opencloning 0.4.7__py3-none-any.whl → 0.5__py3-none-any.whl

opencloning/pydantic_models.py

@@ -1,516 +1,16 @@
-from pydantic import BaseModel, Field, model_validator, field_validator, Discriminator, Tag
-from typing import Optional, List, Union, Annotated
-from pydantic_core import core_schema
+from pydantic import BaseModel, Field, field_validator
+from typing import Optional, List
+
 from ._version import __version__
 
-from Bio.SeqFeature import (
-    SeqFeature,
-    Location,
-    SimpleLocation,
-    FeatureLocation as BioFeatureLocation,
-    LocationParserError,
-)
-from Bio.SeqIO.InsdcIO import _insdc_location_string as format_feature_location
-from Bio.Restriction.Restriction import RestrictionType, RestrictionBatch
-from Bio.SeqRecord import SeqRecord as _SeqRecord
-from pydna.primer import Primer as _PydnaPrimer
+from pydna.opencloning_models import SequenceLocationStr
+
 from opencloning_linkml.datamodel import (
-    OligoHybridizationSource as _OligoHybridizationSource,
-    PolymeraseExtensionSource as _PolymeraseExtensionSource,
-    GenomeCoordinatesSource as _GenomeCoordinatesSource,
-    RepositoryIdSource as _RepositoryIdSource,
-    ManuallyTypedSource as _ManuallyTypedSource,
-    UploadedFileSource as _UploadedFileSource,
-    SequenceFileFormat as _SequenceFileFormat,
-    RestrictionEnzymeDigestionSource as _RestrictionEnzymeDigestionSource,
-    RestrictionSequenceCut as _RestrictionSequenceCut,
-    TextFileSequence as _TextFileSequence,
-    AssemblySource as _AssemblySource,
-    PCRSource as _PCRSource,
-    HomologousRecombinationSource as _HomologousRecombinationSource,
-    GibsonAssemblySource as _GibsonAssemblySource,
-    RestrictionAndLigationSource as _RestrictionAndLigationSource,
-    LigationSource as _LigationSource,
-    CRISPRSource as _CRISPRSource,
-    Primer as _Primer,
-    AssemblyFragment as _AssemblyFragment,
-    AddgeneIdSource as _AddgeneIdSource,
-    WekWikGeneIdSource as _WekWikGeneIdSource,
-    BenchlingUrlSource as _BenchlingUrlSource,
     CloningStrategy as _CloningStrategy,
-    OverlapExtensionPCRLigationSource as _OverlapExtensionPCRLigationSource,
-    SnapGenePlasmidSource as _SnapGenePlasmidSource,
-    EuroscarfSource as _EuroscarfSource,
-    GatewaySource as _GatewaySource,
-    InFusionSource as _InFusionSource,
-    AnnotationSource as _AnnotationSource,
-    IGEMSource as _IGEMSource,
-    ReverseComplementSource as _ReverseComplementSource,
-    SEVASource as _SEVASource,
-    CreLoxRecombinationSource as _CreLoxRecombinationSource,
-    InVivoAssemblySource as _InVivoAssemblySource,
-    SourceInput as _SourceInput,
-    OpenDNACollectionsSource as _OpenDNACollectionsSource,
-)
-from pydna.assembly2 import (
-    edge_representation2subfragment_representation,
-    subfragment_representation2edge_representation,
+    Primer as PrimerModel,
+    TextFileSequence as _TextFileSequence,
+    Source as _Source,
 )
-from pydna.utils import location_boundaries, shift_location
-
-
-SequenceFileFormat = _SequenceFileFormat
-
-
-class TextFileSequence(_TextFileSequence):
-    pass
-
-
-class SourceInput(_SourceInput):
-    pass
-
-
-class PrimerModel(_Primer):
-    """Called PrimerModel not to be confused with the class from pydna."""
-
-    def to_pydna_primer(self) -> _PydnaPrimer:
-        """
-        Convert the PrimerModel to a pydna Primer object.
-
-        Returns:
-            _PydnaPrimer: A pydna Primer object with the same sequence and name as the PrimerModel.
