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Augur
development version (ec95d57c)

Table of contents

  • Installation
  • Using Augur
    • Augur subcommands
      • augur parse
      • augur curate
        • normalize-strings
        • passthru
      • augur index
      • augur filter
      • augur mask
      • augur align
      • augur tree
      • augur refine
      • augur ancestral
      • augur translate
      • augur reconstruct-sequences
      • augur clades
      • augur traits
      • augur sequence-traits
      • augur lbi
      • augur distance
      • augur titers
      • augur frequencies
      • augur export
      • augur validate
      • augur version
      • augur import
      • augur measurements
    • Format of augur output
    • Environment variables
  • Augur Releases & Upgrading
    • Changelog
    • Augur v6 Release Notes
    • Migrating from augur v5 to v6
    • Breaking Changes to augur
    • Compatibility between Augur & Auspice versions
  • Frequently Asked Questions
    • The concept of a ‘build’
    • Preparing Your Metadata
    • Labeling clades
    • Specifying `refine` rates
    • Creating a tree using your own tree builder
  • Examples of Augur in the wild
  • Python Public API
    • augur.io
  • Developer API
    • augur
      • augur.align
      • augur.ancestral
      • augur.clades
      • augur.dates
        • augur.dates.ambiguous_date
        • augur.dates.errors
      • augur.distance
      • augur.errors
      • augur.export
      • augur.export_v1
      • augur.export_v2
      • augur.filenames
      • augur.filter
        • augur.filter._run
        • augur.filter.include_exclude_rules
        • augur.filter.io
        • augur.filter.subsample
        • augur.filter.validate_arguments
      • augur.frequencies
      • augur.frequency_estimators
      • augur.import
      • augur.index
      • augur.io
        • augur.io.file
        • augur.io.json
        • augur.io.metadata
        • augur.io.print
        • augur.io.sequences
        • augur.io.shell_command_runner
        • augur.io.vcf
      • augur.lbi
      • augur.mask
      • augur.measurements
        • augur.measurements.concat
        • augur.measurements.export
      • augur.parse
      • augur.reconstruct_sequences
      • augur.refine
      • augur.sequence_traits
      • augur.titer_model
      • augur.titers
      • augur.traits
      • augur.translate
      • augur.tree
      • augur.types
      • augur.util_support
        • augur.util_support.color_parser
        • augur.util_support.color_parser_line
        • augur.util_support.node_data
        • augur.util_support.node_data_file
        • augur.util_support.node_data_reader
      • augur.utils
      • augur.validate
      • augur.validate_export
      • augur.version
  • Authors
Augur
  • Home
  • Augur
  • Developer API
  • augur
  • Edit on GitHub

augur.filter

Filter and subsample a sequence set.

augur.filter.register_arguments(parser)

Add arguments to parser. Kept as a separate function than register_parser to continue to support unit tests that use this function to create argparser.

augur.filter.register_parser(parent_subparsers)
augur.filter.run(args)

filter and subsample a set of sequences into an analysis set

  • augur.filter._run
    • run()
  • augur.filter.include_exclude_rules
    • apply_filters()
    • construct_filters()
    • filter_by_ambiguous_date()
    • filter_by_date()
    • filter_by_exclude()
    • filter_by_exclude_all()
    • filter_by_exclude_where()
    • filter_by_max_date()
    • filter_by_min_date()
    • filter_by_non_nucleotide()
    • filter_by_query()
    • filter_by_sequence_index()
    • filter_by_sequence_length()
    • force_include_strains()
    • force_include_where()
    • parse_filter_query()
  • augur.filter.io
    • cleanup_outputs()
    • filter_kwargs_to_str()
    • read_priority_scores()
  • augur.filter.subsample
    • PriorityQueue
      • PriorityQueue.add()
      • PriorityQueue.get_items()
    • TooManyGroupsError
    • calculate_sequences_per_group()
    • create_queues_by_group()
    • get_groups_for_subsampling()
  • augur.filter.validate_arguments
    • validate_arguments()
Previous Next

Revision ec95d57c.

Hadfield et al., Nextstrain: real-time tracking of pathogen evolution , Bioinformatics (2018)

The core Nextstrain team is

Trevor Bedford , Richard Neher , Ivan Aksamentov , Jennifer Chang , James Hadfield , Emma Hodcroft , John Huddleston , Jover Lee , Victor Lin , Cornelius Roemer , Thomas Sibley

Please see the team page for more details.


All source code for Nextstrain is freely available under the terms of an open-source license, typically AGPL-3.0 or MIT. Refer to specific projects for details. Screenshots may be used under a CC-BY-4.0 license and attribution to nextstrain.org must be provided.
This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, Josh Batson, David Blazes, Jesse Bloom, Peter Bogner, Anderson Brito, Matt Cotten, Ana Crisan, Tulio de Oliveira, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Nate Grubaugh, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Duncan MacCannell, Erick Matsen, Sebastian Maurer-Stroh, Placide Mbala, Danny Park, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Cecile Viboud for comments, suggestions and data sharing.

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© Copyright 2014–2023 Trevor Bedford and Richard Neher
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