opencloning 0.2.7.3__py3-none-any.whl → 0.2.8__py3-none-any.whl

opencloning/cre_lox.py

@@ -0,0 +1,29 @@
+from itertools import product
+from pydna.dseqrecord import Dseqrecord
+
+from .dna_utils import compute_regex_site, dseqrecord_finditer
+
+# This is the original loxP sequence, here for reference
+LOXP_SEQUENCE = 'ATAACTTCGTATAGCATACATTATACGAAGTTAT'
+
+# This is a consensus sequence, from this Addgene blog post: https://blog.addgene.org/plasmids-101-cre-lox
+# IMPORTANT: Because it is palyndromic, we only look for it in the forward direction, if this was changed
+# to a non-palindromic sequence, you would need to look for matches reversing it, like in Gateway cloning
+LOXP_CONSENSUS = 'ATAACTTCGTATANNNTANNNTATACGAAGTTAT'
+
+
+loxP_regex = compute_regex_site(LOXP_CONSENSUS)
+
+
+def cre_loxP_overlap(x: Dseqrecord, y: Dseqrecord, _l: None = None) -> list[tuple[int, int, int]]:
+    """Find matching loxP sites between two sequences."""
+    out = list()
+    matches_x = dseqrecord_finditer(loxP_regex, x)
+    matches_y = dseqrecord_finditer(loxP_regex, y)
+
+    for match_x, match_y in product(matches_x, matches_y):
+        value_x = match_x.group()
+        value_y = match_y.group()
+        if value_x == value_y:
+            out.append((match_x.start(), match_y.start(), len(value_x)))
+    return out

opencloning/dna_utils.py

@@ -11,9 +11,15 @@ import os
 import shutil
 from pydna.parsers import parse
 from Bio.Align import PairwiseAligner
+from Bio.Data.IUPACData import ambiguous_dna_values as _ambiguous_dna_values
+import re
 
 aligner = PairwiseAligner(scoring='blastn')
 
+ambiguous_only_dna_values = {**_ambiguous_dna_values}
+for normal_base in 'ACGT':
+    del ambiguous_only_dna_values[normal_base]
+
 
 def sum_is_sticky(three_prime_end: tuple[str, str], five_prime_end: tuple[str, str], partial: bool = False) -> int:
     """Return the overlap length if the 3' end of seq1 and 5' end of seq2 ends are sticky and compatible for ligation.
@@ -144,3 +150,20 @@ def align_sanger_traces(dseqr: Dseqrecord, sanger_traces: list[str]) -> list[str
         sanger_traces = traces_oriented
 
     return align_with_mafft([query_str, *sanger_traces], True)
+
+
+def compute_regex_site(site: str) -> str:
+    upper_site = site.upper()
+    for k, v in ambiguous_only_dna_values.items():
+        if len(v) > 1:
+            upper_site = upper_site.replace(k, f"[{''.join(v)}]")
+
+    # Make case insensitive
+    upper_site = f'(?i){upper_site}'
+    return upper_site
+
+
+def dseqrecord_finditer(pattern: str, seq: Dseqrecord) -> list[re.Match]:
+    query = str(seq.seq) if not seq.circular else str(seq.seq) * 2
+    matches = re.finditer(pattern, query)
+    return (m for m in matches if m.start() <= len(seq))