-        """
-        return _PydnaPrimer(self.sequence, name=self.name, id=str(self.id))
-
-
-class SeqFeatureModel(BaseModel):
-    type: str
-    qualifiers: dict[str, list[str]] = {}
-    location: str
-
-    def convert_to_seq_feature(self) -> SeqFeature:
-        return SeqFeature(location=Location.fromstring(self.location), type=self.type, qualifiers=self.qualifiers)
-
-    def read_from_seq_feature(sf: SeqFeature) -> 'SeqFeatureModel':
-        return SeqFeatureModel(
-            type=sf.type, qualifiers=sf.qualifiers, location=format_feature_location(sf.location, None)
-        )
-
-
-# Sources =========================================
-
-
-def input_discriminator(v) -> str | None:
-    """
-    Discriminator that yields SourceInput by default
-    """
-    if isinstance(v, dict):
-        input_type = v.get('type', None)
-        if input_type is None:
-            return 'SourceInput'
-        else:
-            return input_type
-    elif isinstance(v, SourceInput):
-        return v.type
-    return None
-
-
-class SourceCommonClass(BaseModel):
-    input: Optional[List[SourceInput]] = Field(
-        default_factory=list,
-        description="""The sequences that are an input to this source. If the source represents external import of a sequence, it's empty.""",
-        json_schema_extra={'linkml_meta': {'alias': 'input', 'domain_of': ['Source']}},
-    )
-
-
-class ManuallyTypedSource(SourceCommonClass, _ManuallyTypedSource):
-    """Describes a sequence that is typed manually by the user"""
-
-    @model_validator(mode='after')
-    def validate_circularity(self):
-        # Do the validation instead of printing
-        if self.circular:
-            assert self.overhang_crick_3prime == 0, 'Circular sequences cannot have overhangs.'
-            assert self.overhang_watson_3prime == 0, 'Circular sequences cannot have overhangs.'
-        return self
-
-
-class UploadedFileSource(SourceCommonClass, _UploadedFileSource):
-    coordinates: Optional['SequenceLocationStr'] = Field(
-        default=None,
-        description="""If provided, coordinates within the sequence of the file to extract a subsequence""",
-        json_schema_extra={'linkml_meta': {'alias': 'coordinates', 'domain_of': ['UploadedFileSource']}},
-    )
-
-    @field_validator('coordinates', mode='before')
-    def parse_coordinates(cls, v):
-        if v is None:
-            return None
-        return SequenceLocationStr.field_validator(v)
-
-
-class RepositoryIdSource(SourceCommonClass, _RepositoryIdSource):
-    pass
-
-
-class AddgeneIdSource(SourceCommonClass, _AddgeneIdSource):
-    # TODO: add this to LinkML
-    # repository_name: RepositoryName = RepositoryName('addgene')
-    pass
-
-
-class WekWikGeneIdSource(SourceCommonClass, _WekWikGeneIdSource):
-    pass
-
-
-class BenchlingUrlSource(SourceCommonClass, _BenchlingUrlSource):
-    pass
-
-
-class SnapGenePlasmidSource(SourceCommonClass, _SnapGenePlasmidSource):
-    pass
-
-
-class EuroscarfSource(SourceCommonClass, _EuroscarfSource):
-    pass
-
-
-class IGEMSource(SourceCommonClass, _IGEMSource):
-
-    @model_validator(mode='after')
-    def validate_repository_id(self):
-        file_name = self.sequence_file_url.split('/')[-1]
-        assert file_name.endswith('.gb'), 'The sequence file must be a GenBank file'
-        return self
-
-
-class OpenDNACollectionsSource(SourceCommonClass, _OpenDNACollectionsSource):
-    pass
-
-
-class SEVASource(SourceCommonClass, _SEVASource):
-    pass
-
-
-class GenomeCoordinatesSource(SourceCommonClass, _GenomeCoordinatesSource):
-    pass
-
-
-class AnnotationSource(SourceCommonClass, _AnnotationSource):
-    pass
-
-
-class ReverseComplementSource(SourceCommonClass, _ReverseComplementSource):
-    pass
-
-
-class RestrictionSequenceCut(_RestrictionSequenceCut):
-
-    @classmethod
-    def from_cutsite_tuple(cls, cutsite_tuple: tuple[tuple[int, int], RestrictionType]):
-        cut_watson, ovhg = cutsite_tuple[0]
-        enzyme = str(cutsite_tuple[1])
-
-        return cls(
-            cut_watson=cut_watson,
-            overhang=ovhg,
-            restriction_enzyme=enzyme,
-        )
-
-    def to_cutsite_tuple(self) -> tuple[tuple[int, int], RestrictionType]:
-        restriction_enzyme = RestrictionBatch(first=[self.restriction_enzyme]).pop()
-        return ((self.cut_watson, self.overhang), restriction_enzyme)
-
-
-class RestrictionEnzymeDigestionSource(SourceCommonClass, _RestrictionEnzymeDigestionSource):
-    """Documents a restriction enzyme digestion, and the selection of one of the fragments."""
