openvariant.plugins.get_AF package#

Submodules#

class openvariant.plugins.get_AF.get_AF.Get_afContext(row: dict, field_name: str, file_path: str)[source]

Bases: openvariant.plugins.context.Context

Get_afContext class generated by OpenVariant

row

Main method to execute data transformation in each row.

field_name

Name of the corresponding column that was described on the annotation schema.

file_path

Path of the Input file that is being parsed.

class openvariant.plugins.get_AF.get_AF.Get_afPlugin[source]

Bases: openvariant.plugins.plugin.Plugin

This plugin get alternate allele frequency of a sample in a .vcf. It will be in located in ‘subAF’ field and will get the float number with regexp.

run(context: Get_afContext)[source]: Main method to execute data transformation in each row.

run(context: openvariant.plugins.get_AF.get_AF.Get_afContext) → str[source]

Extract allele frequency from the input row.

Parameters: context (Get_afContext) – Representation of the row to be parsed.
Returns: The value of the field transformed.
Return type: float or int or str

openvariant.plugins.alteration_type package

Examples