opencloning/endpoints/assembly.py

@@ -5,7 +5,7 @@ from pydna.primer import Primer as PydnaPrimer
 from pydna.crispr import cas9
 from pydantic import conlist, create_model
 from Bio.Restriction.Restriction import RestrictionBatch
-
+from opencloning.cre_lox import cre_loxP_overlap
 from ..dna_functions import (
     get_invalid_enzyme_names,
     format_sequence_genbank,
@@ -24,6 +24,8 @@ from ..pydantic_models import (
     AssemblySource,
     OverlapExtensionPCRLigationSource,
     GatewaySource,
+    CreLoxRecombinationSource,
+    InVivoAssemblySource,
 )
 from ..assembly2 import (
     Assembly,
@@ -159,6 +161,7 @@ def generate_assemblies(
     allow_insertion_assemblies: bool,
     assembly_kwargs: dict | None = None,
     product_callback: Callable[[Dseqrecord], Dseqrecord] = lambda x: x,
+    recombination_mode: bool = False,
 ) -> dict[Literal['sources', 'sequences'], list[AssemblySource] | list[TextFileSequence]]:
     if assembly_kwargs is None:
         assembly_kwargs = {}
@@ -175,10 +178,15 @@ def generate_assemblies(
             circular_assemblies = asm.get_circular_assemblies()
             out_sources += [create_source(a, True) for a in circular_assemblies]
             if not circular_only:
-                out_sources += [
-                    create_source(a, False)
-                    for a in filter_linear_subassemblies(asm.get_linear_assemblies(), circular_assemblies, fragments)
-                ]
+                if not recombination_mode:
+                    out_sources += [
+                        create_source(a, False)
+                        for a in filter_linear_subassemblies(
+                            asm.get_linear_assemblies(), circular_assemblies, fragments
+                        )
+                    ]
+                else:
+                    out_sources += [create_source(a, False) for a in asm.get_insertion_assemblies()]
         else:
             asm = SingleFragmentAssembly(fragments, algorithm=algo, **assembly_kwargs)
             out_sources.extend(create_source(a, True) for a in asm.get_circular_assemblies())
@@ -385,13 +393,16 @@ async def homologous_recombination(
     '/gibson_assembly',
     response_model=create_model(
         'GibsonAssemblyResponse',
-        sources=(list[Union[GibsonAssemblySource, OverlapExtensionPCRLigationSource, InFusionSource]], ...),
+        sources=(
+            list[Union[GibsonAssemblySource, OverlapExtensionPCRLigationSource, InFusionSource, InVivoAssemblySource]],
+            ...,
+        ),
         sequences=(list[TextFileSequence], ...),
     ),
 )
 async def gibson_assembly(
     sequences: conlist(TextFileSequence, min_length=1),
-    source: Union[GibsonAssemblySource, OverlapExtensionPCRLigationSource, InFusionSource],
+    source: Union[GibsonAssemblySource, OverlapExtensionPCRLigationSource, InFusionSource, InVivoAssemblySource],
     minimal_homology: int = Query(
         40, description='The minimum homology between consecutive fragments in the assembly.'
     ),
@@ -522,3 +533,30 @@ async def gateway(
         return {'sources': sources, 'sequences': sequences}
 
     return resp
+
+
+@router.post(
+    '/cre_lox_recombination',
+    response_model=create_model(
+        'CreLoxRecombinationResponse',
+        sources=(list[CreLoxRecombinationSource], ...),
+        sequences=(list[TextFileSequence], ...),
+    ),
+)
+async def cre_lox_recombination(source: CreLoxRecombinationSource, sequences: conlist(TextFileSequence, min_length=1)):
+    fragments = [read_dsrecord_from_json(seq) for seq in sequences]
+
+    # Lambda function for code clarity
+    def create_source(a, is_circular):
+        return CreLoxRecombinationSource.from_assembly(
+            assembly=a, circular=is_circular, id=source.id, fragments=fragments
+        )
+
+    resp = generate_assemblies(
+        source, create_source, fragments, False, cre_loxP_overlap, True, recombination_mode=True
+    )
+
+    if len(resp['sources']) == 0:
+        raise HTTPException(400, 'No compatible Cre/Lox recombination was found.')
+
+    return resp

