Commit 823a9d8c authored by Pradat Yoann's avatar Pradat Yoann

update run_example_tcga_HS

parent 39fb9c11
......@@ -15,8 +15,6 @@ Example
python examples/run_example_tcga_HS.py \
--i_split 1 \
--n_split 1 \
--vcf2maf ~/Documents/biotools/informatics/VCF/vcf2maf/vcf2maf.pl \
--vep_folder ~/Documents/biotools/informatics/VCF/ensembl-vep \
--vep_data ~/.vep \
--vep_n_fork 4 \
--fasta ~/.vep/homo_sapiens/101_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
......@@ -34,14 +32,15 @@ from src.main import run_annotator
#### # SCRIPT PARAMETERS
#### #####################################################################################################
default_vep_data = os.path.expanduser("~/.vep")
default_fasta = os.path.expanduser("~/.vep/homo_sapiens/101_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa")
parser = argparse.ArgumentParser()
parser.add_argument('--i_split' , type=int , default=1 , help='the split processed')
parser.add_argument('--n_split' , type=int , default=1 , help='total number of splits')
parser.add_argument('--vcf2maf' , type=str , default="" , help='path to the vcf2maf perl script')
parser.add_argument('--vep_folder' , type=str , default="" , help='path to the folder of the vep command')
parser.add_argument('--vep_data' , type=str , default="" , help='path to the .vep data folder')
parser.add_argument('--vep_n_fork' , type=int , default=4 , help='number of forks to be used by VEP')
parser.add_argument('--fasta' , type=str , default="" , help='path to reference genome FASTA file')
parser.add_argument('--i_split' , type=int , default=1 , help='the split processed')
parser.add_argument('--n_split' , type=int , default=1 , help='total number of splits')
parser.add_argument('--vep_data' , type=str , default=default_vep_data , help='path to the .vep data folder')
parser.add_argument('--vep_n_fork' , type=int , default=4 , help='number of forks to be used by VEP')
parser.add_argument('--fasta' , type=str , default=default_fasta , help='path to reference genome FASTA file')
args = parser.parse_args()
print("Parameters", flush=True)
......@@ -94,7 +93,26 @@ if __name__ == "__main__":
count = 0
count_total = len(vcf_files)
#### # 3. PROCESS
#### # 3. CONFIG
#### # ##################################################################################################
#### configure vep (for inside vcf2maf and for custom if set to use custom vep commands)
vep_config = VepConfig(
data = args.vep_data,
n_fork = args.vep_n_fork,
fasta = args.fasta,
custom_run = False,
# custom_opt = "~/.vep/custom/ClinVar/clinvar.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN",
custom_overwrite = True,
)
#### configure vcf2maf
vcf2maf_config = Vcf2mafConfig(
run = True,
overwrite = True
)
#### # 4. PROCESS
#### # ##################################################################################################
#### loop over the list
......@@ -139,14 +157,8 @@ if __name__ == "__main__":
tumor_id = tumor_id,
infos_n_reads = infos_n_reads,
infos_other = infos_other,
vcf2maf = args.vcf2maf,
vep_folder = args.vep_folder,
vep_data = args.vep_data,
# vep_custom = "~/.vep/custom/ClinVar/clinvar.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNDN",
vep_n_fork = args.vep_n_fork,
vep_overwrite = True,
vcf2maf_overwrite = True,
fasta = args.fasta,
dt_folders = dt_folders,
dt_identifiers = dt_identifiers
vep_config = vep_config,
vcf2maf_config = vcf2maf_config
)
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