openvariant.plugins.alteration_type package#

Submodules#

openvariant.plugins.alteration_type.alteration_type module#

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

Bases: openvariant.plugins.context.Context

The context of this plugin will be the simplest one, without any added property or methods.

row

The row that data transformation will be applied.

Type

dict

field_name

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

Type

str

file_path

Path of the Input file that is being parsed.

Type

str

class openvariant.plugins.alteration_type.alteration_type.Alteration_typePlugin[source]

Bases: openvariant.plugins.plugin.Plugin

This plugin identifies the alteration type. Classifies the alteration type: checking POSITION, REF and ALT fields.

run(context: openvariant.plugins.alteration_type.alteration_type.Alteration_typeContext) → str[source]

Extract alteration type from the input row.

Parameters

context (Alteration_typeContext) – Representation of the row to be parsed.

Returns

The value of ALT_TYPE field.

Return type

str

Module contents#

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openvariant.plugins.get_AF package