("Filtering events...")
filter_exonizations(
output_path + "/non_mutated_exonizations.tab", "Missing",
output_path + "/exonizations_by_sample_Intropolis.tab",
output_path + "/non_mutated_exonizations_filtered.tab",
control_path)
filter_exonizations_CHESS(
output_path + "/non_mutated_exonizations_filtered.tab",
CHESS_SE_path,
output_path + "/non_mutated_exonizations_filtered2.tab")
# 11. Join the mutated and non_mutated cases
output_path_aux13 = output_path + "/all_exonizations.tab"
command3 = "cat " + output_path + "/mutated_exonizations.tab" + " > " + output_path_aux13 + ";tail -n+2 " + output_path + "/non_mutated_exonizations_filtered2.tab" + " >> " + output_path_aux13
os.system(command3)
else:
# 11. Join the mutated and non_mutated cases
output_path_aux13 = output_path + "/all_exonizations.tab"
command3 = "cat " + output_path + "/mutated_exonizations.tab" + " > " + output_path_aux13 + ";tail -n+2 " + output_path + "/non_mutated_exonizations.tab" + " >> " + output_path_aux13
os.system(command3)
# 12. Get the peptide sequence associated
logger.info("Part11...")
output_path_aux13 = output_path + "/all_exonizations.tab"
output_path_peptide = output_path + "/exonizations_peptide_sequence.fa"
output_path_dna = output_path + "/exonizations_fasta_sequence.fa"
output_path_aux14 = output_path + "/all_exonizations_ORF.tab"
output_path_aux15 = output_path + "/all_exonizations_ORF_sequences.tab"
output_path_aux16 = output_path + "/all_exonizations_Interpro.tab"
output_path_aux17 = output_path + "/all_exonizations_IUPred.tab"
get_peptide_sequence(output_path_aux13, transcript_expression_path,
gtf_path, output_path_peptide, output_path_dna,
output_path_aux14, output_path_aux15,
output_path_aux16, output_path_aux17, mosea_path,
genome_path, orfs_scripts, remove_temp_files)
# 13. Filter the significant results
logger.info("Part12...")
output_path_aux18 = output_path + "/all_exonizations_filtered.tab"
output_path_aux19 = output_path + "/all_exonizations_filtered_peptide_change.tab"
command4 = "Rscript " + dir_path + "/lib/Exonization/filter_results.R " + output_path_aux14 + " " + output_path_aux18 + " " + output_path_aux19
os.system(command4)
# 14. Select the fasta candidates for being run to the epitope analysis
logger.info("Part13...")
output_path_aux20 = output_path + "/exonizations_peptide_sequence.fa"
output_path_aux21 = output_path + "/exonizations_peptide_sequence_filtered.fa"
#Create the folder, if it doesn't exists
if not os.path.exists(output_path + "/exonization_fasta_files"):
os.makedirs(output_path + "/exonization_fasta_files")
select_fasta_candidates(output_path_aux19, output_path_aux20,
output_path_aux21,
output_path + "/exonization_fasta_files")
# 15. Run netMHC-4.0_part1
logger.info("Part14...")
if not os.path.exists(output_path + "/exonizations_NetMHC-4.0_files"):
os.makedirs(output_path + "/exonizations_NetMHC-4.0_files")
run_netMHC_classI_slurm_part1(
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)
# 16. Run netMHCpan-4.0_part1
logger.info("Part15...")
if not os.path.exists(output_path +
"/exonizations_NetMHCpan-4.0_files"):
os.makedirs(output_path + "/exonizations_NetMHCpan-4.0_files")
run_netMHCpan_classI_slurm_part1(
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)
logger.info(
"Wait until all jobs have finished. Then, go on with part3")
logger.info("Done. Exiting program.")
