kb_python.config
¶
Module Contents¶
Classes¶
Typed version of namedtuple. |
Functions¶
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Finds platform-dependent kallisto binary included with the installation. |
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Finds platform-dependent bustools binary included with the installation. |
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Finds platform-dependent kallisto binary compiled with compile. |
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Finds platform-dependent bustools binary compiled with compile. |
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Dummy function that simply returns the current value of |
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Dummy function that simply returns the current value of |
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Helper function to set the |
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Helper function to set the |
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Set this run to be a dry run. |
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Return whether the current run is a dry run. |
Turn off validation. |
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Return whether validation is turned on. |
Attributes¶
- 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 asKALLISTO_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 asBUSTOOLS_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