-
-    # TODO: maybe a better way? They have to be redefined here because
-    # we have overriden the original class
-
-    left_edge: Optional[RestrictionSequenceCut] = Field(None)
-    right_edge: Optional[RestrictionSequenceCut] = Field(None)
-
-    @classmethod
-    def from_cutsites(
-        cls,
-        left: tuple[tuple[int, int], RestrictionType],
-        right: tuple[tuple[int, int], RestrictionType],
-        input: list[int],
-        id: int,
-    ):
-        return cls(
-            id=id,
-            left_edge=None if left is None else RestrictionSequenceCut.from_cutsite_tuple(left),
-            right_edge=None if right is None else RestrictionSequenceCut.from_cutsite_tuple(right),
-            input=input,
-        )
-
-    # TODO could be made into a computed field?
-    def get_enzymes(self) -> list[str]:
-        """Returns the enzymes used in the digestion"""
-        out = list()
-        if self.left_edge is not None:
-            out.append(self.left_edge.restriction_enzyme)
-        if self.right_edge is not None:
-            out.append(self.right_edge.restriction_enzyme)
-        # Unique values, sorted the same way
-        return sorted(list(set(out)), key=out.index)
-
-
-class SequenceLocationStr(str):
-    """A string representation of a sequence location, genbank-like."""
-
-    # TODO: this should handle origin-spanning simple locations (splitted)
-    @classmethod
-    def from_biopython_location(cls, location: Location):
-        return cls(format_feature_location(location, None))
-
-    @classmethod
-    def from_start_and_end(cls, start: int, end: int, seq_len: int | None = None, strand: int | None = 1):
-        if end >= start:
-            return cls.from_biopython_location(SimpleLocation(start, end, strand=strand))
-        else:
-            if seq_len is None:
-                raise ValueError('Sequence length is required to handle origin-spanning simple locations')
-            unwrapped_location = SimpleLocation(start, end + seq_len, strand=strand)
-            wrapped_location = shift_location(unwrapped_location, 0, seq_len)
-            return cls.from_biopython_location(wrapped_location)
-
-    def to_biopython_location(self) -> BioFeatureLocation:
-        return Location.fromstring(self)
-
-    @classmethod
-    def field_validator(cls, v):
-        if isinstance(v, str):
-            value = cls(v)
-            try:
-                value.to_biopython_location()
-            except LocationParserError:
-                raise ValueError(f'Location "{v}" is not a valid location')
-            return value
-        raise ValueError(f'Location must be a string or a {cls.__name__}')
-
-    @property
-    def start(self) -> int:
-        return location_boundaries(self.to_biopython_location())[0]
-
-    @property
-    def end(self) -> int:
-        return location_boundaries(self.to_biopython_location())[1]
-
-    @classmethod
-    def __get_pydantic_core_schema__(
-        cls,
-        source_type,
-        handler,
-    ) -> core_schema.CoreSchema:
-        """Generate Pydantic core schema for SequenceLocationStr."""
-        return core_schema.with_info_after_validator_function(
-            cls._validate,
-            core_schema.str_schema(),
-        )
-
-    @classmethod
-    def _validate(cls, value: str, info):
-        """Validate and create SequenceLocationStr instance."""