exit(0)
except Exception as error:
logger.error('ERROR: ' + repr(error))
logger.error("Aborting execution")
sys.exit(1)
def main():
try:
logger.info("Starting execution exonizations_ePydoor_part2")
tumor_specific = True
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"
mutations_path = "/projects_rg/babita/TCGA/mutation/mut_pipeline/juanlu_sclc/src_files/SCLC_mutations_sorted.bed.mut.out"
repeats_path = "/projects_rg/SCLC_cohorts/cis_analysis/tables/hg19_repeats.bed"
CHESS_SE_path = "/projects_rg/SCLC_cohorts/annotation/chess2.0_assembly_hg19_CrossMap.events_SE_strict.ioe"
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
threshold2 = 10
name_user = "******"
output_path = "/users/genomics/juanluis/SCLC_cohorts/Smart/epydoor/exonizations"
# 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...")
dir_path = os.path.dirname(os.path.realpath(__file__))
get_coverageBed_adapter(output_path + "/exonizations_by_sample.tab",
output_path + "/random_exonizations.bed",
output_path + "/coverageBed", output_path,
name_user)
# 7.2. Assemble all pieces into one single file
command2 = "awk 'FNR==1 && NR!=1{next;}{print}' " + output_path + "/get_coverageBed_*.tab > " + output_path + "/exonizations_by_sample_coverage.tab"
os.system(command2)
# 8. Check if in the exonizations there are mutations nearby
logger.info("Part8...")
check_mutations_nearby(
output_path + "/exonizations_by_sample_coverage.tab",
mutations_path, 200,
output_path + "/exonizations_by_sample_coverage_mut.tab")
# 9. Separate between mutated and non-mutated cases
logger.info("Part9...")
command2="module load R; Rscript "+dir_path+"/lib/Exonization/separate_mutated_cases.R "+output_path + \
"/exonizations_by_sample_coverage_mut.tab"+" "+output_path + "/mutated_exonizations.tab"+" "+output_path + "/non_mutated_exonizations.tab"
# print(command2)
os.system(command2)
# 10. Get the tumor specific events
if (tumor_specific):
# Get also the significant exonizations from Rudin and Intropolis
output_Rudin_path_aux2 = output_path + "/new_exonized_junctions_Rudin_normal_reads.tab"
readCounts_Rudin_path = "/projects_rg/SCLC_cohorts/Rudin/STAR/v1/normal_readCounts.tab"
get_reads_exonizations(output_path + "/new_exonized_junctions.tab",
readCounts_Rudin_path,
output_Rudin_path_aux2)
output_Rudin_path_aux3 = output_path + "/new_exonized_junctions_Rudin_normal_reads_repeatitions.tab"
overlap_with_repeats(output_Rudin_path_aux2, repeats_path,
output_Rudin_path_aux3)
output_Rudin_path_aux4 = output_path + "/exonizations_by_sample_Rudin_normal.tab"
get_significant_exonizations(output_Rudin_path_aux3, threshold2,
output_Rudin_path_aux4)
output_Intropolis_path_aux2 = output_path + "/new_exonized_junctions_Intropolis_reads.tab"
get_reads_exonizations(output_path + "/new_exonized_junctions.tab",
readcounts_path,
output_Intropolis_path_aux2)
output_Intropolis_path_aux3 = output_path + "/new_exonized_junctions_Intropolis_reads_repeatitions.tab"
overlap_with_repeats(output_Intropolis_path_aux2, repeats_path,
output_Intropolis_path_aux3)
output_Intropolis_path_aux4 = output_path + "/exonizations_by_sample_Intropolis.tab"
get_significant_exonizations(output_Intropolis_path_aux3,
threshold2,
output_Intropolis_path_aux4)
output_Rudin_path_aux4 = output_path + "/exonizations_by_sample_Rudin_normal.tab"
output_Intropolis_path_aux4 = output_path + "/exonizations_by_sample_Intropolis.tab"
output_path_aux11 = output_path + "/non_mutated_exonizations_filtered.tab"
filter_exonizations(output_path + "/non_mutated_exonizations.tab",
output_Rudin_path_aux4,
output_Intropolis_path_aux4, output_path_aux11,
flag_Rudin)
output_path_aux12 = output_path + "/non_mutated_exonizations_filtered2.tab"
filter_exonizations_CHESS(output_path_aux11, CHESS_SE_path,
output_path_aux12)
# 11. Join the mutated and non_mutated cases
logger.info("Part10...")
