config module

CharGerConfig

class CharGerConfig(*, input=None, output=None, hotspot3d_cluster=None, pathogenic_variant=None, override_variant_info=False, include_vcf_details=False, clinvar_table=None, rare_threshold=0.0005, common_threshold=0.005, acmg_module_scores=NOTHING, charger_module_scores=NOTHING, min_pathogenic_score=9, min_likely_pathogenic_score=5, max_likely_benign_score=- 4, max_benign_score=- 8, disease_specific=False, inheritance_gene_table=None, PP2_gene_list=None, BP1_gene_list=None)[source]

Bases: object

CharGer configuration.

CharGer can be configured programatically using this object.

Examples

>>> config = CharGerConfig()
Parameters
Return type

None

input: Optional[pathlib.Path]

Path to the input VCF.

output: Optional[pathlib.Path]

Path to the CharGer output.

hotspot3d_cluster: Optional[pathlib.Path]
pathogenic_variant: Optional[pathlib.Path]
override_variant_info: bool
include_vcf_details: bool
clinvar_table: Optional[pathlib.Path]

Path the the Tabix indexed ClinVar database table.

rare_threshold: float
common_threshold: float
acmg_module_scores: Dict[str, int]
charger_module_scores: Dict[str, int]
min_pathogenic_score: int
min_likely_pathogenic_score: int
max_likely_benign_score: int
max_benign_score: int
disease_specific: bool

Whether to enable disease specific detection for inheritance_gene_table.

inheritance_gene_table: Optional[pathlib.Path]

Path to a TSV table of inheritance genes.

The table columns must have these three columns in order: gene, diseases, modes_of_inheritance. The first row is header and will be ignored.

  • gene: Gene symbol.

  • diseases: Name of the diseases seperated by comma.

  • modes_of_inheritance: Name of the inheritance modes seperated by comma. Possible modes: autosomal recessive, autosomal dominant, Y-linked, X-linked recessive, X-link dominant, unknown.

Example table of inheritance_gene_table

gene

diseases

modes_of_inheritance

BRCA2

BRCA, OV

autosomal recessive, autosomal dominant

NF1

Neurofibroma

autosomal dominant
PP2_gene_list: Optional[pathlib.Path]

Path to the list of genes for PP2 module.

The given file has one gene symbol per line.

BP1_gene_list: Optional[pathlib.Path]

Path to the list of genes for BP1 module.

The given file has one gene symbol per line.

Constants and helpers

ACMG_MODULES: Dict[str, List[str]] = {'b_moderate': [], 'b_standalone': ['BA1'], 'b_strong': ['BS1', 'BS2', 'BS3', 'BS4'], 'b_support': ['BP1', 'BP2', 'BP3', 'BP4', 'BP5', 'BP6', 'BP7'], 'p_moderate': ['PM1', 'PM2', 'PM3', 'PM4', 'PM5', 'PM6'], 'p_strong': ['PS1', 'PS2', 'PS3', 'PS4'], 'p_support': ['PP1', 'PP2', 'PP3', 'PP4', 'PP5'], 'p_very_strong': ['PVS1']}

All ACMG modules.

CHARGER_MODULES: Dict[str, List[str]] = {'b_moderate': ['BMC1'], 'b_strong': ['BSC1'], 'b_support': [], 'p_moderate': ['PMC1'], 'p_strong': ['PSC1'], 'p_support': ['PPC1', 'PPC2']}

All CharGer modules.

_default_acmg_scores: Dict[str, int] = {'BA1': -8, 'BP1': -1, 'BP2': -1, 'BP3': -1, 'BP4': -1, 'BP5': -1, 'BP6': -1, 'BP7': -1, 'BS1': -4, 'BS2': -4, 'BS3': -4, 'BS4': -4, 'PM1': 2, 'PM2': 2, 'PM3': 2, 'PM4': 2, 'PM5': 2, 'PM6': 2, 'PP1': 1, 'PP2': 1, 'PP3': 1, 'PP4': 1, 'PP5': 1, 'PS1': 7, 'PS2': 4, 'PS3': 4, 'PS4': 4, 'PVS1': 8}

Default scores for ACMG modules.

_default_charger_scores: Dict[str, int] = {'BMC1': -2, 'BSC1': -6, 'PMC1': 2, 'PPC1': 1, 'PPC2': 1, 'PSC1': 4}

Default scores for CharGer modules.