add_germline_annotations

Convert IgLabel-style labels in an alignment file to dummy IUIS format

usage: add_germline_annotations [-h] [-c CALL_COLUMNS] [-s DUMMY_SUBGROUP] [-a DUMMY_ALLELE] [-u] input_file output_file germline_set

Positional Arguments

input_file

alignments to annotate (csv, tsv)

output_file

output with added annotations

germline_set

AIRR standard germline set to use for metadata (JSON)

Named Arguments

-c, --call_columns

Names of one or more columns to be processed, separated by commas

Default: “v_call,d_call,j_call”

-s, --dummy_subgroup

The subgroup to be used, where no value is specified in the germline set metadata

Default: “0”

-a, --dummy_allele

The allele to be used, where no value is specified in the germline set metadata

Default: “00”

-u, --un_dummy

translate dummy names back to label form

Default: False