output_path_aux13 = output_path + "/all_exonizations.tab"
command3 = "cat " + output_path + "/mutated_exonizations.tab" + " > " + output_path_aux13 + ";tail -n+2 " + output_path_aux12 + " >> " + output_path_aux13
os.system(command3)
else:
# 11. Join the mutated and non_mutated cases
logger.info("Part10...")
output_path_aux13 = output_path + "/all_exonizations.tab"
command3 = "cat " + output_path + "/mutated_exonizations.tab" + " > " + output_path_aux13 + ";tail -n+2 " + output_path + "/non_mutated_exonizations.tab" + " >> " + output_path_aux13
os.system(command3)
# 12. Get the peptide sequence associated
logger.info("Part11...")
output_path_aux13 = output_path + "/all_exonizations.tab"
output_path_peptide = output_path + "/exonizations_peptide_sequence.fa"
output_path_dna = output_path + "/exonizations_fasta_sequence.fa"
output_path_aux14 = output_path + "/all_exonizations_ORF.tab"
output_path_aux15 = output_path + "/all_exonizations_ORF_sequences.tab"
output_path_aux16 = output_path + "/all_exonizations_Interpro.tab"
output_path_aux17 = output_path + "/all_exonizations_IUPred.tab"
get_peptide_sequence(output_path_aux13, 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)
# 13. Filter the significant results
logger.info("Part12...")
output_path_aux18 = output_path + "/all_exonizations_filtered.tab"
output_path_aux19 = output_path + "/all_exonizations_filtered_peptide_change.tab"
command4 = "module load R; Rscript " + dir_path + "/lib/Exonization/filter_results.R " + output_path_aux14 + " " + output_path_aux18 + " " + output_path_aux19
os.system(command4)
# 14. Select the fasta candidates for being run to the epitope analysis
logger.info("Part13...")
output_path_aux20 = output_path + "/exonizations_peptide_sequence.fa"
output_path_aux21 = output_path + "/exonizations_peptide_sequence_filtered.fa"
#Create the folder, if it doesn't exists
if not os.path.exists(output_path + "/exonization_fasta_files"):
os.makedirs(output_path + "/exonization_fasta_files")
select_fasta_candidates(output_path_aux19, output_path_aux20,
output_path_aux21,
output_path + "/exonization_fasta_files")
# 15. Run netMHC-4.0_part1
logger.info("Part14...")
if not os.path.exists(output_path + "/exonizations_NetMHC-4.0_files"):
os.makedirs(output_path + "/exonizations_NetMHC-4.0_files")
run_netMHC_classI_slurm_part1(
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_3.tab", output_path +
"/exonizations_NetMHC-4.0_neoantigens_type_3_all.tab",
output_path + "/exonizations_NetMHC-4.0_neoantigens_type_2.tab",
output_path +
"/exonizations_NetMHC-4.0_neoantigens_type_2_all.tab",
output_path +
"/exonizations_NetMHC-4.0_junctions_ORF_neoantigens.tab",
netMHC_path)
# 16. Run netMHCpan-4.0_part1
logger.info("Part15...")
if not os.path.exists(output_path +
"/exonizations_NetMHCpan-4.0_files"):
os.makedirs(output_path + "/exonizations_NetMHCpan-4.0_files")
run_netMHCpan_classI_slurm_part1(
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_3.tab", output_path +
"/exonizations_NetMHCpan-4.0_neoantigens_type_3_all.tab",
output_path + "/exonizations_NetMHCpan-4.0_neoantigens_type_2.tab",
output_path +
"/exonizations_NetMHCpan-4.0_neoantigens_type_2_all.tab",
output_path +
"/exonizations_NetMHCpan-4.0_junctions_ORF_neoantigens.tab",
netMHC_pan_path)
logger.info(
"Wait until all jobs have finished. Then, go on with part3")
logger.info("Done. Exiting program.")
exit(0)
except Exception as error:
logger.error('ERROR: ' + repr(error))
logger.error("Aborting execution")
sys.exit(1)