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Augur
version 30.0.1

Table of contents

  • Installation
  • Using Augur
    • Augur subcommands
      • augur parse
      • augur curate
        • passthru
        • normalize-strings
        • format-dates
        • titlecase
        • apply-geolocation-rules
        • apply-record-annotations
        • abbreviate-authors
        • parse-genbank-location
        • transform-strain-name
        • rename
      • augur merge
      • 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
      • augur read-file
      • augur write-file
    • Format of augur output
    • Environment variables
  • Augur Releases & Upgrading
    • Changelog
    • Deprecated features
    • Augur v6 Release Notes
    • Migrating from augur v5 to v6
    • Compatibility between Augur & Auspice versions
  • Frequently Asked Questions
    • What is a “build”?
    • How do I prepare metadata?
    • How do I label clades?
    • How do I specify refine rates?
    • How do I use my own tree builder?
  • Examples of Augur in the wild
  • Python Public API
    • augur.io
  • Developer API
    • augur package
      • augur.curate package
        • augur.curate.abbreviate_authors module
        • augur.curate.apply_geolocation_rules module
        • augur.curate.apply_record_annotations module
        • augur.curate.format_dates module
        • augur.curate.format_dates_directives module
        • augur.curate.normalize_strings module
        • augur.curate.parse_genbank_location module
        • augur.curate.passthru module
        • augur.curate.rename module
        • augur.curate.titlecase module
        • augur.curate.transform_strain_name module
      • augur.data package
      • augur.dates package
        • augur.dates.ambiguous_date module
        • augur.dates.errors module
      • augur.filter package
        • augur.filter.constants module
        • augur.filter.include_exclude_rules module
        • augur.filter.io module
        • augur.filter.subsample module
        • augur.filter.validate_arguments module
        • augur.filter.weights_file module
      • augur.import_ package
        • augur.import_.beast module
      • augur.io package
        • augur.io.file module
        • augur.io.json module
        • augur.io.metadata module
        • augur.io.print module
        • augur.io.sequences module
        • augur.io.shell_command_runner module
        • augur.io.strains module
        • augur.io.vcf module
      • augur.measurements package
        • augur.measurements.concat module
        • augur.measurements.export module
      • augur.util_support package
        • augur.util_support.auspice_config module
        • augur.util_support.color_parser module
        • augur.util_support.color_parser_line module
        • augur.util_support.node_data module
        • augur.util_support.node_data_file module
        • augur.util_support.node_data_reader module
        • augur.util_support.warnings module
      • augur.align module
      • augur.ancestral module
      • augur.argparse_ module
      • augur.clades module
      • augur.debug module
      • augur.distance module
      • augur.errors module
      • augur.export module
      • augur.export_v1 module
      • augur.export_v2 module
      • augur.frequencies module
      • augur.frequency_estimators module
      • augur.index module
      • augur.lbi module
      • augur.mask module
      • augur.merge module
      • augur.parse module
      • augur.read_file module
      • augur.reconstruct_sequences module
      • augur.refine module
      • augur.sequence_traits module
      • augur.titer_model module
      • augur.titers module
      • augur.traits module
      • augur.translate module
      • augur.tree module
      • augur.types module
      • augur.utils module
      • augur.validate module
      • augur.validate_export module
      • augur.version module
      • augur.write_file module
  • Authors
Augur
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  • Augur
  • Developer API
  • augur package
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augur.io package

Interfaces for reading and writing data also known as input/output (I/O)

Submodules

  • augur.io.file module
    • open_file()
  • augur.io.json module
    • JSONDecodeError
      • JSONDecodeError.CONTEXT_LENGTH
    • JsonEncoder
      • JsonEncoder.default()
    • as_json()
    • contextualize_char()
    • dump_ndjson()
    • load_json()
    • load_ndjson()
    • mark_char()
    • shorten_as_json()
    • shorten_left()
  • augur.io.metadata module
    • InvalidDelimiter
    • Metadata
      • Metadata.columns
      • Metadata.delimiter
      • Metadata.id_column
      • Metadata.open()
      • Metadata.path
      • Metadata.rows()
    • read_metadata()
    • read_metadata_with_sequences()
    • read_table_to_dict()
    • write_records_to_tsv()
  • augur.io.print module
    • print_debug()
    • print_err()
  • augur.io.sequences module
    • get_biopython_format()
    • read_sequences()
    • read_single_sequence()
    • write_records_to_fasta()
    • write_sequences()
  • augur.io.shell_command_runner module
    • ShellCommandRunner
      • ShellCommandRunner.invoke_command()
      • ShellCommandRunner.modified_env
      • ShellCommandRunner.print_error()
      • ShellCommandRunner.print_error_message()
      • ShellCommandRunner.run()
      • ShellCommandRunner.shell_args
      • ShellCommandRunner.shell_executable
      • ShellCommandRunner.signal_from_error()
    • run_shell_command()
  • augur.io.strains module
    • read_strains()
  • augur.io.vcf module
    • is_vcf()
    • write_VCF_translation()
    • write_vcf()
Previous Next

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

The core Nextstrain team is

Trevor Bedford , Richard Neher , Ivan Aksamentov , John SJ Anderson , Kim Andrews , 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 2014–2025 Trevor Bedford and Richard Neher

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