kb_python.config

Module Contents

Functions

get_provided_kallisto_path()	Finds platform-dependent kallisto binary included with the installation.
get_provided_bustools_path()	Finds platform-dependent bustools binary included with the installation.
get_kallisto_binary_path()	Dummy function that simply returns the current value of KALLISTO_PATH.
get_bustools_binary_path()	Dummy function that simply returns the current value of BUSTOOLS_PATH.
set_kallisto_binary_path(path)	Helper function to set the KALLISTO_PATH variable. Automatically finds the
set_bustools_binary_path(path)	Helper function to set the BUSTOOLS_PATH variable. Automatically finds the
set_dry()	Set this run to be a dry run.
is_dry()	Return whether the current run is a dry run.
no_validate()	Turn off validation.
is_validate()	Return whether validation is turned on.

Attributes

PACKAGE_PATH
PLATFORM
BINS_DIR
TEMP_DIR
DRY
VALIDATE
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 = bins

kb_python.config.TEMP_DIR = tmp

kb_python.config.DRY = False

kb_python.config.VALIDATE = True

kb_python.config.get_provided_kallisto_path()

Finds platform-dependent kallisto binary included with the installation.

Returns

path to the binary, None if not found

Return type

str

kb_python.config.get_provided_bustools_path()

Finds platform-dependent bustools binary included with the installation.

Returns

path to the binary, None if not found

Return type

str

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.UnsupportedOSException

Bases: Exception

Common base class for all non-exit exceptions.

exception kb_python.config.NotExecutableException

Bases: Exception

Common base class for all non-exit exceptions.

kb_python.config.get_kallisto_binary_path()

Dummy function that simply returns the current value of KALLISTO_PATH.

kb_python.config.get_bustools_binary_path()

Dummy function that simply returns the current value of BUSTOOLS_PATH.

kb_python.config.set_kallisto_binary_path(path)

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

kb_python.config.set_bustools_binary_path(path)

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

kb_python.config.set_dry()

Set this run to be a dry run.

kb_python.config.is_dry()

Return whether the current run is a dry run.

Returns

whether the current run is a dry run

Return type

bool

kb_python.config.no_validate()

Turn off validation.

kb_python.config.is_validate()

Return whether validation is turned on.

Returns

whether validation is on

Return type

bool