veoibd_synapse.rules package

Module contents

Provide code supporting the running and automating of Snakemake rules.

veoibd_synapse.rules.apply_template(template, keywords)

Return a list of strings of form template with values in keywords 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.

veoibd_synapse.rules.pathify_by_key_ends(dictionary)

Return a dict that has had all values with keys containing the suffixes: ‘_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 veoibd_synapse.rules.SnakeRun(cfg, snakefile)

Bases: object

Initialize and manage information common to the whole run.

__init__(cfg, snakefile)

Initialize common information for a run.

class veoibd_synapse.rules.SnakeRule(run, name, pretty_name=None)

Bases: object

Manage the initialization and deployment of rule-specific information.

__init__(run, name, pretty_name=None)

Initialize logs, inputs, outputs, params, etc for a single rule.

_import_config_dict()

Import configuration values set for this rule so they are directly accessable as attributes.

veoibd_synapse.rules.recode_graph(dot, new_dot, pretty_names, rules_to_drop, color=None, use_pretty_names=True)

Change dot label info to pretty_names and alter styling.