checkQC.runfolder_reader module

class checkQC.runfolder_reader.RunfolderReader

Bases: object

This class provides methods to read files such as the runParameters.xml and RunInfo.xml files, which often need to be read to pick up info about what type of run we are looking at etc.

static find_run_parameters_xml(runfolder)

Finds the path to the [r|R]unParameters.xml :param runfolder: to look in :return: the path to the [r|R]unParameters.xml

static get_nbr_of_lanes(runfolder)

static read_run_info_xml(runfolder)

Read the RunInfo.xml and return it as a dict :param runfolder: to look in :return: RunInfo.xml data as a dict

static read_run_parameters_xml(runfolder)

Read the run parameters of an Illumina instrument are recorded in a file called runParameters or RunParameters depending on the exact instrument type. This method will read it and return it as a dict. :param runfolder: to look in :return: the [R|r]unParameters.xml as a dict :raises: RunParametersNotFound if no [R|r]unParameters.xml was found