def iterate_taxon(taxid=9606):
"""
This is an ad hoc fix to fix humans or similar. For full deployment use ProteomeParser.
:param taxid:
:return:
"""
path = os.path.join(global_settings.pickle_folder, f'taxid{taxid}')
for pf in os.listdir(path):
try:
protein = ProteinGatherer().load(file=os.path.join(path, pf))
protein.gnomAD = []
protein.parse_gnomAD()
protein.get_PTM()
protein.compute_params()
protein.dump()
#michelanglo_protein.get_offsets().parse_gnomAD().compute_params()
#michelanglo_protein.dump()
except:
pass
namedexfile=os.path.join(global_settings.dictionary_folder,
'taxid9606-names2uniprot.json'),
folder=os.path.join(global_settings.temp_folder, 'gnomAD')).split()
if __name__ == '__main__':
global_settings.verbose = True #False
global_settings.error_tolerant = True
global_settings.startup(data_folder='../protein-data')
global_settings.retrieve_references(ask=False, refresh=False)
## Phosphosite
#Phosphosite().split().write()
message('Phosphosite split')
## Uniprot
UniprotMasterReader(first_n_protein=0)
message('Uniprot split')
# gnomAD data needs to be split up after that the dictionaries are made.
# _gnomad()
message('gnomAD split')
taxid = 9606 # that's humans
path = os.path.join(global_settings.pickle_folder, f'taxid{taxid}')
for pf in os.listdir(path):
try:
protein = ProteinGatherer().load(file=os.path.join(path, pf))
protein.gnomAD = []
protein.parse_gnomAD()
protein.get_PTM()
protein.dump()
except:
pass
message('Done.')