bcftbx.Experiment

Legacy module for handling SOLiD experiments (groups of primary data sets from a SOLiD sequencing run).

The functionality of the module has been moved to the ‘platforms.solid.experiment’ module, which supersedes this one. This module is now deprecated and will be removed in a future release.

The legacy classes have been reimplemented as wrappers to the classes in the newer module, to preserve backwards compatibility.

class bcftbx.Experiment.Experiment

Class defining an experiment from a SOLiD run.

An ‘experiment’ is a collection of related data.

class bcftbx.Experiment.ExperimentList(solid_run_dir=None)

Container for a collection of Experiments

addDuplicateExperiment(expt)

Duplicate an existing Experiment and add to the list

addExperiment(name)

Create a new Experiment and add to the list

buildAnalysisDirs(top_dir=None, dry_run=False, link_type='relative', naming_scheme='partial')

Construct and populate analysis directories for the experiments

getLastExperiment()

Return the last Experiment added to the list

class bcftbx.Experiment.LinkNames(scheme)

Class to construct names for links to primary data files