def map_to_up_primary(ids):
primary_ids = []
for up_id in ids:
if not uniprot_client.is_secondary(up_id):
primary_ids.append(up_id)
continue
primary_id = uniprot_client.get_primary_id(up_id)
primary_ids.append(primary_id)
# If there are no primary IDs, we return None
if not primary_ids:
return None
# Try to get primary IDs if there are
# If there is more than one primary ID then we return the first one
elif len(primary_ids) > 1:
human_upids = [
id for id in primary_ids if uniprot_client.is_human(id)
]
if not human_upids:
logger.info('More than one primary id but none human, '
'choosing the first: %s' %
','.join(primary_ids))
primary_id = primary_ids[0]
elif len(human_upids) > 1:
logger.info('More than one human primary id, choosing '
'the first: %s' % ','.join(human_upids))
primary_id = human_upids[0]
# Only one, so use it
else:
primary_id = human_upids[0]
# One primary ID, so use it
else:
primary_id = primary_ids[0]
# Make sure it's unicode
return str(primary_id)
def test_all_uniprot_ids():
for obj in bp.model.getObjects().toArray():
bpe = bpc._cast_biopax_element(obj)
if bpc._is_protein(bpe):
uniprot_id = bp._get_uniprot_id(bpe)
if uniprot_id is not None:
assert (not uniprot_client.is_secondary(uniprot_id))
assert (unicode_strs(uniprot_id))
def test_all_uniprot_ids():
for obj in bp.model.getObjects().toArray():
bpe = bpc._cast_biopax_element(obj)
if bpc._is_protein(bpe):
uniprot_id = bp._get_uniprot_id(bpe)
if uniprot_id is not None:
assert(not uniprot_client.is_secondary(uniprot_id))
assert(unicode_strs(uniprot_id))
def map_to_up_primary(ids):
primary_ids = []
for up_id in ids:
if not uniprot_client.is_secondary(up_id):
primary_ids.append(up_id)
continue
primary_id = uniprot_client.get_primary_id(up_id)
primary_ids.append(primary_id)
# If there are no primary IDs, we return None
if not primary_ids:
return None
# Try to get primary IDs if there are
# If there is more than one primary ID then we return the first one
if len(primary_ids) > 1:
logger.info('More than one primary id: %s' %
','.join(primary_ids))
# Make sure it's unicode
primary_id = str(primary_ids[0])
return primary_id
def test_is_secondary_secondary():
assert uniprot_client.is_secondary('Q96J62')
def test_is_secondary_primary():
assert not uniprot_client.is_secondary('Q02750')
def test_is_secondary_secondary():
assert uniprot_client.is_secondary('Q96J62')
def test_is_secondary_primary():
assert not uniprot_client.is_secondary('Q02750')