Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
def link(in_files, out_file, keep_subelements, params):
in_types = set(pms.FileHandler.getType(in_) for in_ in in_files)
if in_types == set((pms.Type.CONSENSUSXML,)):
link_features = False
elif in_types == set((pms.Type.FEATUREXML,)):
link_features = True
else:
raise Exception("different kinds of input files")
algorithm_parameters = params.copy("algorithm:", True)
algorithm = pms.FeatureGroupingAlgorithmQT()
algorithm.setParameters(algorithm_parameters)
out_map = pms.ConsensusMap()
fds = out_map.getColumnHeaders()
if link_features:
f = pms.FeatureXMLFile()
def align(in_files, out_files, out_trafos, reference_index,
reference_file, params):
in_types = set(pms.FileHandler.getType(in_) for in_ in in_files)
if in_types <= set((pms.Type.MZML, pms.Type.MZXML, pms.Type.MZDATA)):
align_features = False
elif in_types == set((pms.Type.FEATUREXML,)):
align_features = True
else:
raise Exception("different kinds of input files")
algorithm = pms.MapAlignmentAlgorithmPoseClustering()
alignment_params = params.copy("algorithm:", True)
algorithm.setParameters(alignment_params)
algorithm.setLogType(pms.LogType.CMD)
plog = pms.ProgressLogger()
plog.setLogType(pms.LogType.CMD)
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_)
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_)