This Python script provides a class CatSalutSomaticTiers to classify clinically actionable variants supported by CatSalut The official instruction is available at: Perfil genetic tumors sòlids 2022

No installation is required. Simply download the cat_salut_somatic_tiers.py file and import it into your Python project.

To use the CatSalutSomaticTiers class, you need to provide a TSV (tab-separated values) file containing the list of known tier variants.

There's a tsv file with variant-specific rules file at test/tiers/Tiers_cancer.v1.tsv

Here's an example of how to use the class:

from cat_salut_somatic_tiers import CatSalutSomaticTiers

variants_tsv = "path/to/your/variants.tsv"
cat_salut = CatSalutSomaticTiers(variants_tsv)

gene = "BRAF"
variant_type = "SNV"
exon = "15"
csq = "missense_variant"
hgvsp = "p.V600E"

tier = cat_salut.classify(gene, variant_type, exon=exon, csq=csq, hgvsp=hgvsp)
print(f"Tier classification: {tier}")
Each row should represent a known tier variant with the corresponding information.

The main methods provided by the CatSalutSomaticTiers class are: __init__(self, variants_tsv: str): Initializes the class with the given TSV file containing known tier variants. load_known_tier_variants(self): Reads the TSV file and stores the tier variants in a dictionary. classify(self, gene: str, variant_type: str, exon: Optional[str] = None, intron: Optional[str] = None, csq: Optional[str] = None, hgvsp: Optional[str] = None, force_gene: bool = False): Classifies a given variant based on the gene, variant type, and other optional parameters. Returns the tier classification.

The module defines the following custom exceptions: InvalidTsvSchema: Raised when the provided TSV file has an incorrect schema. MissingGene: Raised when the provided gene is not found in the known tier variants. InvalidAlteration: Raised when the provided variant type is not valid.

The input TSV file should have the following header: Gene, Exon, Intron, Alteration, Alteration Comments, Consequence, HGVSp, Exclusion Criteria, ESCAT, Treatments, Treatment Lines, Comments, Clinical Trials, Tier, Automatized, Skip, Version, Date

Each row should represent a known tier variant with the corresponding information.

python -m pytest test/ 

Currently it is only supported the analysis of LUAD. In addition, the current version does not support the automatic annotation of all available mutation classes:

• EGFR uncommon mutations.
• ALK mutations of resistance.
• RET mutations of resistance.
• NTRK mutations of resistance.