bcftbx.SolidData

Legacy module providing classes for extracting data about SOLiD runs from directory structure, data files and naming conventions.

The functionality of the module has been moved to the ‘platforms.solid.data’ 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.

SolidRun

class bcftbx.SolidData.SolidRun(solid_run_dir)

Describe a SOLiD run.

class bcftbx.SolidData.SolidRunInfo(run_name)

Extract data about a run from the run name

Parameters:

run_name – the name of the run, e.g. solid0123_20130426_FRAG_BC_2. NB this is not a path to a run directory

class bcftbx.SolidData.SolidRunDefinition(run_definition_file)

Class to store data from a SOLiD run definition file

Parameters:

run_definition_file (str) – name of run definition file (including any leading path) from which to extract data

class bcftbx.SolidData.SolidBarcodeStatistics(barcode_statistics_file)

Store data from a SOLiD BarcodeStatistics file

class bcftbx.SolidData.SolidProject(name, run=None, sample=None)

Class to hold information about a SOLiD ‘project’

Parameters:

  • name (str) – the name of the project.

  • run (SolidRun) – (optional) the parent SolidRun for the project

  • sample (SolidSample) – (optional) the parent SolidSample for the project

SolidSample

class bcftbx.SolidData.SolidSample(name, parent_run=None)

Store information about a sample in a SOLiD run.

Parameters:

  • name (str) – name of the sample (e.g. AS_XC_pool)

  • parent_run (SolidRun) – (optional) the parent SolidRun object

SolidLibrary

class bcftbx.SolidData.SolidLibrary(name, parent_sample=None)

Store information about a SOLiD library.

Parameters:

  • name (str) – name of the library (e.g. AS_07)

  • parent_sample (SolidSample) – (optional) parent SolidSample object

SolidPrimaryData

class bcftbx.SolidData.SolidPrimaryData

Class to store references to primary data files

Functions

bcftbx.SolidData.extract_library_timestamp(path)

Extract the timestamp string from a path

bcftbx.SolidData.get_primary_data_file_pair(dirn)

Return csfasta/qual file pair from specified directory

bcftbx.SolidData.is_paired_end(solid_run)

Determine if a SolidRun instance is a paired-end run

bcftbx.SolidData.match(pattern, word)

Check if a word matches pattern

bcftbx.SolidData.slide_layout(n_samples)

Description of the slide layout based on number of samples