opencloning 0.3.4__tar.gz → 0.3.5__tar.gz

{opencloning-0.3.4 → opencloning-0.3.5}/PKG-INFO

@@ -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 → opencloning-0.3.5}/pyproject.toml

@@ -8,7 +8,7 @@ authors = ["Manuel Lera-Ramirez <manulera14@gmail.com>"]
 description = "Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others."
 license = "MIT"
 name = "opencloning"
-version = "0.3.4"
+version = "0.3.5"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"

{opencloning-0.3.4 → opencloning-0.3.5}/src/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-0.3.4 → opencloning-0.3.5}/src/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: