CharGer Internals

Here documents CharGer’s internal design by modules:

• config module
  • CharGerConfig
  • Constants and helpers
• classifier module
  • CharGer
  • Module helper classes
• result module
  • CharGerResult
  • Module helper classes
• acmg_modules module
  • Pathogenic
• custom_modules module
  • Pathogenic
• variant module
  • Variant
  • GeneInheritanceMode
  • ClinicalSignificance
  • Helpers
• csq module
  • CSQ
  • Constants and helpers
• io module
  • read_tsv
  • read_csv
  • read_lines
  • Helpers
• console module
• argtype module

Reuse CharGer modules

The module can be accessed externally by charger.<module_name>. For example,

from charger.classifier import CharGer
from charger.config import CharGerConfig
from charger.console import setup_logger
from charger.variant import Variant

The following script programmatically calls CharGer:

# Enable logging to stderr
setup_logger()

# Configure CharGer
config = CharGerConfig(
    input=path_in_repo(
        "tests/examples/10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz"
    ),
    pathogenic_variant=path_in_repo(
        "tests/examples/annotations/grch37_pathogenic_variants.vcf.gz"
    ),
    inheritance_gene_table=path_in_repo(
        "tests/examples/annotations/inheritance_gene_table.tsv.gz"
    ),
    PP2_gene_list=path_in_repo("tests/examples/annotations/pp2_gene_list.txt.gz"),
    clinvar_table=path_in_repo(
        "tests/examples/annotations/clinvar_chrom_22_only.b37.tsv.gz"
    ),
)

# Initiate and run the CharGer classifier
charger = CharGer(config)
charger.setup()
charger.run_acmg_modules()
charger.run_charger_modules()