How to use the pyopenms.IdXMLFile function in pyopenms

To help you get started, we’ve selected a few pyopenms examples, based on popular ways it is used in public projects.

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OpenMS / OpenMS / pyOpenMS / pyTOPP / IDMapper.py View on Github

def id_mapper(in_file, id_file, out_file, params, use_centroid_rt,
        use_centroid_mz, use_subelements ):

    in_type = pms.FileHandler.getType(in_file)

    protein_ids = []
    peptide_ids = []

    pms.IdXMLFile().load(id_file, protein_ids, peptide_ids)

    mapper = pms.IDMapper()
    mapper.setParameters(params)

    if in_type == pms.Type.CONSENSUSXML:
        file_ = pms.ConsensusXMLFile()
        map_ = pms.ConsensusMap()
        file_.load(in_file, map_)
        mapper.annotate(map_, peptide_ids, protein_ids, use_subelements)
        addDataProcessing(map_, params, pms.ProcessingAction.IDENTIFICATION_MAPPING)
        file_.store(out_file, map_)

    elif in_type == pms.Type.FEATUREXML:
        file_ = pms.FeatureXMLFile()
        map_ = pms.FeatureMap()
        file_.load(in_file, map_)

OpenMS / OpenMS / src / pyOpenMS / pyTOPP / IDMapper.py View on Github

def id_mapper(in_file, id_file, out_file, params, use_centroid_rt,
        use_centroid_mz, use_subelements ):

    in_type = pms.FileHandler.getType(in_file)

    protein_ids = []
    peptide_ids = []

    pms.IdXMLFile().load(id_file, protein_ids, peptide_ids)

    mapper = pms.IDMapper()
    mapper.setParameters(params)

    if in_type == pms.Type.CONSENSUSXML:
        file_ = pms.ConsensusXMLFile()
        map_ = pms.ConsensusMap()
        file_.load(in_file, map_)
        mapper.annotate(map_, peptide_ids, protein_ids, use_subelements)
        addDataProcessing(map_, params, pms.ProcessingAction.IDENTIFICATION_MAPPING)
        file_.store(out_file, map_)

    elif in_type == pms.Type.FEATUREXML:
        file_ = pms.FeatureXMLFile()
        map_ = pms.FeatureMap()
        file_.load(in_file, map_)

How to use the pyopenms.IdXMLFile function in pyopenms

To help you get started, we’ve selected a few pyopenms examples, based on popular ways it is used in public projects.

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