opencloning 0.2.8.1__py3-none-any.whl → 0.2.8.3__py3-none-any.whl

opencloning/dna_functions.py

@@ -241,16 +241,23 @@ def find_sequence_regex(pattern: str, seq: str, is_circular: bool) -> list[Locat
 def oligonucleotide_hybridization_overhangs(
     fwd_oligo_seq: str, rvs_oligo_seq: str, minimal_annealing: int
 ) -> list[int]:
+    """
+    Returns possible overhangs between two oligos, and returns an error if mismatches are found.
+
+    see https://github.com/manulera/OpenCloning_backend/issues/302 for notation
+
+    """
     matches = common_sub_strings(fwd_oligo_seq.lower(), reverse_complement(rvs_oligo_seq.lower()), minimal_annealing)
 
-    for m in matches:
-        if not (
-            (m[0] == 0 and m[1] + m[2] == len(fwd_oligo_seq)) or (m[1] == 0 and m[0] + m[2] == len(rvs_oligo_seq))
+    for pos_fwd, pos_rvs, length in matches:
+
+        if (pos_fwd != 0 and pos_rvs != 0) or (
+            pos_fwd + length < len(fwd_oligo_seq) and pos_rvs + length < len(rvs_oligo_seq)
         ):
             raise ValueError('The oligonucleotides can anneal with mismatches')
 
     # Return possible overhangs
-    return [start_on_rvs - start_on_fwd for start_on_fwd, start_on_rvs, length in matches]
+    return [pos_rvs - pos_fwd for pos_fwd, pos_rvs, length in matches]
 
 
 class MyGenBankScanner(GenBankScanner):

{opencloning-0.2.8.1.dist-info → opencloning-0.2.8.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.2.8.1
+Version: 0.2.8.3
 Summary: Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.
 License: MIT
 Author: Manuel Lera-Ramirez
@@ -18,7 +18,7 @@ Requires-Dist: httpx (>=0.25.0,<0.26.0)
 Requires-Dist: opencloning-linkml (==0.2.6.1a0)
 Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
-Requires-Dist: primer3-py (>=2.0.3,<3.0.0)
+Requires-Dist: primer3-py (==2.0.3)
 Requires-Dist: pydantic (>=2.7.1,<3.0.0)
 Requires-Dist: pydna (==5.5.0)
 Requires-Dist: python-multipart

{opencloning-0.2.8.1.dist-info → opencloning-0.2.8.3.dist-info}/RECORD

@@ -20,7 +20,7 @@ opencloning/batch_cloning/ziqiang_et_al2024/__init__.py,sha256=zZUbj3uMzd9rKMXi5
 opencloning/batch_cloning/ziqiang_et_al2024/index.html,sha256=EDncANDhhQkhi5FjnnAP6liHkG5srf4_Y46IrnMUG5g,4607
 opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=mB81j2qWam7uRc-980YFjfqq2CiWTXJYfKFAoKuGtRw,157148
 opencloning/cre_lox.py,sha256=mb2ZddjrPIrUBT3xxMub5-c97WkKZ4Z-HkGFVzuR8pQ,2031
-opencloning/dna_functions.py,sha256=W-SxEfvYpN1JVZbTeCNitpQXkazEHvFyqZBUndd-jpY,16329
+opencloning/dna_functions.py,sha256=ivepJM2wRTIW0ArSiQ5s-XuqBd69giEQijaWXXGT64E,16536
 opencloning/dna_utils.py,sha256=uv97aO04dbk3NnqbN6GlnwOu0MOpK88rl2np2QcEQ4Y,6301
 opencloning/ebic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 opencloning/ebic/primer_design.py,sha256=gPZTF9w5SV7WGgnefp_HBM831y0z73M1Kb0QUPnbfIM,2270
@@ -40,7 +40,7 @@ opencloning/primer_design.py,sha256=nqCmYIZ7UvU4CQwVGJwX7T5LTHwt3-51_ZcTZZAgT_Y,
 opencloning/pydantic_models.py,sha256=gsipVXhjQOXVz2NL-MiNpLuOZYDVo2Pli9F--bp6tjs,15345
 opencloning/request_examples.py,sha256=QAsJxVaq5tHwlPB404IiJ9WC6SA7iNY7XnJm63BWT_E,2944
 opencloning/utils.py,sha256=wsdTJYliap-t3oa7yQE3pWDa1CR19mr5lUQfocp4hoM,1875
-opencloning-0.2.8.1.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
-opencloning-0.2.8.1.dist-info/METADATA,sha256=rp3mHAG3x49YfumIjM5teZL6iAtRbhQG1tl64bOjPfI,8429
-opencloning-0.2.8.1.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-opencloning-0.2.8.1.dist-info/RECORD,,
+opencloning-0.2.8.3.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.2.8.3.dist-info/METADATA,sha256=Wox-THlR-NrqHBqQ5Fo8PG_-2Vl55dvNS6rRZlpkRMs,8422
+opencloning-0.2.8.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+opencloning-0.2.8.3.dist-info/RECORD,,

{opencloning-0.2.8.1.dist-info → opencloning-0.2.8.3.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.2
+Generator: poetry-core 2.1.3
 Root-Is-Purelib: true
 Tag: py3-none-any