opencloning 0.4.7__tar.gz → 0.4.8__tar.gz

{opencloning-0.4.7 → opencloning-0.4.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: opencloning
-Version: 0.4.7
+Version: 0.4.8
 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

{opencloning-0.4.7 → opencloning-0.4.8}/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 = "0.4.7"
+version = "0.4.8"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"

{opencloning-0.4.7 → opencloning-0.4.8}/src/opencloning/ebic/primer_design.py

@@ -1,16 +1,15 @@
 from pydna.dseqrecord import Dseqrecord
 from Bio.SeqFeature import SimpleLocation
-from ..primer3_functions import primer3_design_primers
+from ..primer3_functions import PrimerDesignSettings, primer3_design_primers
 
 from ..pydantic_models import PrimerModel
 from .primer_design_settings import amanda_settings
 
-padding = 1000
-
 adapter_left_fwd = 'ataGGTCTCtGGAG'
 adapter_left_rvs = 'ataGGTCTCtCATT'
 adapter_right_fwd = 'ataGGTCTCtGCTT'
 adapter_right_rvs = 'ataGGTCTCtAGCG'
+default_settings = PrimerDesignSettings()
 
 
 def ebic_primers(
@@ -20,36 +19,47 @@ def ebic_primers(
     max_outside: int,
     target_tm: float,
     target_tm_tolerance: float,
+    padding_left: int = 1000,
+    padding_right: int = 1000,
+    settings: PrimerDesignSettings = default_settings,
 ) -> tuple[PrimerModel, PrimerModel, PrimerModel, PrimerModel]:
     """Design primers for EBIC"""
 
     # First, we keep only the part within the padding
-    edge_left = location.start - padding
-    edge_right = location.end + padding
+    edge_left = location.start - padding_left
+    edge_right = location.end + padding_right
     if edge_left < 0 or edge_right > len(input_seq):
         raise ValueError('The template is too short for the padding.')
 
     template_seq = str(input_seq.seq[edge_left:edge_right])
-    inside_edge = padding + max_inside
-    outside_edge = padding - max_outside
+    inside_edge_left = padding_left + max_inside
+    inside_edge_right = padding_right + max_inside
+    outside_edge_left = padding_left - max_outside
 
-    left_template = template_seq[:inside_edge]
-    right_template = template_seq[-inside_edge:]
+    left_template = template_seq[:inside_edge_left]
+    right_template = template_seq[-inside_edge_right:]
 
     seq_args_left = {
-        'SEQUENCE_PRIMER_PAIR_OK_REGION_LIST': f'0,{int(padding/2)},{outside_edge},{max_outside + max_inside}',
+        'SEQUENCE_PRIMER_PAIR_OK_REGION_LIST': f'0,{int(padding_left/2)},{outside_edge_left},{max_outside + max_inside}',
     }
     seq_args_right = {
-        'SEQUENCE_PRIMER_PAIR_OK_REGION_LIST': f'0,{max_outside + max_inside},{len(right_template) - int(padding/2)},{int(padding/2)}',
+        'SEQUENCE_PRIMER_PAIR_OK_REGION_LIST': f'0,{max_outside + max_inside},{len(right_template) - int(padding_right/2)},{int(padding_right/2)}',
     }
 
     global_args = amanda_settings.copy()
     global_args['PRIMER_OPT_TM'] = target_tm
     global_args['PRIMER_MIN_TM'] = target_tm - target_tm_tolerance
     global_args['PRIMER_MAX_TM'] = target_tm + target_tm_tolerance
+    global_args['PRIMER_SALT_MONOVALENT'] = settings.primer_salt_monovalent
+    global_args['PRIMER_SALT_DIVALENT'] = settings.primer_salt_divalent
+    global_args['PRIMER_DNA_CONC'] = settings.primer_dna_conc
+    global_args_left = global_args.copy()
+    global_args_right = global_args.copy()
+    global_args_left['PRIMER_PRODUCT_SIZE_RANGE'] = [[max(100, padding_left - 100), padding_left]]
+    global_args_right['PRIMER_PRODUCT_SIZE_RANGE'] = [[max(100, padding_right - 100), padding_right]]
 
-    report_left = primer3_design_primers(left_template, seq_args_left, global_args)
-    report_right = primer3_design_primers(right_template, seq_args_right, global_args)
+    report_left = primer3_design_primers(left_template, seq_args_left, global_args_left)
+    report_right = primer3_design_primers(right_template, seq_args_right, global_args_right)
     primer_names = ['left_fwd', 'left_rvs', 'right_fwd', 'right_rvs']
     primer_seqs = [
         adapter_left_fwd + report_left['PRIMER_LEFT'][0]['SEQUENCE'],

{opencloning-0.4.7 → opencloning-0.4.8}/src/opencloning/endpoints/primer_design.py