-        return cls.field_validator(value)
-
-
-class AssemblyFragment(_AssemblyFragment, SourceInput):
-    left_location: Optional[SequenceLocationStr] = None
-    right_location: Optional[SequenceLocationStr] = None
-
-    def to_fragment_tuple(self, fragments) -> tuple[int, Location, Location]:
-        fragment_ids = [int(f.id) for f in fragments]
-        # By convention, these have no strand
-        left_loc = None if self.left_location is None else self.left_location.to_biopython_location()
-        right_loc = None if self.right_location is None else self.right_location.to_biopython_location()
-        if left_loc is not None:
-            left_loc.strand = None
-        if right_loc is not None:
-            right_loc.strand = None
-
-        return (
-            (fragment_ids.index(self.sequence) + 1) * (-1 if self.reverse_complemented else 1),
-            left_loc,
-            right_loc,
-        )
-
-    @field_validator('left_location', 'right_location', mode='before')
-    def parse_location(cls, v):
-        if v is None:
-            return None
-        return SequenceLocationStr.field_validator(v)
-
-
-class AssemblySourceCommonClass(SourceCommonClass):
-    # TODO: This is different in the LinkML model, because there it is not required,
-    # and here we make it default to list.
-    input: Optional[
-        List[
-            Annotated[
-                Union[
-                    Annotated[SourceInput, Tag('SourceInput')],
-                    Annotated['AssemblyFragment', Tag('AssemblyFragment')],
-                ],
-                Discriminator(input_discriminator),
-            ]
-        ]
-    ] = Field(
-        default_factory=list,
-        description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
-        json_schema_extra={'linkml_meta': {'alias': 'input', 'domain_of': ['Source'], 'slot_uri': 'schema:object'}},
-    )
-
-    def minimal_overlap(self):
-        """Returns the minimal overlap between the fragments in the assembly"""
-        all_overlaps = list()
-        for f in self.input:
-            if f.left_location is not None:
-                all_overlaps.append(f.left_location.end - f.left_location.start)
-            if f.right_location is not None:
-                all_overlaps.append(f.right_location.end - f.right_location.start)
-        return min(all_overlaps)
-
-    def get_assembly_plan(self, fragments: list[_SeqRecord]) -> tuple:
-        """Returns the assembly plan"""
-        subf = [f.to_fragment_tuple(fragments) for f in self.input if f.type == 'AssemblyFragment']
-        return subfragment_representation2edge_representation(subf, self.circular)
-
-    def is_assembly_complete(self) -> bool:
-        """Returns True if the assembly is complete"""
-        return any(f.type == 'AssemblyFragment' for f in self.input)
-
-    @classmethod
-    def from_assembly(
-        cls,
-        assembly: list[tuple[int, int, Location, Location]],
-        id: int,
-        circular: bool,
-        fragments: list[_SeqRecord],
-        **kwargs,
-    ):
-
-        # Replace the positions with the actual ids
-        fragment_ids = [int(f.id) for f in fragments]
-
-        # Here the ids are still the positions in the fragments list
-        fragment_assembly_positions = edge_representation2subfragment_representation(assembly, circular)
-        assembly_fragments = [
-            AssemblyFragment(
-                sequence=fragment_ids[abs(pos) - 1],
-                left_location=None if left_loc is None else SequenceLocationStr.from_biopython_location(left_loc),
-                right_location=None if right_loc is None else SequenceLocationStr.from_biopython_location(right_loc),
-                reverse_complemented=pos < 0,
-            )
-            for pos, left_loc, right_loc in fragment_assembly_positions
-        ]
-        return cls(
-            id=id,
-            input=assembly_fragments,
-            circular=circular,
-            **kwargs,
-        )
-
-
-class AssemblySource(AssemblySourceCommonClass, _AssemblySource):
-    pass
-
-
-class PCRSource(AssemblySourceCommonClass, _PCRSource):
-    pass
-
-
-class LigationSource(AssemblySourceCommonClass, _LigationSource):
