cowidev.variants¶

cowidev.variants.main¶

cowidev.variants.__main__.run_step(step: str)[source]¶

cowidev.variants._parser¶

cowidev.variants._parser._parse_args()[source]¶

cowidev.variants.etl¶

class cowidev.variants.etl.VariantsETL[source]¶

Bases: object

property _parse_last_update_date¶

extract() → dict[source]¶

json_to_df(data: dict) → DataFrame[source]¶

load(df: DataFrame, output_path: str) → None[source]¶

pipe_check_variants(df: DataFrame) → DataFrame[source]¶

pipe_correct_excess_percentage(df: DataFrame) → DataFrame[source]¶

pipe_cumsum(df: DataFrame) → DataFrame[source]¶

pipe_date(df: DataFrame) → DataFrame[source]¶

pipe_dtypes(df: DataFrame) → DataFrame[source]¶

pipe_filter_by_num_sequences(df: DataFrame) → DataFrame[source]¶

pipe_filter_locations(df: DataFrame) → DataFrame[source]¶

pipe_group_by_variants(df: DataFrame) → DataFrame[source]¶

pipe_location(df: DataFrame) → DataFrame[source]¶

pipe_omicron(df: DataFrame) → DataFrame[source]¶

pipe_out(df: DataFrame) → DataFrame[source]¶

pipe_per_capita(df: DataFrame) → DataFrame[source]¶

pipe_percent(df: DataFrame) → DataFrame[source]¶

pipe_rename_columns(df: DataFrame) → DataFrame[source]¶

pipe_variant_dominant(df)[source]¶

pipe_variant_non_who(df: DataFrame) → DataFrame[source]¶

pipe_variant_others(df: DataFrame) → DataFrame[source]¶

pipe_variant_totals(df: DataFrame) → DataFrame[source]¶

pipe_variants(df: DataFrame) → DataFrame[source]¶

run()[source]¶

transform(data: dict) → DataFrame[source]¶

transform_seq(df: DataFrame) → DataFrame[source]¶

property variants_mapping¶

property variants_who¶

cowidev.variants.etl.run_etl()[source]¶

cowidev.variants.grapher¶

cowidev.variants.grapher.filter_by_num_sequences(df: DataFrame) → DataFrame[source]¶

cowidev.variants.grapher.run_db_updater(input_path: str)[source]¶

cowidev.variants.grapher.run_explorerizer()[source]¶

cowidev.variants.grapher.run_grapheriser()[source]¶

cowidev.variants.grapher.variant_url_frienldy_name(df: DataFrame) → DataFrame[source]¶

python -m cowidev.variants etl python -m cowidev.variants grapher-file