kb_python.config

Module Contents

Classes

Technology

Typed version of namedtuple.

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

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
class kb_python.config.Technology

Bases: NamedTuple

Typed version of namedtuple.

Usage in Python versions >= 3.6:

class Employee(NamedTuple):
    name: str
    id: int

This is equivalent to:

Employee = collections.namedtuple('Employee', ['name', 'id'])

The resulting class has extra __annotations__ and _field_types attributes, giving an ordered dict mapping field names to types. __annotations__ should be preferred, while _field_types is kept to maintain pre PEP 526 compatibility. (The field names are in the _fields attribute, which is part of the namedtuple API.) Alternative equivalent keyword syntax is also accepted:

Employee = NamedTuple('Employee', name=str, id=int)

In Python versions <= 3.5 use:

Employee = NamedTuple('Employee', [('name', str), ('id', int)])
name :str
description :str
chemistry :ngs_tools.chemistry.Chemistry
show :bool = True
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