def get_phospho_antibody_map(fname=antibody_map_file):
# First gather the annotations for the phosphosites
df = pandas.read_csv(fname, index_col=None, sep=',', encoding='utf8')
antibody_map = {}
for _, row in df.iterrows():
ps = row['phosphosite']
sub_upid = row['SUB_ID']
if not pandas.isnull(sub_upid):
if sub_upid.find('-') != -1:
sub_upid = sub_upid.split('-')[0]
sub_hgnc_symbol = uniprot_client.get_gene_name(sub_upid)
sub_hgnc = hgnc_client.get_hgnc_id(sub_hgnc_symbol)
else:
sub_hgnc_symbol = row['SUB_GENE']
sub_hgnc_id = hgnc_client.get_hgnc_id(sub_hgnc_symbol)
sub_upid = hgnc_client.get_uniprot_id(sub_hgnc_id)
if sub_upid is None:
continue
sub = Agent(sub_hgnc_symbol,
db_refs={
'UP': sub_upid,
'HGNC': sub_hgnc
})
residue = row['Actual_site'][0]
if len(row['Actual_site']) > 1:
position = row['Actual_site'][1:]
else:
position = None
mc = ModCondition('phosphorylation', residue, position)
sub.mods = [mc]
if ps in antibody_map:
found = False
for p in antibody_map[ps]:
if p.name == sub.name and p.mods[0].residue == residue and \
p.mods[0].position == position:
found = True
break
if not found:
antibody_map[ps].append(sub)
else:
antibody_map[ps] = [sub]
return antibody_map
