opencloning 0.2.8.3__py3-none-any.whl → 0.3.1__py3-none-any.whl

opencloning/_version.py

@@ -0,0 +1,7 @@
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version(__name__.split('.')[0])
+except PackageNotFoundError:
+    # package not installed
+    __version__ = '0.0.0'

opencloning/assembly2.py

@@ -465,6 +465,17 @@ def assemble(fragments, assembly, is_insertion=False):
         is_circular = assembly_is_circular(assembly, fragments)
 
     subfragment_representation = edge_representation2subfragment_representation(assembly, is_circular)
+
+    # Sanity check
+    for asm_edge in assembly:
+        u, v, loc_u, loc_v = asm_edge
+        f_u = fragments[u - 1] if u > 0 else fragments[-u - 1].reverse_complement()
+        f_v = fragments[v - 1] if v > 0 else fragments[-v - 1].reverse_complement()
+        seq_u = str(loc_u.extract(f_u).seq).upper()
+        seq_v = str(loc_v.extract(f_v).seq).upper()
+        if seq_u != seq_v:
+            raise ValueError('Mismatch in assembly')
+
     # We transform into Dseqrecords (for primers)
     dseqr_fragments = [f if isinstance(f, _Dseqrecord) else _Dseqrecord(f) for f in fragments]
     subfragments = get_assembly_subfragments(dseqr_fragments, subfragment_representation)

opencloning/batch_cloning/pombe/__init__.py

@@ -9,9 +9,7 @@ from .pombe_summary import main as pombe_summary
 from .pombe_gather import main as pombe_gather
 import shutil
 import traceback
-import json
 from ...get_router import get_router
-from ...utils import api_version
 from fastapi import Request
 
 router = get_router()
@@ -75,10 +73,6 @@ async def post_batch_cloning(
         except Exception:
             raise HTTPException(status_code=400, detail='Summary failed')
 
-        # Write the version
-        with open(os.path.join(temp_dir, 'version.json'), 'w') as f:
-            f.write(json.dumps(api_version(), indent=2))
-
         # zip the temp dir and return it
         zip_filename = f'{temp_dir}_archive'
         shutil.make_archive(zip_filename, 'zip', temp_dir)