Convert: COSMIC

Scripts

map_cosmic_tsv.py

Procedure

Run map_cosmic_tsv.py

Summary

The python script map_cosmic_tsv.py will take the output of the TCGA download step and:

• Map the data to:

  • uniprot accessions

  • doid parent terms

• Rename fields

• Reformat fields

  • amino acid change and position

  • chromosome id

  • genomic location

  • nucleotide change

Script Specifications

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

Input

• -i : A path to the cosmic tsv mutation file

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

• -d : The name of the doid to cosmic cancer type mapping file

• -e : The name of the enst to uniprot accession mapping file

• -o : A path to the the folder to export the final mapped mutations

Output

• A mutation file with COSMIC mutations mapped to doid terms and uniprot accessions

Usage

• map_cosmic_tsv -h

*Gives a description of the neccessary commands

• python map_cosmic_tsv.py -i <path/cosmic_file_name.tsv> -m <path/mapping_folder> -d <doid_mapping_file_name> -e <enst_mapping_file_name> -o <path/output_folder>

*Runs the script with the given input tsv and outputs a tsv with Biomuta formatting.

Additional Notes

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

The mapping files used for converting the COSMIC tsv are:

DOID: cosmic_doid_mapping.csv

COSMIC tissue site terms were mapped to DOID parent terms using the following table (generated from previous Biomuta mapping):

Primary Site	Top_Level_Organ_system
NS	NA
adrenal_gland	DOID:3953 / adrenal gland cancer
autonomic_ganglia	NA
biliary_tract	DOID:4606 / bile duct cancer
bone	DOID:184 / bone cancer
breast	DOID:1612 / breast cancer
central_nervous_system	DOID:1319 / brain cancer
cervix	DOID:4362 / cervical cancer
endometrium	DOID:363 / uterine cancer
eye	DOID:2174 / ocular cancer
fallopian_tube	DOID:1964 / fallopian tube cancer
female_genital_tract_(site_indeterminate)
female_genitourinary_system	NA
gastrointestinal_tract_(site_indeterminate)	DOID:3119 / gastrointestinal system cancer
genital_tract	NA
haematopoietic_and_lymphoid_tissue	DOID:2531 / hematologic cancer
kidney	DOID:263 / kidney cancer
large_intestine	DOID:9256 / colorectal cancer
liver	DOID:3571 / liver cancer
lung	DOID:1324 / lung cancer
mediastinum	NA
meninges	DOID:3565 / meningioma
oesophagus	DOID:5041 / esophageal cancer
ovary	DOID:2394 / ovarian cancer
pancreas	DOID:1793 / pancreatic cancer
paratesticular_tissues	NA
parathyroid	DOID:1540 / parathyroid carcinoma
penis	DOID:11615 / penile cancer
pericardium	NA
perineum	DOID:4045 / muscle cancer
peritoneum	DOID:1725 / peritoneum cancer
pituitary	DOID:1785 / pituitary cancer
placenta	DOID:2021 / placenta cancer
pleura	DOID:5158 / pleural cancer
prostate	DOID:10283 / prostate cancer
retroperitoneum	DOID:5875 / retroperitoneal cancer
salivary_gland	DOID:8618 / oral cavity cancer
skin	DOID:4159 / skin cancer
small_intestine	DOID:9253 / gastrointestinal stromal tumor
soft_tissue	NA
stomach	DOID:10534 / stomach cancer
testis	DOID:2998 / testicular cancer
thymus	DOID:3277 / thymus cancer
thyroid	DOID:1781 / thyroid gland cancer
upper_aerodigestive_tract	DOID:8618 / oral cavity cancer
urinary_tract	DOID:11054 / urinary bladder cancer
uterine_adnexa	NA
vagina	DOID:119 / vaginal cancer
vulva	DOID:1245 / vulva cancer

Uniprot Accession: human_protein_transcriptlocus.csv

Transcript ID (starts with ENST) 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