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
  • AugurJSONEncoder
    • AugurJSONEncoder.default()
  • BytesWrittenCounterIO
    • BytesWrittenCounterIO.write()
    • BytesWrittenCounterIO.written
  • JSONDecodeError
    • JSONDecodeError.CONTEXT_LENGTH
  • JsonEncoder
    • JsonEncoder.default()
  • as_json()
  • contextualize_char()
  • dump_ndjson()
  • json_size()
  • load_json()
  • load_ndjson()
  • mark_char()
  • shorten_as_json()
  • shorten_left()
  • write_json()
• augur.io.metadata module
  • InvalidDelimiter
  • Metadata
    • Metadata.columns
    • Metadata.delimiter
    • Metadata.id_column
    • Metadata.open()
    • Metadata.path
    • Metadata.rows()
  • read_csv_with_index_col()
  • read_metadata()
  • read_metadata_with_sequences()
  • read_table_to_dict()
  • write_records_to_tsv()
• augur.io.print module
  • indented_list()
  • print_debug()
  • print_err()
• augur.io.sequences module
  • find_feature_errors()
  • get_biopython_format()
  • is_vcf()
  • load_features()
  • read_sequence_ids()
  • read_sequences()
  • read_single_sequence()
  • seqkit()
  • subset_fasta()
  • write_VCF_translation()
  • write_records_to_fasta()
  • write_sequences()
  • write_vcf()
• 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()