Command Line Interface¶

pybel-tools¶

PyBEL-Tools v0.7.1-dev Command Line Interface on /home/docs/checkouts/readthedocs.org/user_builds/pybel-tools/envs/develop/bin/python with PyBEL v0.13.1

pybel-tools [OPTIONS] COMMAND [ARGS]...

Options

--version¶: Show the version and exit.

annotation¶

Annotation file utilities.

pybel-tools annotation [OPTIONS] COMMAND [ARGS]...

convert-to-namespace¶

Convert an annotation file to a namespace file.

pybel-tools annotation convert-to-namespace [OPTIONS]

Options

-f, --file <file>¶: Path to input BEL Namespace file

-o, --output <output>¶: Path to output converted BEL Namespace file

--keyword <keyword>¶: Set custom keyword. useful if the annotation keyword is too long

document¶

BEL document utilities.

pybel-tools document [OPTIONS] COMMAND [ARGS]...

boilerplate¶

Build a template BEL document with the given PubMed identifiers.

pybel-tools document boilerplate [OPTIONS] NAME CONTACT DESCRIPTION [PMIDS]...

Options

--version <version>¶

--copyright <copyright>¶

--authors <authors>¶

--licenses <licenses>¶

--disclaimer <disclaimer>¶

--output <output>¶

Arguments

NAME¶: Required argument

CONTACT¶: Required argument

DESCRIPTION¶: Required argument

PMIDS¶: Optional argument(s)

serialize-namespaces¶

Parse a BEL document then serializes the given namespaces (errors and all) to the given directory.

pybel-tools document serialize-namespaces [OPTIONS] [NAMESPACES]...

Options

-c, --connection <connection>¶: Database connection string. [default: sqlite:////home/docs/.pybel/pybel_0.13.0_cache.db]

-p, --path <path>¶: Input BEL file path. Defaults to stdin.

-d, --directory <directory>¶: Output folder. Defaults to current working directory /home/docs/checkouts/readthedocs.org/user_builds/pybel-tools/checkouts/develop/docs/source)

Arguments

NAMESPACES¶: Optional argument(s)

io¶

Upload and conversion utilities

pybel-tools io [OPTIONS] COMMAND [ARGS]...

Options

-c, --connection <connection>¶: Database connection string. [default: sqlite:////home/docs/.pybel/pybel_0.13.0_cache.db]

get-pmids¶

Output PubMed identifiers from a graph to a stream.

pybel-tools io get-pmids [OPTIONS] path

Options

-o, --output <output>¶

Arguments

path¶: Required argument

namespace¶

Namespace file utilities.

pybel-tools namespace [OPTIONS] COMMAND [ARGS]...

convert-to-annotation¶

Convert a namespace file to an annotation file.

pybel-tools namespace convert-to-annotation [OPTIONS]

Options

-f, --file <file>¶: Path to input BEL Namespace file

-o, --output <output>¶: Path to output converted BEL Annotation file

write¶

Build a namespace from items.

pybel-tools namespace write [OPTIONS] NAME KEYWORD DOMAIN CITATION

Options

--author <author>¶

--description <description>¶

--species <species>¶

--version <version>¶

--contact <contact>¶

--license <license>¶

--values <values>¶: A file containing the list of names

--output <output>¶

Arguments

NAME¶: Required argument

KEYWORD¶: Required argument

DOMAIN¶: Required argument

CITATION¶: Required argument