opencloning/gateway.py

@@ -1,31 +1,10 @@
-from Bio.Data.IUPACData import ambiguous_dna_values as _ambiguous_dna_values
 from Bio.Seq import reverse_complement
 from pydna.dseqrecord import Dseqrecord as _Dseqrecord
 import re
 import itertools as _itertools
 from Bio.SeqFeature import SimpleLocation, SeqFeature
 from pydna.utils import shift_location
-
-ambiguous_only_dna_values = {**_ambiguous_dna_values}
-for normal_base in 'ACGT':
-    del ambiguous_only_dna_values[normal_base]
-
-
-def compute_regex_site(site: str) -> str:
-    upper_site = site.upper()
-    for k, v in ambiguous_only_dna_values.items():
-        if len(v) > 1:
-            upper_site = upper_site.replace(k, f"[{''.join(v)}]")
-
-    # Make case insensitive
-    upper_site = f'(?i){upper_site}'
-    return upper_site
-
-
-def dseqrecord_finditer(pattern: str, seq: _Dseqrecord) -> list[re.Match]:
-    query = str(seq.seq) if not seq.circular else str(seq.seq) * 2
-    matches = re.finditer(pattern, query)
-    return (m for m in matches if m.start() <= len(seq))
+from .dna_utils import compute_regex_site, dseqrecord_finditer
 
 
 raw_gateway_common = {

opencloning/pydantic_models.py

@@ -45,6 +45,8 @@ from opencloning_linkml.datamodel import (
     IGEMSource as _IGEMSource,
     ReverseComplementSource as _ReverseComplementSource,
     SEVASource as _SEVASource,
+    CreLoxRecombinationSource as _CreLoxRecombinationSource,
+    InVivoAssemblySource as _InVivoAssemblySource,
 )
 from pydna.utils import shift_location as _shift_location
 from .assembly2 import edge_representation2subfragment_representation, subfragment_representation2edge_representation
@@ -338,6 +340,10 @@ class InFusionSource(AssemblySourceCommonClass, _InFusionSource):
     pass
 
 
+class InVivoAssemblySource(AssemblySourceCommonClass, _InVivoAssemblySource):
+    pass
+
+
 class CRISPRSource(AssemblySourceCommonClass, _CRISPRSource):
 
     # TODO
@@ -384,6 +390,10 @@ class GatewaySource(AssemblySourceCommonClass, _GatewaySource):
         return super().from_assembly(assembly, id, circular, fragments, reaction_type=reaction_type)
 
 
+class CreLoxRecombinationSource(AssemblySourceCommonClass, _CreLoxRecombinationSource):
+    pass
+
+
 class OligoHybridizationSource(SourceCommonClass, _OligoHybridizationSource):
     pass
 

{opencloning-0.2.7.3.dist-info → opencloning-0.2.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.2.7.3
+Version: 0.2.8
 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
@@ -15,7 +15,7 @@ Requires-Dist: beautifulsoup4 (>=4.11.1,<5.0.0)
 Requires-Dist: biopython (==1.84)
 Requires-Dist: fastapi
 Requires-Dist: httpx (>=0.25.0,<0.26.0)
-Requires-Dist: opencloning-linkml (==0.2.5.2a0)
+Requires-Dist: opencloning-linkml (==0.2.6a0)
 Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: primer3-py (>=2.0.3,<3.0.0)

