mqrun.mqparams.xml_to_data

mqrun.mqparams.xml_to_data(xml_tree, logger=None)

Extract parameters and file-paths from MaxQuant configuration file

Parameters:

• xml_tree (xml.etree.ElementTree.Element.Tree) – MaxQuant configuration file.
• logger (logging.Logger, optional) – Logger for the conversion process. Use logging.getLogger('mqparams') if not specified.

Returns:

• params (dict) – Parameters as described in module doc
• path_data (mqparams.ExtraMQData) – Path information from xml file
• extra_data has the following attributes
• file_paths (dict) – Mapping from names for input files to paths
• fasta_paths (dict # TODO merge with file_paths) – Same for fasta files
• output_dir (pathlib.Path) – Path to the output directory
• tmp_dir (pathlib.Path) – Path to temporary directory