augur.filter.io module

augur.filter.io.cleanup_outputs(args)

Remove output files. Useful when terminating midway through a loop of metadata chunks.

augur.filter.io.column_type_pair(input)

Get a 2-tuple for column name to type.

Intended to be used as the argument type converter for argparse options that take type maps in a ‘column:type’ format.

augur.filter.io.get_useful_metadata_columns(args, id_column, all_columns)

Return a list of column names that are used in augur filter. This allows reading only the necessary columns.

augur.filter.io.read_priority_scores(fname)

augur.filter.io.write_metadata_based_outputs(input_metadata_path, delimiters, id_columns, output_metadata_path, output_strains_path, ids_to_write)

Write output metadata and/or strains file given input metadata information and a set of IDs to write.