{opencloning-0.2.7.3.dist-info → opencloning-0.2.8.dist-info}/RECORD

@@ -19,27 +19,28 @@ opencloning/batch_cloning/pombe/pombe_summary.py,sha256=W9DLpnCuwK7w2DhHLu60N7L6
 opencloning/batch_cloning/ziqiang_et_al2024/__init__.py,sha256=zZUbj3uMzd9rKMXi5s9LQ1yUg7sccdS0f_4kpw7SQlk,7584
 opencloning/batch_cloning/ziqiang_et_al2024/index.html,sha256=EDncANDhhQkhi5FjnnAP6liHkG5srf4_Y46IrnMUG5g,4607
 opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=mB81j2qWam7uRc-980YFjfqq2CiWTXJYfKFAoKuGtRw,157148
+opencloning/cre_lox.py,sha256=ocPx3EVkecoZjHx_ENhk5pEteRXRtiN5z5URmrIcCPw,1194
 opencloning/dna_functions.py,sha256=W-SxEfvYpN1JVZbTeCNitpQXkazEHvFyqZBUndd-jpY,16329
-opencloning/dna_utils.py,sha256=emms1omBhQKuVNEv6YXcHReP69tvUU1iRpLgjXn5p9o,5541
+opencloning/dna_utils.py,sha256=uv97aO04dbk3NnqbN6GlnwOu0MOpK88rl2np2QcEQ4Y,6301
 opencloning/ebic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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=0kcWchgN5ulj_I7ZOpFhsgq74SBT_7A7xbZz7s5-1C0,19330
+opencloning/endpoints/assembly.py,sha256=H1b7CRx1JZ5pcUGd3uyJG2syYugkXiIo8HRCA11TQfE,20704
 opencloning/endpoints/external_import.py,sha256=dDG7DiNb8WYE46nLGnkyRbGVVNUDXp3h0_1ixsJAh5o,16242
 opencloning/endpoints/no_assembly.py,sha256=NY6rhEDCNoZVn6Xk81cen2n-FkMr7ierfxM8G0npbQs,4722
 opencloning/endpoints/no_input.py,sha256=DuqKD3Ph3a44ZxPMEzZv1nwD5xlxYsN7YyxXcfjSUFc,3844
 opencloning/endpoints/other.py,sha256=TzfCJLDmZFWeKYxKhEfXOvlQrWWyBIGJ5FR0yA7tuvI,1673
 opencloning/endpoints/primer_design.py,sha256=ItPUa7bBW9JOOfTuLj0yNnF9UmQ-I_0l3i8wHpnUc6k,12854
-opencloning/gateway.py,sha256=qaefWKjfASuVU_nXnCCoDepQq1jhNINNW0VifkCLVC0,9123
+opencloning/gateway.py,sha256=jzpLbB8UCSlks0S6Qe9PXJ7CdzHiH2ko_O7MzYQLR14,8435
 opencloning/get_router.py,sha256=l2DXaTbeL2tDqlnVMlcewutzt1sjaHlxku1X9HVUwJk,252
 opencloning/main.py,sha256=l9PrPBMtGMEWxAPiPWR15Qv2oDNnRoNd8H8E3bZW6Do,3750
 opencloning/ncbi_requests.py,sha256=JrFc-Ugr1r1F4LqsdpJZEiERj7ZemvZSgiIltl2Chx8,5547
 opencloning/primer_design.py,sha256=nqCmYIZ7UvU4CQwVGJwX7T5LTHwt3-51_ZcTZZAgT_Y,9175
-opencloning/pydantic_models.py,sha256=S3ehXeynVlYJQK-G96D0jApMp7dn-eRg1di9d0DbsEc,15045
+opencloning/pydantic_models.py,sha256=gsipVXhjQOXVz2NL-MiNpLuOZYDVo2Pli9F--bp6tjs,15345
 opencloning/request_examples.py,sha256=QAsJxVaq5tHwlPB404IiJ9WC6SA7iNY7XnJm63BWT_E,2944
 opencloning/utils.py,sha256=wsdTJYliap-t3oa7yQE3pWDa1CR19mr5lUQfocp4hoM,1875
-opencloning-0.2.7.3.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
-opencloning-0.2.7.3.dist-info/METADATA,sha256=SFtmhPNvDi61Qp9JYNcsiQop9I_zYOPyGfeus-Etbf4,8429
-opencloning-0.2.7.3.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-opencloning-0.2.7.3.dist-info/RECORD,,
+opencloning-0.2.8.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.2.8.dist-info/METADATA,sha256=0kyQ2RhJcsCrkjRR6usNPg4LswxSYq71A61MY0ro0Yw,8425
+opencloning-0.2.8.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+opencloning-0.2.8.dist-info/RECORD,,