Commit 37d89f1f authored by Pradat Yoann's avatar Pradat Yoann

[dev] minor fixes

parent 5a5941bb
......@@ -12,7 +12,7 @@ Example of how to annotate a list of VCF from one project/study.
Example
-----------
python main/data/vcf/run/vcf2maf_tcga_GA.py \
python examples/run_example_tcga_GA.py \
--i_split 1 \
--n_split 1 \
--vcf2maf ~/Documents/biotools/informatics/VCF/mskcc-vcf2maf-5453f80/vcf2maf.pl \
......@@ -106,7 +106,7 @@ if __name__ == "__main__":
mask_vcf_file = df_meta["file_name_GA"] == vcf_file
index_vcf_file = mask_vcf_file[mask_vcf_file].index[0]
vcf_identifiers = {
dt_identifiers = {
"Tumor_Sample" : df_meta.loc[index_vcf_file, "tumor_sample"],
"Tumor_Sample_Barcode" : df_meta.loc[index_vcf_file, "tumor_sample_barcode"],
"Matched_Norm_Sample_Barcode" : df_meta.loc[index_vcf_file, "normal_sample_barcode"],
......@@ -115,27 +115,28 @@ if __name__ == "__main__":
#### get parameter values
col_normal = "NORMAL"
if vcf_identifiers["Tumor_Sample_Site"] == "01":
if dt_identifiers["Tumor_Sample_Site"] == "01":
col_tumor = "PRIMARY"
else:
col_tumor = "METASTATIC"
normal_id = vcf_identifiers["Matched_Norm_Sample_Barcode"],
tumor_id = vcf_identifiers["Tumor_Sample_Barcode"],
normal_id = dt_identifiers["Matched_Norm_Sample_Barcode"],
tumor_id = dt_identifiers["Tumor_Sample_Barcode"],
infos_n_reads = ["AD", "DP", "FA"]
infos_other = ["SS", "GT"]
run_annotator(
vcf_folder = vcf_folder,
vcf_file = vcf_file,
col_normal = col_normal,
col_tumor = col_tumor,
normal_id = normal_id,
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,
fasta = args.fasta,
dt_folders = dt_folders
vcf_folder = vcf_folder,
vcf_file = vcf_file,
col_normal = col_normal,
col_tumor = col_tumor,
normal_id = normal_id,
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,
fasta = args.fasta,
dt_folders = dt_folders,
dt_identifiers = dt_identifiers
)
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