augur.filter module

Filter and subsample a sequence set.

exception augur.filter.TooManyGroupsError(msg)

Bases: ValueError

augur.filter.filter_by_query(sequences, metadata_file, query)

Filter a set of sequences using Pandas DataFrame querying against the metadata file.

Parameters
  • sequences (list[str]) – List of sequence names to filter

  • metadata_file (str) – Path to the metadata associated wtih the sequences

  • query (str) – Query string for the dataframe.

Returns

List of sequence names that match the given query

Return type

list[str]

augur.filter.numeric_date(date)

Converts the given date string to a float.

date may be given as a number (a float) with year as the integer part, or in the YYYY-MM-DD (ISO 8601) syntax.

>>> numeric_date("2020.42")
2020.42
>>> numeric_date("2020-06-04")
2020.42486...
augur.filter.read_priority_scores(fname)
augur.filter.read_vcf(filename)
augur.filter.register_arguments(parser)
augur.filter.run(args)

filter and subsample a set of sequences into an analysis set

augur.filter.write_vcf(input_filename, output_filename, dropped_samps)