lib5c.core.mixins module

class lib5c.core.mixins.Annotatable

Mixin class for storing and accessing arbitrary annotation information on object instances.

data

Dict to store arbitrary annotation data. Typically, the keys will be strings.

Type:dict

Notes

This mixin requires initialization. Subclasses must explicitly call

Annotatable.__init__(self)

somewhere in their constructor.

When a subclass’s bound functions return a new instance, the following guidelines are recommended:

• addition/summing operations: create a new dict and update it
• other operations: copy a reference to data into the new instance

get_data()

Get this instance’s data attribute.

Returns:This instance’s data attribute. Return type:dict

get_value(key)

Get the value of some key in data. This is equivalent to a get-or-None function for data[key].

Parameters:key (str) – The key to search for in this instance’s data. Returns:The value of data[key], or None if the key does not exist. Return type:any

Examples

>>> from lib5c.core.loci import Locus
>>> locus = Locus('chr3', 34109023, 34113109, num_genes=10)
>>> locus.get_value('num_genes')
10
>>> locus.get_value('num_ctcf_sites') is None
True

set_data(data)

Overwrite this instance’s data attribute with a passed dict.

Parameters:data (dict) – The dict to put in this instance’s data attribute.

set_value(key, value)

Set the value for a specific key in this instance’s data attribute.

Parameters:

• key (str) – The key to set.
• value (any) – The value to store.

class lib5c.core.mixins.Loggable

Mixin class for supporting object event logging.

log

Each string in the list describes an event in this object’s history.

Type:list of str

Notes

This mixin requires initialization. Subclasses must explicitly call

Loggable.__init__(self)

somewhere in their constructor.

When a subclass’s bound functions return a new instance, the following guidelines are recommended:

• addition/summing operations: use the empty log of the new instance
• other operations: copy a reference to log into the new instance

get_log()

Get this instance’s log.

Returns:This instance’s log. Return type:list of str

log_event(event)

Add an event to the log.

Parameters:event (str) – A string describing the event.

print_log()

Print this instance’s log to the console.

class lib5c.core.mixins.Picklable

Mixin class for providing easy reading and writing of instances to disk via the pickle module.

classmethod from_pickle(filename)

Create a new instance of the class from a pickle file.

Parameters:filename (str) – String reference to a pickle file to read from. Returns:Unpickled instance. Return type:cls

to_pickle(filename)

Write this instance to a pickle file.

Parameters:filename (str) – String reference to the file to write this instance to.