snaketools package¶
Submodules¶
snaketools.errors module¶
Provide error classes for snaketools.
-
exception
snaketools.errors.
NotImplementedYet
(msg=None)[source]¶ Bases:
NotImplementedError
,snaketools.errors.SnaketoolsError
Raise when a section of code that has been left for another time is asked to execute.
-
exception
snaketools.errors.
SnaketoolsError
[source]¶ Bases:
Exception
Base error class for veoibd-synapse-data-manager.
-
exception
snaketools.errors.
ValidationError
[source]¶ Bases:
snaketools.errors.SnaketoolsError
Raise when a validation/sanity check comes back with unexpected value.
snaketools.snaketools module¶
Provide code supporting the running and automating of Snakemake rules.
-
snaketools.snaketools.
apply_template
(template, keywords)[source]¶ Return a list of strings of form
template
with values inkeywords
inserted.Parameters: - template (
str
) – a string containing keywords ({kw_name}
). - keywords (
dict
-like) – dict with keys of appropriate keyword names and values as equal length ORDERED lists with the correct values to be inserted.
- template (
-
snaketools.snaketools.
pathify_by_key_ends
(dictionary)[source]¶ Return a dict that has had all values with keys containing the suffixes: ‘_FILE’, ‘_PATH’ or ‘_DIR’ converted to Path() instances.
Parameters: dictionary (dict-like) – Usually the loaded, processed config file as a dict. Returns: Modified version of the input. Return type: dict-like
-
class
snaketools.snaketools.
SnakeRun
(cfg, snakefile)[source]¶ Bases:
object
Initialize and manage information common to the whole run.
-
class
snaketools.snaketools.
SnakeRule
(run, name, pretty_name=None)[source]¶ Bases:
object
Manage the initialization and deployment of rule-specific information.
Module contents¶
Top-level package for SnakeTools.