augur.io

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

• augur.io.file
  • open_file()
• augur.io.json
  • 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
  • read_metadata()
  • read_metadata_with_sequences()
  • read_table_to_dict()
  • write_records_to_tsv()
• augur.io.print
  • print_err()
• augur.io.sequences
  • read_sequences()
  • write_records_to_fasta()
  • write_sequences()
• augur.io.shell_command_runner
  • 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.vcf
  • is_vcf()
  • read_vcf()
  • write_VCF_translation()
  • write_vcf()