pyani.scripts.subcommands.subcmd_report module

Provides the report subcommand for pyani.

class pyani.scripts.subcommands.subcmd_report.ReportParams

Bases: tuple

Report query/header data.

headers

Alias for field number 2

name

Alias for field number 0

statement

Alias for field number 1

pyani.scripts.subcommands.subcmd_report.process_formats(args: argparse.Namespace) → List[str]

Return processed list of output formats for writing reports.

Parameters:args – Namespace of command-line arguments

pyani.scripts.subcommands.subcmd_report.report(args: argparse.Namespace, session, formats: List[str], params: pyani.scripts.subcommands.subcmd_report.ReportParams) → None

Write tabular report of pyani runs from database.

Parameters:

• args – Namespace of command-line arguments
• session – SQLAlchemy database session
• formats – list of output formats
• params – ReportParams namedtuple

pyani.scripts.subcommands.subcmd_report.subcmd_report(args: argparse.Namespace) → int

Present report on ANI results and/or database contents.

Parameters:args – Namespace, command-line arguments

The report subcommand takes any of several long options that do one of two things:

1. perform a single action.
2. set a parameter/format

These will typically take an output path to a file or directory into which the report will be written (whatever form it takes). By default, text output is written in plain text format, but for some outputs this can be modified by an ‘excel’ or ‘html’ format specifier, which writes outputs in that format, where possible.