coverage for variant caller (add two cases, find one bug ...)

countess/utils/variant.py

@@ -22,6 +22,11 @@ def translate_aa(aa_seq: str) -> str:
 
  >>> translate_aa("HYPERSENSITIVITIES")
  'HisTyrProGluArgSerGluAsnSerIleThrIleValIleThrIleGluSer'
+
+ >>> translate_aa("SYZYGY")
+ Traceback (most recent call last):
+ ...
+ ValueError: Invalid AA Sequence
  """
 
  try:
@@ -323,11 +328,21 @@ def find_variant_protein(ref_seq: str, var_seq: str, offset: int = 0):
  >>> list(find_variant_protein("ATGGTTGGTTCA", "ATGGGTTCA"))
  ['Val2del']
 
+ a double AA deletion:
+
+ >>> list(find_variant_protein("ATGGTTGGTTCAGGC", "ATGTCAGGC"))
+ ['Val2_Gly3del']
+
  a single AA duplication:
 
  >>> list(find_variant_protein("ATGGTTGGTTCA", "ATGGTTGGTGGTTCA"))
  ['Gly3dup']
 
+ a double AA duplication:
+
+ >>> list(find_variant_protein("ATGGTTGGTTCA", "ATGGTTGGTGTTGGTTCA"))
+ ['Val2_Gly3dup']
+
  a single AA insertion
  >>> list(find_variant_protein("ATGGTTGGTTCA", "ATGGTTGGTAAATCA"))
  ['Gly3_Ser4insLys']
@@ -364,17 +379,16 @@ def find_variant_protein(ref_seq: str, var_seq: str, offset: int = 0):
 
  >>> list(find_variant_protein("ATGGCCCCCAAATAA", "ATGGCGCCAAATTAA"))
  ['Ala2_Pro3=', 'Lys4Asn']
-
  """
 
  ref_seq = ref_seq.strip().upper()
  var_seq = var_seq.strip().upper()
 
  if not re.match("[AGTCN]+$", ref_seq):
- raise ValueError("Invalid reference sequence")
+ raise ValueError("Invalid reference sequence") # pragma: no cover
 
  if not re.match("[AGTCN]+$", var_seq):
- raise ValueError("Invalid variant sequence")
+ raise ValueError("Invalid variant sequence") # pragma: no cover
 
  frame = (3 - offset) % 3
  ref_pro = translate_dna(ref_seq[frame:])[0]
@@ -415,7 +429,7 @@ def _ref(pos):
  if len(dest_pro) == 1:
  yield f"{_ref(start-1)}dup"
  else:
- yield f"{_ref(start-len(dest_pro))}_{_ref(start)}dup"
+ yield f"{_ref(start-len(dest_pro))}_{_ref(start-1)}dup"
  elif start == len(ref_pro):
  # 'extension', not quite standards compliant
  yield f"{_ref(start-1)}ext{translate_aa(dest_pro)}"