kb_python.config

Module Contents

Functions

get_provided_kallisto_path() → Optional[str]	Finds platform-dependent kallisto binary included with the installation.
get_provided_bustools_path() → Optional[str]	Finds platform-dependent bustools binary included with the installation.
get_compiled_kallisto_path(alias: str = COMPILED_DIR) → Optional[str]	Finds platform-dependent kallisto binary compiled with compile.
get_compiled_bustools_path(alias: str = COMPILED_DIR) → Optional[str]	Finds platform-dependent bustools binary compiled with compile.
get_kallisto_binary_path() → str	Dummy function that simply returns the current value of KALLISTO_PATH.
get_bustools_binary_path() → str	Dummy function that simply returns the current value of BUSTOOLS_PATH.
set_kallisto_binary_path(path: str)	Helper function to set the KALLISTO_PATH variable. Automatically
set_bustools_binary_path(path: str)	Helper function to set the BUSTOOLS_PATH variable. Automatically
set_dry()	Set this run to be a dry run.
is_dry() → bool	Return whether the current run is a dry run.
no_validate()	Turn off validation.
is_validate() → bool	Return whether validation is turned on.

Attributes

PACKAGE_PATH
PLATFORM
BINS_DIR
COMPILED_DIR
TEMP_DIR
DRY
VALIDATE
GITHUB_API_URL
KALLISTO_REPO_URL
BUSTOOLS_REPO_URL
KALLISTO_RELEASES_URL
BUSTOOLS_RELEASES_URL
KALLISTO_TARBALL_URL
BUSTOOLS_TARBALL_URL
KALLISTO_PATH
BUSTOOLS_PATH
Technology
TECHNOLOGIES
TECHNOLOGIES_MAPPING
Reference
REFERENCES
REFERENCES_MAPPING

kb_python.config.PACKAGE_PATH

kb_python.config.PLATFORM

kb_python.config.BINS_DIR

kb_python.config.COMPILED_DIR

kb_python.config.TEMP_DIR = tmp

kb_python.config.DRY = False

kb_python.config.VALIDATE = True

kb_python.config.GITHUB_API_URL = https://api.github.com

kb_python.config.KALLISTO_REPO_URL

kb_python.config.BUSTOOLS_REPO_URL

kb_python.config.KALLISTO_RELEASES_URL

kb_python.config.BUSTOOLS_RELEASES_URL

kb_python.config.KALLISTO_TARBALL_URL

kb_python.config.BUSTOOLS_TARBALL_URL

kb_python.config.get_provided_kallisto_path() → Optional[str]

Finds platform-dependent kallisto binary included with the installation.

Returns

Path to the binary, None if not found

kb_python.config.get_provided_bustools_path() → Optional[str]

Finds platform-dependent bustools binary included with the installation.

Returns

Path to the binary, None if not found

kb_python.config.get_compiled_kallisto_path(alias: str = COMPILED_DIR) → Optional[str]

Finds platform-dependent kallisto binary compiled with compile.

Parameters

Alias – Alias of compiled binary.

Returns

Path to the binary, None if not found

kb_python.config.get_compiled_bustools_path(alias: str = COMPILED_DIR) → Optional[str]

Finds platform-dependent bustools binary compiled with compile.

Parameters

Alias – Alias of compiled binary.

Returns

Path to the binary, None if not found

kb_python.config.KALLISTO_PATH

kb_python.config.BUSTOOLS_PATH

kb_python.config.Technology

kb_python.config.TECHNOLOGIES

kb_python.config.TECHNOLOGIES_MAPPING

kb_python.config.Reference

kb_python.config.REFERENCES

kb_python.config.REFERENCES_MAPPING

exception kb_python.config.UnsupportedOSError

Bases: Exception

Common base class for all non-exit exceptions.

exception kb_python.config.ConfigError

Bases: Exception

Common base class for all non-exit exceptions.

kb_python.config.get_kallisto_binary_path() → str

Dummy function that simply returns the current value of KALLISTO_PATH.

kb_python.config.get_bustools_binary_path() → str

Dummy function that simply returns the current value of BUSTOOLS_PATH.

kb_python.config.set_kallisto_binary_path(path: str)

Helper function to set the KALLISTO_PATH variable. Automatically finds the full path to the executable and sets that as KALLISTO_PATH.

Parameters

path – Path to the kallisto binary

Raises

ConfigError – If path could not be resolved or if the executable is not executable.

kb_python.config.set_bustools_binary_path(path: str)

Helper function to set the BUSTOOLS_PATH variable. Automatically finds the full path to the executable and sets that as BUSTOOLS_PATH.

Parameters

path – Path to the bustools binary

Raises

ConfigError – If path could not be resolved or if the executable is not executable.

kb_python.config.set_dry()

Set this run to be a dry run.

kb_python.config.is_dry() → bool

Return whether the current run is a dry run.

Returns

Whether the current run is a dry run

kb_python.config.no_validate()

Turn off validation.

kb_python.config.is_validate() → bool

Return whether validation is turned on.

Returns

Whether validation is on