-    pass
-
-
-class HomologousRecombinationSource(AssemblySourceCommonClass, _HomologousRecombinationSource):
-
-    # TODO: add this to LinkML
-    # This can only take two inputs, the first one is the template, the second one is the insert
-    # input: conlist(int, min_length=2, max_length=2)
-    pass
-
-
-class GibsonAssemblySource(AssemblySourceCommonClass, _GibsonAssemblySource):
-
-    # TODO: add this to LinkML
-    # input: conlist(int, min_length=1)
-    pass
-
-
-class OverlapExtensionPCRLigationSource(AssemblySourceCommonClass, _OverlapExtensionPCRLigationSource):
-    pass
-
-
-class InFusionSource(AssemblySourceCommonClass, _InFusionSource):
-    pass
-
-
-class InVivoAssemblySource(AssemblySourceCommonClass, _InVivoAssemblySource):
-    pass
-
-
-class CRISPRSource(AssemblySourceCommonClass, _CRISPRSource):
-
-    # TODO
-    # input: conlist(int, min_length=2, max_length=2)
-    # circular: bool = False
-
-    @classmethod
-    def from_assembly(
-        cls,
-        assembly: list[tuple[int, int, Location, Location]],
-        id: int,
-        fragments: list[_SeqRecord],
-        guides: list[int],
-    ):
-        source = super().from_assembly(assembly, id, False, fragments)
-        source.input += [SourceInput(sequence=guide) for guide in guides]
-        return source
-
-
-class RestrictionAndLigationSource(AssemblySourceCommonClass, _RestrictionAndLigationSource):
-    # TODO: add this to LinkML
-    # input: conlist(int, min_length=1)
-
-    @classmethod
-    def from_assembly(
-        cls,
-        assembly: list[tuple[int, int, Location, Location]],
-        circular: bool,
-        id: int,
-        fragments: list[_SeqRecord],
-        restriction_enzymes=list['str'],
-    ):
-        return super().from_assembly(assembly, id, circular, fragments, restriction_enzymes=restriction_enzymes)
-
-
-class GatewaySource(AssemblySourceCommonClass, _GatewaySource):
-    @classmethod
-    def from_assembly(
-        cls,
-        assembly: list[tuple[int, int, Location, Location]],
-        circular: bool,
-        id: int,
-        fragments: list[_SeqRecord],
-        reaction_type: str,
-    ):
-        return super().from_assembly(assembly, id, circular, fragments, reaction_type=reaction_type)
-
-
-class CreLoxRecombinationSource(AssemblySourceCommonClass, _CreLoxRecombinationSource):
-    pass
-
-
-class OligoHybridizationSource(SourceCommonClass, _OligoHybridizationSource):
-    pass
-
-
-class PolymeraseExtensionSource(SourceCommonClass, _PolymeraseExtensionSource):
-    pass
 
 
 class BaseCloningStrategy(_CloningStrategy):
@@ -536,7 +36,7 @@ class BaseCloningStrategy(_CloningStrategy):
     def next_id(self):
         return max([s.id for s in self.sources + self.sequences + self.primers], default=0) + 1
 
-    def add_source_and_sequence(self, source: SourceCommonClass, sequence: TextFileSequence):
+    def add_source_and_sequence(self, source: _Source, sequence: _TextFileSequence):
         if source in self.sources:
             if sequence not in self.sequences:
                 raise ValueError(
@@ -566,7 +66,7 @@ class BaseCloningStrategy(_CloningStrategy):
 
 class PrimerDesignQuery(BaseModel):
     model_config = {'arbitrary_types_allowed': True}
-    sequence: TextFileSequence
+    sequence: _TextFileSequence
     location: SequenceLocationStr
     forward_orientation: bool = True
 

opencloning/request_examples.py

@@ -3,58 +3,48 @@ genome_region_examples = {
         'summary': 'All parameters provided',
         'value': {
             'id': 1,
-            'sequence_accession': 'NC_003424.3',
+            'repository_id': 'NC_003424.3',
             'assembly_accession': 'GCF_000002945.2',
             'locus_tag': 'SPOM_SPAPB1A10.09',
             'gene_id': 2543372,
-            'start': 1877009,
-            'end': 1881726,
-            'strand': 1,
+            'coordinates': '1877009..1881726',
         },
     },
     'full_with_genbank_accession': {
         'summary': 'All parameters provided, but sequence accession is GenBank',
         'value': {
             'id': 1,
-            'sequence_accession': 'CU329670.1',
+            'repository_id': 'CU329670.1',
