opencloning 0.4.2__py3-none-any.whl → 0.4.3__py3-none-any.whl

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/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/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]
 

{opencloning-0.4.2.dist-info → opencloning-0.4.3.dist-info}/METADATA

@@ -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.dist-info → opencloning-0.4.3.dist-info}/RECORD

@@ -5,13 +5,13 @@ opencloning/app_settings.py,sha256=FJFayBMLtE9gRC1e0ns5sVQRUb9DVXJ8o-ix4bTlPmI,2
 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
-opencloning/batch_cloning/EBIC/example.py,sha256=1OENMoPVn5lhTall_DvD7qx7t021a2HMV11kpStVs88,6851
+opencloning/batch_cloning/EBIC/example.py,sha256=tCXbxJtn4O0PxxAnm1UlxlrTlFHSK5C8R9D_6Br_8HE,7048
 opencloning/batch_cloning/EBIC/primer_design_settings.py,sha256=MVML1r1ciJYMFUJoqZVcGLoPM-f28oBN1wSDzlD0y64,1896
 opencloning/batch_cloning/__init__.py,sha256=uDxAa45g30_S6dJScNMlIxubQXlLRUsWoLX4S4y-l88,244
 opencloning/batch_cloning/index.html,sha256=HDqPHrJxrrKfGmy_dwYHhOsdUgZHHIch7Z0ey8qyvZI,1332
 opencloning/batch_cloning/pombe/__init__.py,sha256=Fq7SroO0Fer5CtFBRWdduIvzp1_dTUZwBb8IjBtRQO0,3332
 opencloning/batch_cloning/pombe/index.html,sha256=3YchoKGpcKDfvTOW1Rdih4PkbZIkMjKIQ0PaVXfV3e8,8348
-opencloning/batch_cloning/pombe/pombe_clone.py,sha256=3Z51NA0rhU-e4SxuLnlV5iDWeQrqECJTfe8IfiDoiow,7996
+opencloning/batch_cloning/pombe/pombe_clone.py,sha256=JlaTKcPBH8pR94FVgTPCopGRBCjS2VKvkkxZLjJdyb4,8056
 opencloning/batch_cloning/pombe/pombe_gather.py,sha256=qI-biMZGLxVDV-vOf3sT6bS1BawtTihZNcSYNlnnEi8,2432
 opencloning/batch_cloning/pombe/pombe_get_primers.py,sha256=nrn6V4_l8FWWfqS4WU3qPt95KwzvCXxETh8E-zWbRhM,3968
 opencloning/batch_cloning/pombe/pombe_summary.py,sha256=DBpoSEV1xPFm8TFDhrxS4tjqxJVrfH-ttM_0ELjQqok,4350
@@ -28,7 +28,7 @@ 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=KdVi63Bjmb7qwCQrwMUkRK6lAhlAJvBcHLqj1VJtuAQ,21584
+opencloning/endpoints/assembly.py,sha256=xkvChfwspdh2lnCi9tQFfTQuEhJfNXNjDb4wRKymZV8,21727
 opencloning/endpoints/external_import.py,sha256=Z9zd94kzmnbLG_yEAjI-1HK7sIAMcLz3FSZZR66BV-U,18386
 opencloning/endpoints/no_assembly.py,sha256=F6mRZFGUAASZ0v7EhPyBgmn_O-YLySMR1a_0aUH2U70,4806
 opencloning/endpoints/no_input.py,sha256=0wc5sTD6nL0SrsXmT__x0g-m6m45ID5hq-D8KDKy98Y,4170
@@ -43,7 +43,7 @@ opencloning/primer_design.py,sha256=nqCmYIZ7UvU4CQwVGJwX7T5LTHwt3-51_ZcTZZAgT_Y,
 opencloning/pydantic_models.py,sha256=N18tl8r6owDxTBRtrvB7DU3kmp59sBc8gYxujT9q6jE,19900
 opencloning/request_examples.py,sha256=_VvY4lNpgqhLTM6O_OUs1TujhL7RUbRFZ9ptyssbxLk,2934
 opencloning/utils.py,sha256=0Lvw1h1AsUJTK2b9mNzYVi_DBeWmWCFA5dIPl_gERcI,1479
-opencloning-0.4.2.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
-opencloning-0.4.2.dist-info/METADATA,sha256=jdAjLsb539U782FhTf2O7jV3UdQ-07mlCvu4LnFyd-c,9138
-opencloning-0.4.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-opencloning-0.4.2.dist-info/RECORD,,
+opencloning-0.4.3.dist-info/METADATA,sha256=fCbNrI65QXY0C6J_kMt5M0jMPo5TbzZasWaBxWqYheo,9211
+opencloning-0.4.3.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+opencloning-0.4.3.dist-info/licenses/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.4.3.dist-info/RECORD,,

{opencloning-0.4.2.dist-info → opencloning-0.4.3.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: poetry-core 2.2.1
 Root-Is-Purelib: true
 Tag: py3-none-any