opencloning 0.3.4__py3-none-any.whl → 0.3.5__py3-none-any.whl

opencloning/assembly2.py

@@ -745,7 +745,14 @@ class Assembly:
     Examples
     --------
 
-    from assembly2 import Assembly, example_fragments, assembly2str
+    from assembly2 import Assembly, assembly2str
+    from pydna.dseqrecord import Dseqrecord
+
+    example_fragments = (
+        Dseqrecord('AacgatCAtgctcc', name='a'),
+        Dseqrecord('TtgctccTAAattctgc', name='b'),
+        Dseqrecord('CattctgcGAGGacgatG', name='c'),
+    )
 
     asm = Assembly(example_fragments, limit=5, use_fragment_order=False)
     print('Linear ===============')
@@ -1337,22 +1344,3 @@ class SingleFragmentAssembly(Assembly):
 
     def get_linear_assemblies(self):
         raise NotImplementedError('Linear assembly does not make sense')
-
-
-example_fragments = (
-    _Dseqrecord('AacgatCAtgctcc', name='a'),
-    _Dseqrecord('TtgctccTAAattctgc', name='b'),
-    _Dseqrecord('CattctgcGAGGacgatG', name='c'),
-)
-
-
-'CattctgcGAGGacgatCAtgctcc'
-
-linear_results = (
-    _Dseqrecord('AacgatCAtgctccTAAattctgcGAGGacgatG', name='abc'),
-    _Dseqrecord('ggagcaTGatcgtCCTCgcagaatG', name='ac_rc'),
-    _Dseqrecord('AacgatG', name='ac'),
-)
-
-
-circular_results = (_Dseqrecord('acgatCAtgctccTAAattctgcGAGG', name='abc', circular=True),)

opencloning/endpoints/assembly.py

@@ -39,6 +39,7 @@ from ..assembly2 import (
     blunt_overlap,
     combine_algorithms,
     annotate_primer_binding_sites,
+    common_sub_strings,
 )
 
 from ..gateway import gateway_overlap, find_gateway_sites, annotate_gateway_sites
@@ -417,8 +418,9 @@ async def gibson_assembly(
     def create_source(a, is_circular):
         return source.__class__.from_assembly(assembly=a, circular=is_circular, id=source.id, fragments=fragments)
 
+    algo = gibson_overlap if not isinstance(source, InVivoAssemblySource) else common_sub_strings
     resp = generate_assemblies(
-        source, create_source, fragments, circular_only, gibson_overlap, False, {'limit': minimal_homology}
+        source, create_source, fragments, circular_only, algo, False, {'limit': minimal_homology}
     )
 
     if len(resp['sources']) == 0:

{opencloning-0.3.4.dist-info → opencloning-0.3.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.3.4
+Version: 0.3.5
 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

{opencloning-0.3.4.dist-info → opencloning-0.3.5.dist-info}/RECORD

@@ -2,7 +2,7 @@ opencloning/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 opencloning/_version.py,sha256=6QbWXLSZypjtWL_CwJFHH4dzMRK3AUH4B0YudzvGz9s,200
 opencloning/api_config_utils.py,sha256=inAXPGYNDz-DuEoSqitImj0Vv5TpQSbMZH9D3dQb5P0,4319
 opencloning/app_settings.py,sha256=MScy0le1Dn00rxqDkpeoBLWwjWQTyzHBQ-MqSDdmoe4,2054
-opencloning/assembly2.py,sha256=_UdQCnjc2wmWoeVT9NKwXcYUAEBrBT0OSBNMbGYAIL8,57041
+opencloning/assembly2.py,sha256=GEHii1WSXoUFjJDeCBXsCxQ6tIqhwF77DeRnsxkrtMM,56770
 opencloning/batch_cloning/EBIC/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 opencloning/batch_cloning/EBIC/barcode.gb,sha256=G6kP6MuY23S-n3xg16LQaTasFtYFqik5eEgcooZ9ATM,815
 opencloning/batch_cloning/EBIC/common_plasmid.gb,sha256=At1HJjqJ2MsLMEx6W3MihJy7tgdtDu3fhwF4YGuw8Dk,13068
@@ -30,7 +30,7 @@ opencloning/ebic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,
 opencloning/ebic/primer_design.py,sha256=gPZTF9w5SV7WGgnefp_HBM831y0z73M1Kb0QUPnbfIM,2270
 opencloning/ebic/primer_design_settings.py,sha256=OnFsuh0QCvplUEPXLZouzRo9R7rm4nLbcd2LkDCiIDM,1896
 opencloning/endpoints/annotation.py,sha256=3rlIXeNQzoqPD9lJUEBGLGxvlhUCTcfkqno814A8P0U,2283
-opencloning/endpoints/assembly.py,sha256=MMwvlyM2NHnT04Pp7LdKQRvahq0itdqTtZx3OQhOswc,20980
+opencloning/endpoints/assembly.py,sha256=KrrsqG8jgR_Xe9BnfNvpbJce600rvMi8jXFu8wQuXX8,21092
 opencloning/endpoints/external_import.py,sha256=i2hAKSYi2IIdglmDhDhWmBzHbhn6A9A8ybbj4nmhROM,18188
 opencloning/endpoints/no_assembly.py,sha256=NY6rhEDCNoZVn6Xk81cen2n-FkMr7ierfxM8G0npbQs,4722
 opencloning/endpoints/no_input.py,sha256=DuqKD3Ph3a44ZxPMEzZv1nwD5xlxYsN7YyxXcfjSUFc,3844
@@ -45,7 +45,7 @@ opencloning/primer_design.py,sha256=nqCmYIZ7UvU4CQwVGJwX7T5LTHwt3-51_ZcTZZAgT_Y,
 opencloning/pydantic_models.py,sha256=lMO78M4MwDgzTEGz9qzsaADwAFXagWK4qGsF1K1hLZw,18865
 opencloning/request_examples.py,sha256=QAsJxVaq5tHwlPB404IiJ9WC6SA7iNY7XnJm63BWT_E,2944
 opencloning/utils.py,sha256=0Lvw1h1AsUJTK2b9mNzYVi_DBeWmWCFA5dIPl_gERcI,1479
-opencloning-0.3.4.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
-opencloning-0.3.4.dist-info/METADATA,sha256=beszv-cKQj-br6Zcn9kW_v-PiaHe-MIOJ6PUZ7atBPs,9041
-opencloning-0.3.4.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-opencloning-0.3.4.dist-info/RECORD,,
+opencloning-0.3.5.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.3.5.dist-info/METADATA,sha256=y9nmpxH2Ew4kifbNfw7FrhzKS88djzWN_WWyk2A2lYk,9041
+opencloning-0.3.5.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+opencloning-0.3.5.dist-info/RECORD,,