@@ -51,9 +51,7 @@ def validate_spacers(spacers: list[str] | None, nb_templates: int, circular: boo
 async def primer_design_homologous_recombination(
     pcr_template: PrimerDesignQuery,
     homologous_recombination_target: PrimerDesignQuery,
-    settings: PrimerDesignSettings = Body(
-        ..., description='Primer design settings.', default_factory=PrimerDesignSettings
-    ),
+    settings: PrimerDesignSettings = Body(description='Primer design settings.', default_factory=PrimerDesignSettings),
     spacers: list[str] | None = Body(
         None,
         description='Spacers to add at the left and right side of the insertion.',
@@ -103,9 +101,7 @@ async def primer_design_homologous_recombination(
 @router.post('/primer_design/gibson_assembly', response_model=PrimerDesignResponse)
 async def primer_design_gibson_assembly(
     pcr_templates: list[PrimerDesignQuery],
-    settings: PrimerDesignSettings = Body(
-        ..., description='Primer design settings.', default_factory=PrimerDesignSettings
-    ),
+    settings: PrimerDesignSettings = Body(description='Primer design settings.', default_factory=PrimerDesignSettings),
     spacers: list[str] | None = Body(
         None,
         description='Spacers to add between the restriction site and the 5\' end of the primer footprint (the part that binds the DNA).',
@@ -156,9 +152,7 @@ async def primer_design_simple_pair(
         None,
         description='Spacers to add between the restriction site and the 5\' end of the primer footprint (the part that binds the DNA).',
     ),
-    settings: PrimerDesignSettings = Body(
-        ..., description='Primer design settings.', default_factory=PrimerDesignSettings
-    ),
+    settings: PrimerDesignSettings = Body(description='Primer design settings.', default_factory=PrimerDesignSettings),
     minimal_hybridization_length: int = Query(
         ..., description='The minimal length of the hybridization region in bps.'
     ),
@@ -219,6 +213,7 @@ async def primer_design_simple_pair(
 @router.post('/primer_design/ebic', response_model=PrimerDesignResponse)
 async def primer_design_ebic(
     template: PrimerDesignQuery,
+    settings: PrimerDesignSettings = Body(description='Primer design settings.', default_factory=PrimerDesignSettings),
     max_inside: int = Query(..., description='The maximum length of the inside edge of the EBIC primer.'),
     max_outside: int = Query(..., description='The maximum length of the outside edge of the EBIC primer.'),
     target_tm: float = Query(
@@ -227,11 +222,25 @@ async def primer_design_ebic(
     target_tm_tolerance: float = Query(
         3, description='The tolerance for the desired melting temperature for the hybridization part of the primer.'
     ),
+    padding_left: int = Query(..., description='The padding length on the left side of the template.'),
+    padding_right: int = Query(..., description='The padding length on the right side of the template.'),
 ):
     """Design primers for EBIC"""
     dseqr = read_dsrecord_from_json(template.sequence)
     location = template.location.to_biopython_location()
-    return {'primers': ebic_primers(dseqr, location, max_inside, max_outside, target_tm, target_tm_tolerance)}
+    return {
+        'primers': ebic_primers(
+            dseqr,
+            location,
+            max_inside,
+            max_outside,
+            target_tm,
+            target_tm_tolerance,
+            padding_left,
+            padding_right,
+            settings,
+        )
+    }
 
 
 # @router.post('/primer_design/gateway_attB', response_model=PrimerDesignResponse)
@@ -279,9 +288,7 @@ class PrimerDetailsResponse(BaseModel):
 @router.post('/primer_details', response_model=PrimerDetailsResponse)
 async def primer_details(
     sequence: str = Body(..., description='Primer sequence', pattern=r'^[ACGTacgt]+$'),
-    settings: PrimerDesignSettings = Body(
-        ..., description='Primer design settings.', default_factory=PrimerDesignSettings
-    ),
+    settings: PrimerDesignSettings = Body(description='Primer design settings.', default_factory=PrimerDesignSettings),
 ):
     """Get information about a primer"""
     sequence = sequence.upper()
@@ -303,9 +310,7 @@ async def primer_details(
 async def primer_heterodimer(
     sequence1: str = Body(..., description='First primer sequence', pattern=r'^[ACGTacgt]+$'),
     sequence2: str = Body(..., description='Second primer sequence', pattern=r'^[ACGTacgt]+$'),
-    settings: PrimerDesignSettings = Body(
-        ..., description='Primer design settings.', default_factory=PrimerDesignSettings
-    ),
+    settings: PrimerDesignSettings = Body(description='Primer design settings.', default_factory=PrimerDesignSettings),
 ):
     """Get information about a primer pair"""
 

{opencloning-0.4.7 → opencloning-0.4.8}/src/opencloning/primer3_functions.py

@@ -62,7 +62,7 @@ class ThermodynamicResult(BaseModel):
         )
 
 
-def get_sequence_thermodynamic_result(sequence: str, method: callable) -> ThermodynamicResult | None:
+def get_sequence_thermodynamic_result(sequence: str, method: callable):
     """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."""
     sequence = sequence.upper()
@@ -80,13 +80,13 @@ def get_sequence_thermodynamic_result(sequence: str, method: callable) -> Thermo
     return ThermodynamicResult.from_binding(result)
 
 
-def primer3_calc_homodimer(seq: str, settings: PrimerDesignSettings) -> ThermodynamicResult:
+def primer3_calc_homodimer(seq: str, settings: PrimerDesignSettings):
     return get_sequence_thermodynamic_result(
         seq, lambda x: _calc_homodimer(x, output_structure=True, **settings.to_primer3_args())
     )
 
 
-def primer3_calc_hairpin(seq: str, settings: PrimerDesignSettings) -> ThermodynamicResult:
+def primer3_calc_hairpin(seq: str, settings: PrimerDesignSettings):
     return get_sequence_thermodynamic_result(
         seq, lambda x: _calc_hairpin(x, output_structure=True, **settings.to_primer3_args())
     )