opencloning 0.2.7__tar.gz → 0.2.7.2__tar.gz

{opencloning-0.2.7 → opencloning-0.2.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.2.7
+Version: 0.2.7.2
 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-0.2.7 → opencloning-0.2.7.2}/pyproject.toml

@@ -3,7 +3,7 @@ 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 = "v0.2.7"
+version = "v0.2.7.2"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"

{opencloning-0.2.7 → opencloning-0.2.7.2}/src/opencloning/endpoints/primer_design.py

@@ -209,8 +209,8 @@ async def primer_design_ebic(
 # @router.post('/primer_design/gateway_attB', response_model=PrimerDesignResponse)
 # async def primer_design_gateway_attB(
 #     template: PrimerDesignQuery,
-#     left_site: str = Query(..., description='The left attB site to recombine.', regex=r'^attB[1-5]$'),
-#     right_site: str = Query(..., description='The right attB site to recombine.', regex=r'^attB[1-5]$'),
+#     left_site: str = Query(..., description='The left attB site to recombine.', pattern=r'^attB[1-5]$'),
+#     right_site: str = Query(..., description='The right attB site to recombine.', pattern=r'^attB[1-5]$'),
 #     spacers: list[str] | None = Body(None, description='Spacers to add between the attB site and the primer.'),
 #     filler_bases: str = Query(
 #         'GGGG',
@@ -276,7 +276,7 @@ class PrimerDetailsResponse(BaseModel):
 
 @router.get('/primer_details', response_model=PrimerDetailsResponse)
 async def primer_details(
-    sequence: str = Query(..., description='Primer sequence', regex=r'^[ACGTacgt]+$'),
+    sequence: str = Query(..., description='Primer sequence', pattern=r'^[ACGTacgt]+$'),
 ):
     """Get information about a primer"""
     sequence = sequence.upper()
@@ -299,8 +299,8 @@ async def primer_details(
 
 @router.get('/primer_heterodimer', response_model=ThermodynamicResult | None)
 async def primer_heterodimer(
-    sequence1: str = Query(..., description='First primer sequence', regex=r'^[ACGTacgt]+$'),
-    sequence2: str = Query(..., description='Second primer sequence', regex=r'^[ACGTacgt]+$'),
+    sequence1: str = Query(..., description='First primer sequence', pattern=r'^[ACGTacgt]+$'),
+    sequence2: str = Query(..., description='Second primer sequence', pattern=r'^[ACGTacgt]+$'),
 ):
     """Get information about a primer pair"""
 

{opencloning-0.2.7 → opencloning-0.2.7.2}/src/opencloning/primer_design.py

@@ -7,6 +7,13 @@ from .pydantic_models import PrimerModel
 from Bio.Seq import reverse_complement
 from Bio.Restriction.Restriction import RestrictionType
 from Bio.Data.IUPACData import ambiguous_dna_values as _ambiguous_dna_values
+from primer3.bindings import calc_tm as _calc_tm
+from typing import Callable
+
+
+def primer3_calc_tm(seq: str) -> float:
+    return _calc_tm(seq.upper())
+
 
 ambiguous_dna_values = _ambiguous_dna_values.copy()
 # Remove acgt
@@ -24,10 +31,18 @@ def homologous_recombination_primers(
     insert_forward: bool,
     target_tm: float,
     spacers: list[str] | None = None,
+    tm_func: Callable[[str], float] = primer3_calc_tm,
+    estimate_function: Callable[[str], float] | None = None,
 ) -> tuple[str, str]:
 
     fragment2amplify = pcr_loc.extract(pcr_seq)
-    amplicon = primer_design(fragment2amplify, limit=minimal_hybridization_length, target_tm=target_tm)
+    amplicon = primer_design(
+        fragment2amplify,
+        limit=minimal_hybridization_length,
+        target_tm=target_tm,
+        tm_func=tm_func,
+        estimate_function=estimate_function,
+    )
 
     if insert_forward:
         fwd_primer, rvs_primer = amplicon.primers()
@@ -76,10 +91,19 @@ def gibson_assembly_primers(
     target_tm: float,
     circular: bool,
     spacers: list[str] | None = None,
+    tm_func: Callable[[str], float] = primer3_calc_tm,
+    estimate_function: Callable[[str], float] | None = None,
 ) -> list[PrimerModel]:
 
     initial_amplicons = [
-        primer_design(template, limit=minimal_hybridization_length, target_tm=target_tm) for template in templates
+        primer_design(
+            template,
+            limit=minimal_hybridization_length,
+            target_tm=target_tm,
+            tm_func=tm_func,
+            estimate_function=estimate_function,
+        )
+        for template in templates
     ]
 
     for i, amplicon in enumerate(initial_amplicons):
@@ -133,6 +157,8 @@ def simple_pair_primers(
     spacers: list[str] | None = None,
     left_enzyme_inverted: bool = False,
     right_enzyme_inverted: bool = False,
+    tm_func: Callable[[str], float] = primer3_calc_tm,
+    estimate_function: Callable[[str], float] | None = None,
 ) -> tuple[PrimerModel, PrimerModel]:
     """
     Design primers to amplify a DNA fragment, if left_enzyme or right_enzyme are set, the primers will be designed
@@ -145,7 +171,13 @@ def simple_pair_primers(
     if len(spacers) != 2:
         raise ValueError("The 'spacers' list must contain exactly two elements.")
 
-    amplicon = primer_design(template, limit=minimal_hybridization_length, target_tm=target_tm)
+    amplicon = primer_design(
+        template,
+        limit=minimal_hybridization_length,
+        target_tm=target_tm,
+        tm_func=tm_func,
+        estimate_function=estimate_function,
+    )
     fwd_primer, rvs_primer = amplicon.primers()
 
     if fwd_primer is None or rvs_primer is None: