Convert: TCGA

Scripts

process_tcga_download.py

Procedure

Run process_tcga_download.py

Summary

The python script process_tcga_download.py will take the output of the TCGA download step and:
  • Map the data to:

    • uniprot accession

    • doid parent terms

  • Rename fields

  • Reformat fields

    • amino acid change and position

    • chromosome id

  • Filter out unnecessary fields

Script Specifications

The script must be called from the command line and takes specific command line arguments

Input

  • -i : A path to the input csv to reformat

  • -m : A path to the folder containing mapping files

  • -d : A path to the tcga study to doid mapping file

  • -e : A path to the ENSP to uniprot mapping file

  • -o : A path to the output folder

Output

  • A data report comparing new AA sites to old AA sites for Biomuta

Usage

  • python process_tcga_download.py -h

*Gives a description of the neccessary commands

  • python process_tcga_download.py -i <path/input_file.vcf> -m <path/> -d <doid_mapping.csv -e <ensp_mapping.csv> -o <path/>

*Runs the script with the given input tcga csv and output a formatted csv

Additional Notes

All the mapping files are available in the repository folder pipeline/convert_step2/mapping

The mapping files used for converting TCGA are:

DOID: tcga_doid_mapping.csv

TCGA Projects were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping):

DO_slim_id

DO_slim_name

TCGA_project

DOID:5041

esophageal cancer

TCGA-ESCA

DOID:2531

hematologic cancer

TCGA-DLBC

DOID:9256

colorectal cancer

TCGA-READ

DOID:1319

brain cancer

TCGA-GBM

DOID:1319

brain cancer

TCGA-LGG

DOID:1781

thyroid cancer

TCGA-THCA

DOID:11054

urinary bladder cancer

TCGA-BLCA

DOID:363

uterine cancer

TCGA-UCEC

DOID:169

neuroendocrine tumor

TCGA-PCPG

DOID:4362

cervical cancer

TCGA-CESC

DOID:363

uterine cancer

TCGA-UCS

DOID:3277

thymus cancer

TCGA-THYM

DOID:3571

liver cancer

TCGA-LIHC

DOID:11934

head and neck cancer

TCGA-HNSC

DOID:2174

ocular cancer

TCGA-UVM

DOID:4159

skin cancer

TCGA-SKCM

DOID:9256

colorectal cancer

TCGA-COAD

DOID:3953

adrenal gland cancer

TCGA-ACC

DOID:1793

pancreatic cancer

TCGA-PAAD

DOID:2994

germ cell cancer

TCGA-TGCT

DOID:1324

lung cancer

TCGA-LUSC

DOID:1790

malignant mesothelioma

TCGA-MESO

DOID:2394

ovarian cancer

TCGA-OV

DOID:1115

sarcoma

TCGA-SARC

DOID:263

kidney cancer

TCGA-KIRP

DOID:10534

stomach cancer

TCGA-STAD

DOID:2531

hematologic cancer

TCGA-LAML

DOID:10283

prostate cancer

TCGA-PRAD

DOID:1324

lung cancer

TCGA-LUAD

DOID:1612

breast cancer

TCGA-BRCA

DOID:263

kidney cancer

TCGA-KIRC

DOID:263

kidney cancer

TCGA-KICH

Uniprot Accession: human_protein_transcriptlocus.csv

Peptide ID (starts with ENSP) was mapped to uniprot isoform accession

Mapping was NOT performed to uniprot canonical accession as this resulted in an issue with the final dataset in which a mutation for the same canonical accession would be listed with different amino acid changes