opencloning 0.4.2__tar.gz → 0.4.3__tar.gz

{opencloning-0.4.2 → opencloning-0.4.3}/PKG-INFO

@@ -1,8 +1,9 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: opencloning
-Version: 0.4.2
+Version: 0.4.3
 Summary: Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.
 License: MIT
+License-File: LICENSE
 Author: Manuel Lera-Ramirez
 Author-email: manulera14@gmail.com
 Requires-Python: >=3.11,<4.0
@@ -11,6 +12,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Requires-Dist: beautifulsoup4 (>=4.11.1,<5.0.0)
 Requires-Dist: biopython (>=1.85,<2.0)
 Requires-Dist: fastapi

{opencloning-0.4.2 → opencloning-0.4.3}/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 = "0.4.2"
+version = "0.4.3"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"

{opencloning-0.4.2 → opencloning-0.4.3}/src/opencloning/batch_cloning/EBIC/example.py

@@ -4,7 +4,7 @@ from primer3 import bindings
 import json
 from fastapi import UploadFile, Response
 
-from ...pydantic_models import (
+from opencloning.pydantic_models import (
     GenomeCoordinatesSource,
     TextFileSequence,
     PrimerModel,
@@ -13,10 +13,10 @@ from ...pydantic_models import (
     BaseCloningStrategy,
     HomologousRecombinationSource,
 )
-from .primer_design_settings import amanda_settings
-from ...endpoints.external_import import genome_coordinates, read_from_file
-from ...endpoints.assembly import pcr, restriction_and_ligation, homologous_recombination
-from ...dna_functions import read_dsrecord_from_json
+from opencloning.batch_cloning.EBIC.primer_design_settings import amanda_settings
+from opencloning.endpoints.external_import import genome_coordinates, read_from_file
+from opencloning.endpoints.assembly import pcr, restriction_and_ligation, homologous_recombination
+from opencloning.dna_functions import read_dsrecord_from_json
 
 # Settings for design
 padding = 1000
@@ -123,7 +123,9 @@ async def main():
 
     with open(os.path.join(os.path.dirname(__file__), 'barcode.gb'), 'rb') as f:
         dummy_resp = Response()
-        resp = await read_from_file(dummy_resp, UploadFile(file=f, filename='barcode.gb'), None, None, True, 'barcode')
+        resp = await read_from_file(
+            dummy_resp, UploadFile(file=f, filename='barcode.gb'), None, None, True, 'barcode', None, None
+        )
 
     barcode_source = resp['sources'][0]
     barcode_seq: TextFileSequence = resp['sequences'][0]
@@ -132,7 +134,14 @@ async def main():
     with open(os.path.join(os.path.dirname(__file__), 'common_plasmid.gb'), 'rb') as f:
         dummy_resp = Response()
         resp = await read_from_file(
-            dummy_resp, UploadFile(file=f, filename='common_plasmid.gb'), None, None, True, 'common_plasmid'
+            dummy_resp,
+            UploadFile(file=f, filename='common_plasmid.gb'),
+            None,
+            None,
+            True,
+            'common_plasmid',
+            None,
+            None,
         )
 
     common_plasmid_source = resp['sources'][0]

{opencloning-0.4.2 → opencloning-0.4.3}/src/opencloning/batch_cloning/pombe/pombe_clone.py

@@ -1,7 +1,7 @@
 import os
-from ...endpoints.external_import import genome_coordinates, get_from_repository_id_addgene, read_from_file
-from ...endpoints.assembly import pcr, homologous_recombination
-from ...pydantic_models import (
+from opencloning.endpoints.external_import import genome_coordinates, get_from_repository_id_addgene, read_from_file
+from opencloning.endpoints.assembly import pcr, homologous_recombination
+from opencloning.pydantic_models import (
     GenomeCoordinatesSource,
     TextFileSequence,
     AddgeneIdSource,
@@ -12,7 +12,7 @@ from ...pydantic_models import (
     UploadedFileSource,
 )
 
-from ...ncbi_requests import get_annotations_from_query
+from opencloning.ncbi_requests import get_annotations_from_query
 import asyncio
 import json
 from Bio import SeqIO
@@ -78,9 +78,9 @@ async def main(
     # Get plasmid sequence =================s================================================================
     if not isinstance(plasmid, str):
         if plasmid.filename.endswith('.fa') or plasmid.filename.endswith('.fasta'):
-            resp = await read_from_file(plasmid, None, None, True, None)
+            resp = await read_from_file(plasmid, None, None, True, None, None, None)
         else:
-            resp = await read_from_file(plasmid, None, None, None, None)
+            resp = await read_from_file(plasmid, None, None, None, None, None, None)
         # Verify that plasmid is circular
         if not pydna_parse(resp['sequences'][0].file_content)[0].circular:
             raise ValueError('Plasmid is not circular')

{opencloning-0.4.2 → opencloning-0.4.3}/src/opencloning/endpoints/assembly.py

@@ -265,12 +265,16 @@ async def pcr(
     source: PCRSource,
     sequences: Annotated[list[TextFileSequence], Field(min_length=1, max_length=1)],
     primers: Annotated[list[PrimerModel], Field(min_length=1, max_length=2)],
-    minimal_annealing: int = Query(20, description='The minimal annealing length for each primer.'),
+    minimal_annealing: int = Query(
+        14,
+        description='The minimal amount of bases that must match between the primer and the sequence, excluding mismatches.',
+    ),
     allowed_mismatches: int = Query(0, description='The number of mismatches allowed'),
 ):
     if len(primers) != len(sequences) * 2:
         raise HTTPException(400, 'The number of primers should be twice the number of sequences.')
 
+    minimal_annealing = minimal_annealing + allowed_mismatches
     pydna_sequences = [read_dsrecord_from_json(s) for s in sequences]
     pydna_primers = [PydnaPrimer(p.sequence, id=str(p.id), name=p.name) for p in primers]