             'assembly_accession': 'GCF_000002945.2',
             'locus_tag': 'SPOM_SPAPB1A10.09',
             'gene_id': 2543372,
-            'start': 1877009,
-            'end': 1881726,
-            'strand': 1,
+            'coordinates': '1877009..1881726',
         },
     },
     'id_omitted': {
         'summary': 'Gene ID omitted (filled in response)',
         'value': {
             'id': 1,
-            'sequence_accession': 'NC_003424.3',
+            'repository_id': 'NC_003424.3',
             'assembly_accession': 'GCF_000002945.2',
             'locus_tag': 'SPOM_SPAPB1A10.09',
-            'start': 1877009,
-            'end': 1881726,
-            'strand': 1,
+            'coordinates': '1877009..1881726',
         },
     },
     'assembly_accession_omitted': {
         'summary': 'Sequence accession only',
         'value': {
             'id': 1,
-            'sequence_accession': 'NC_003424.3',
-            'start': 1877009,
-            'end': 1881726,
-            'strand': 1,
+            'repository_id': 'NC_003424.3',
+            'coordinates': '1877009..1881726',
         },
     },
     'viral_sequence': {
         'summary': 'Viral sequence not associated with assembly',
         'value': {
             'id': 1,
-            'sequence_accession': 'DQ208311.2',
-            'start': 20,
-            'end': 2050,
-            'strand': -1,
+            'repository_id': 'DQ208311.2',
+            'coordinates': 'complement(20..2050)',
         },
     },
 }
@@ -84,7 +74,6 @@ benchling_url_examples = {
         'summary': 'Typical example',
         'value': {
             'id': 0,
-            'repository_name': 'benchling',
             'repository_id': 'https://benchling.com/siverson/f/lib_B94YxDHhQh-cidar-moclo-library/seq_kryGidaz-c0062_cd.gb',
         },
     },
@@ -95,7 +84,6 @@ snapgene_plasmid_examples = {
         'summary': 'Typical example',
         'value': {
             'id': 0,
-            'repository_name': 'snapgene',
             'repository_id': 'basic_cloning_vectors/pEASY-T1_(linearized)',
         },
     },

opencloning/temp_functions.py

@@ -0,0 +1,50 @@
+"""
+Functions to be moved to pydna at some point.
+"""
+
+from opencloning_linkml.datamodel import AssemblySource
+from Bio.SeqFeature import Location
+from opencloning_linkml.datamodel import RestrictionEnzymeDigestionSource
+from opencloning_linkml.datamodel import RestrictionSequenceCut
+from opencloning_linkml.datamodel import Primer as PrimerModel
+from Bio.Restriction.Restriction import RestrictionType, RestrictionBatch
+from pydna.primer import Primer as PydnaPrimer
+
+
+def is_assembly_complete(source: AssemblySource) -> bool:
+    return any(f.type == 'AssemblyFragment' for f in source.input)
+
+
+def minimal_assembly_overlap(source: AssemblySource) -> int:
+    all_overlaps = list()
+    for f in source.input:
+        if f.type != 'AssemblyFragment':
+            continue
+        if f.left_location is not None:
+            all_overlaps.append(len(Location.fromstring(f.left_location)))
+        if f.right_location is not None:
+            all_overlaps.append(len(Location.fromstring(f.right_location)))
+    if len(all_overlaps) == 0:
+        raise ValueError('Assembly is not complete')
+    return min(all_overlaps)
+
+
+def get_enzymes_from_source(source: RestrictionEnzymeDigestionSource) -> list[str]:
+    out = list()
+    if source.left_edge is not None:
+        out.append(source.left_edge.restriction_enzyme)
+    if source.right_edge is not None:
+        out.append(source.right_edge.restriction_enzyme)
+    # Unique values, sorted the same way
+    return sorted(list(set(out)), key=out.index)
+
+
+def restriction_sequence_cut_to_cutsite_tuple(
+    restriction_sequence_cut: RestrictionSequenceCut,
+) -> tuple[tuple[int, int], RestrictionType]:
+    restriction_enzyme = RestrictionBatch(first=[restriction_sequence_cut.restriction_enzyme]).pop()
+    return ((restriction_sequence_cut.cut_watson, restriction_sequence_cut.overhang), restriction_enzyme)
+
+
+def primer_model_to_pydna_primer(primer_model: PrimerModel) -> PydnaPrimer:
+    return PydnaPrimer(primer_model.sequence, id=str(primer_model.id), name=primer_model.name)