Fix imgt numbering of CDR1 and CDR2

abnumber/common.py

@@ -40,12 +40,6 @@ def _anarci_align(sequence, scheme, allowed_species, assign_germline=False) -> L
         species = ali['species']
         v_gene = ali['germlines']['v_gene'][0][1] if assign_germline else None
         j_gene = ali['germlines']['j_gene'][0][1] if assign_germline else None
-        if scheme == 'imgt':
-            for (num, letter), aa in positions:
-                if str(num) == '61' and str(letter) == 'A':
-                    raise NotImplementedError(f'Cannot parse sequence "{sequence}", '
-                                              f'ANARCI numbering of IMGT position 61A is currently broken: '
-                                              f'https://github.com/oxpig/ANARCI/issues/14')
         aa_dict = {Position(chain_type=chain_type, number=num, letter=letter, scheme=scheme): aa
                    for (num, letter), aa in positions if aa != '-'}
         tail = sequence[end+1:]

abnumber/position.py

@@ -90,7 +90,7 @@ def chain_type_prefix(self):
     def _sort_key(self):
         letter_ord = ord(self.letter) if self.letter else 0
         if self.scheme == 'imgt':
-            if self.number == 112:
+            if self.number in [33, 61, 112]:
                 # position 112 is sorted in reverse
                 letter_ord = -letter_ord
         elif self.scheme in ['chothia', 'kabat', 'aho']:

test/test_bugs.py

@@ -4,11 +4,29 @@
 
 
 def test_imgt_61A():
-    """Related to ANARCI issue: https://github.com/oxpig/ANARCI/issues/14"""
-    assert Position.from_string('61A', 'H', 'imgt') > Position.from_string('61', 'H', 'imgt')
+    assert Position.from_string('61A', 'H', 'imgt') < Position.from_string('61', 'H', 'imgt')
     seq = 'EVQLVESGGGLVQPGGSLRLSCAASGIILDYYPIGWFRQAPGKEREGVAFITNSDDSTIYTNYADSVKGRFTISRDKNSLYLQMNSLRAEDTAVYYCSSKASFLIGKDDQGIDAGEYDYWGQGTMVTVSS'
-    with pytest.raises(NotImplementedError):
-        chain = Chain(seq, 'imgt')
+    chain = Chain(seq, 'imgt')
+    assert chain.seq == seq
+
+def test_imgt_33A():
+    assert Position.from_string('33A', 'H', 'imgt') < Position.from_string('33', 'H', 'imgt')
+    seq = 'EVQLVESGGGLVQPGGSLRLSCAASGIILELVISDYYPIGWFRQAPGKEREGVAFITNSDDSTIYTNYADSVKGRFTISRDKNSLYLQMNSLRAEDTAVYYCSSKASFLIGKDDQGIDAGEYDYWGQGTMVTVSS'
+    chain = Chain(seq, 'imgt')
+    assert chain.seq == seq
+
+
+def test_kappa_imgt_21():
+    from anarci import run_hmmer
+    sequence = 'DVVMTQSPLSLPVTLGQPASISCRSSQSLVYSDGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGTFGQGTKVEIK'
+    alignment = run_hmmer([('id', sequence)], hmm_database="ALL", hmmerpath="", ncpu=None, bit_score_threshold=80)[0]
+    print(len(alignment))
+    print('---')
+    for pos in alignment:
+        print(pos)
+    print('---')
+    for pos, aa in zip(alignment, sequence):
+        print(pos, aa)
 
 
 def test_light_chain_IMGT_position_21():