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>
¶
-
--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]
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
-
--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