pept.base.LineDataFilter

class pept.base.LineDataFilter

Bases: Filter

An abstract class that defines a filter for samples of pept.LineData.

An implementor must define the method def fit_sample(self, sample).

A default fit method is provided for convenience, calling fit_sample on each sample from an iterable according to a given execution policy (e.g. “sequential”, “joblib”, or concurrent.futures.Executor subclasses, such as ProcessPoolExecutor or MPIPoolExecutor).

__init__(*args, **kwargs)

Methods

__init__(*args, **kwargs)
copy([deep])	Create a deep copy of an instance of this class, including all inner attributes.
fit(line_data[, executor, max_workers, verbose])	Apply self.fit_sample (implemented by subclasses) according to the execution policy.
fit_sample(sample)
load(filepath)	Load a saved / pickled PEPTObject object from filepath.
save(filepath)	Save a PEPTObject instance as a binary pickle object.

fit(line_data, executor='joblib', max_workers=None, verbose=True)

Apply self.fit_sample (implemented by subclasses) according to the execution policy. Simply return a list of processed samples. If you need a reduction step (e.g. stack all processed samples), apply it in the subclass.

copy(deep=True)

Create a deep copy of an instance of this class, including all inner attributes.

abstract fit_sample(sample)

static load(filepath)

Load a saved / pickled PEPTObject object from filepath.

Most often the full object state was saved using the .save method.

Parameters

filepathfilename or file handle

If filepath is a path (rather than file handle), it is relative to where python is called.

Returns

pept.PEPTObject subclass instance

The loaded object.

Examples

Save a LineData instance, then load it back:

>>> lines = pept.LineData([[1, 2, 3, 4, 5, 6, 7]])
>>> lines.save("lines.pickle")

>>> lines_reloaded = pept.LineData.load("lines.pickle")

save(filepath)

Save a PEPTObject instance as a binary pickle object.

Saves the full object state, including inner attributes, in a portable binary format. Load back the object using the load method.

Parameters

filepathfilename or file handle

If filepath is a path (rather than file handle), it is relative to where python is called.

Examples

Save a LineData instance, then load it back:

>>> lines = pept.LineData([[1, 2, 3, 4, 5, 6, 7]])
>>> lines.save("lines.pickle")

>>> lines_reloaded = pept.LineData.load("lines.pickle")