opencloning 0.2.6.4__tar.gz → 0.2.7__tar.gz

{opencloning-0.2.6.4 → opencloning-0.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.2.6.4
+Version: 0.2.7
 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-0.2.6.4 → opencloning-0.2.7}/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 = "v0.2.6.4"
+version = "v0.2.7"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"

{opencloning-0.2.6.4 → opencloning-0.2.7}/src/opencloning/endpoints/primer_design.py

@@ -2,6 +2,9 @@ from fastapi import Body, Query, HTTPException
 from pydantic import create_model
 import re
 from Bio.Restriction import RestrictionBatch
+from Bio.SeqUtils import gc_fraction
+from primer3 import bindings
+from itertools import product
 
 from ..dna_functions import get_invalid_enzyme_names
 from ..pydantic_models import PrimerModel, PrimerDesignQuery
@@ -13,6 +16,7 @@ from ..primer_design import (
 )
 from ..get_router import get_router
 from ..ebic.primer_design import ebic_primers
+from pydantic import BaseModel
 
 router = get_router()
 
@@ -235,3 +239,80 @@ async def primer_design_ebic(
 #         raise HTTPException(400, *e.args)
 
 #     return {'primers': primers}
+
+
+class ThermodynamicResult(BaseModel):
+    melting_temperature: float
+    deltaG: float
+    figure: str | None
+
+    @classmethod
+    def from_binding(cls, result):
+        return cls(
+            melting_temperature=result.tm,
+            deltaG=result.dg,
+            figure='\n'.join(result.ascii_structure_lines),
+        )
+
+
+def get_sequence_thermodynamic_result(sequences: list[str], method: callable) -> ThermodynamicResult | None:
+    """Get the thermodynamic result for a sequence, if the sequence is longer than primer3 60bp limit, it will be split into two
+    and the result with the lowest deltaG will be returned."""
+    results = [method(seq, output_structure=True) for seq in sequences]
+    results = [r for r in results if r.structure_found]
+    if len(results) == 0:
+        return None
+
+    result = min(results, key=lambda r: r.dg)
+    return ThermodynamicResult.from_binding(result)
+
+
+class PrimerDetailsResponse(BaseModel):
+    melting_temperature: float
+    gc_content: float
+    homodimer: ThermodynamicResult | None
+    hairpin: ThermodynamicResult | None
+
+
+@router.get('/primer_details', response_model=PrimerDetailsResponse)
+async def primer_details(
+    sequence: str = Query(..., description='Primer sequence', regex=r'^[ACGTacgt]+$'),
+):
+    """Get information about a primer"""
+    sequence = sequence.upper()
+    tm = bindings.calc_tm(sequence)
+    gc_content = gc_fraction(sequence)
+
+    thermodynamic_sequences = [sequence]
+    if len(sequence) > 60:
+        thermodynamic_sequences = [sequence[:60], sequence[-60:]]
+    homodimer = get_sequence_thermodynamic_result(thermodynamic_sequences, bindings.calc_homodimer)
+    hairpin = get_sequence_thermodynamic_result(thermodynamic_sequences, bindings.calc_hairpin)
+
+    return {
+        'melting_temperature': tm,
+        'gc_content': gc_content,
+        'homodimer': homodimer,
+        'hairpin': hairpin,
+    }
+
+
+@router.get('/primer_heterodimer', response_model=ThermodynamicResult | None)
+async def primer_heterodimer(
+    sequence1: str = Query(..., description='First primer sequence', regex=r'^[ACGTacgt]+$'),
+    sequence2: str = Query(..., description='Second primer sequence', regex=r'^[ACGTacgt]+$'),
+):
+    """Get information about a primer pair"""
+
+    if len(sequence1) <= 60 or len(sequence2) <= 60:
+        sequence_pairs = [(sequence1, sequence2)]
+    else:
+        sequence_pairs = list(product((sequence1[:60], sequence1[-60:]), (sequence2[:60], sequence2[-60:])))
+
+    results = [bindings.calc_heterodimer(s1, s2, output_structure=True) for s1, s2 in sequence_pairs]
+    results = [r for r in results if r.structure_found]
+    if len(results) == 0:
+        return None
+
+    result = min(results, key=lambda r: r.dg)
+    return ThermodynamicResult.from_binding(result)