diff --git a/docs/notebooks/history.ipynb b/docs/notebooks/history.ipynb index 7cf5b115..94c3300d 100644 --- a/docs/notebooks/history.ipynb +++ b/docs/notebooks/history.ipynb @@ -186,13 +186,13 @@ "╙── product (Dseqrecord(-18))\n", " └─╼ LigationSource\n", " ├─╼ c (Dseqrecord(-7))\n", - " │ └─╼ Source\n", - " │ └─╼ a (Dseqrecord(-18)) ╾ Source, Source\n", + " │ └─╼ RestrictionEnzymeDigestionSource\n", + " │ └─╼ a (Dseqrecord(-18)) ╾ RestrictionEnzymeDigestionSource, RestrictionEnzymeDigestionSource\n", " ├─╼ d (Dseqrecord(-12))\n", - " │ └─╼ Source\n", + " │ └─╼ RestrictionEnzymeDigestionSource\n", " │ └─╼ ...\n", " └─╼ e (Dseqrecord(-7))\n", - " └─╼ Source\n", + " └─╼ RestrictionEnzymeDigestionSource\n", " └─╼ ...\n" ] } @@ -354,8 +354,8 @@ " └─╼ CreLoxRecombinationSource\n", " └─╼ integration_product (Dseqrecord(-84))\n", " └─╼ CreLoxRecombinationSource\n", - " ├─╼ a (Dseqrecord(-45))\n", - " └─╼ b (Dseqrecord(o39))\n" + " ├─╼ genome (Dseqrecord(-45))\n", + " └─╼ plasmid (Dseqrecord(o39))\n" ] } ], diff --git a/poetry.lock b/poetry.lock index d6dec7ae..ba6af5bf 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. 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a/src/pydna/assembly2.py b/src/pydna/assembly2.py index c896280f..12929aac 100644 --- a/src/pydna/assembly2.py +++ b/src/pydna/assembly2.py @@ -2036,7 +2036,7 @@ def _recast_sources( """ for prod in products: prod.source = source_cls( - **prod.source.model_dump(), + **prod.source.to_unserialized_dict(), **extra_fields, ) return products @@ -2805,7 +2805,8 @@ def crispr_integration( # The second element of product.source.input is conventionally the insert/repair fragment # The other two (first and third) are the two bits of the genome repair_start = _location_boundaries(product.source.input[0].right_location)[0] - repair_end = _location_boundaries(product.source.input[2].left_location)[1] + # Here we do +1 because the position of the cut marks the boundary (e.g. 0:10, 10:20 if a cut is at pos 10) + repair_end = _location_boundaries(product.source.input[2].left_location)[1] + 1 repair_location = create_location(repair_start, repair_end, len(genome)) some_cuts_inside_repair = [] all_cuts_inside_repair = [] diff --git a/src/pydna/genbank.py b/src/pydna/genbank.py index 6cd96043..2b21e719 100644 --- a/src/pydna/genbank.py +++ b/src/pydna/genbank.py @@ -12,12 +12,13 @@ `pydna.ini` file. See the documentation of :func:`pydna.open_config_folder`""" # from pydna.utils import memorize as _memorize -from pydna.opencloning_models import RepositoryIdSource +from pydna.opencloning_models import NCBISequenceSource from pydna.genbankrecord import GenbankRecord as _GenbankRecord from pydna.readers import read as _read from Bio import Entrez as _Entrez from Bio.SeqFeature import SimpleLocation + from typing import Literal as _Literal, Optional as _Optional import re as _re import os as _os @@ -175,11 +176,17 @@ def nucleotide( # _module_logger.info("text[:160] %s", text[:160]) result = _read(text) + # TODO: Address this for cases where only one is defined + if seq_start is not None and seq_stop is not None: + location = SimpleLocation( + int(seq_start) - 1, int(seq_stop), -1 if strand == 2 else strand + ) + else: + location = None - result.source = RepositoryIdSource( + result.source = NCBISequenceSource( repository_id=item, - repository_name="genbank", - location=SimpleLocation(seq_start, seq_stop, strand), + coordinates=location, ) return result diff --git a/src/pydna/oligonucleotide_hybridization.py b/src/pydna/oligonucleotide_hybridization.py new file mode 100644 index 00000000..d7a8db8f --- /dev/null +++ b/src/pydna/oligonucleotide_hybridization.py @@ -0,0 +1,124 @@ +# -*- coding: utf-8 -*- +""" +This module contains the functions for oligonucleotide hybridization. +""" + +from pydna.common_sub_strings import common_sub_strings +from Bio.Seq import reverse_complement +from pydna.primer import Primer +from pydna.dseqrecord import Dseqrecord +from pydna.dseq import Dseq +from pydna.opencloning_models import OligoHybridizationSource, SourceInput + + +def oligonucleotide_hybridization_overhangs( + fwd_oligo_seq: str, rvs_oligo_seq: str, minimal_annealing: int +) -> list[int]: + """ + Returns possible overhangs between two oligos given a minimal annealing length, and + returns an error if mismatches are found. + + see https://github.com/manulera/OpenCloning_backend/issues/302 for notation + + >>> from pydna.oligonucleotide_hybridization import oligonucleotide_hybridization_overhangs + >>> oligonucleotide_hybridization_overhangs("ATGGC", "GCCAT", 3) + [0] + >>> oligonucleotide_hybridization_overhangs("aATGGC", "GCCAT", 5) + [-1] + >>> oligonucleotide_hybridization_overhangs("ATGGC", "GCCATa", 5) + [1] + >>> oligonucleotide_hybridization_overhangs("ATGGC", "GCCATaaGCCAT", 5) + [0, 7] + + If the minimal annealing length is longer than the length of the shortest oligo, it returns an empty list. + + >>> oligonucleotide_hybridization_overhangs("ATGGC", "GCCATaaGCCAT", 100) + [] + + If it's possible to anneal for ``minimal_annealing`` length, but with mismatches, it raises an error. + + >>> oligonucleotide_hybridization_overhangs("cATGGC", "GCCATa", 5) + Traceback (most recent call last): + ... + ValueError: The oligonucleotides can anneal with mismatches + """ + matches = common_sub_strings( + fwd_oligo_seq.lower(), + reverse_complement(rvs_oligo_seq.lower()), + minimal_annealing, + ) + + for pos_fwd, pos_rvs, length in matches: + + if (pos_fwd != 0 and pos_rvs != 0) or ( + pos_fwd + length < len(fwd_oligo_seq) + and pos_rvs + length < len(rvs_oligo_seq) + ): + raise ValueError("The oligonucleotides can anneal with mismatches") + + # Return possible overhangs + return [pos_rvs - pos_fwd for pos_fwd, pos_rvs, length in matches] + + +def oligonucleotide_hybridization( + fwd_primer: Primer, rvs_primer: Primer, minimal_annealing: int +) -> list[Dseqrecord]: + """ + Returns a list of Dseqrecord objects representing the hybridization of two primers. + + >>> from pydna.primer import Primer + >>> from pydna.oligonucleotide_hybridization import oligonucleotide_hybridization + >>> fwd_primer = Primer("ATGGC") + >>> rvs_primer = Primer("GCCA") + >>> oligonucleotide_hybridization(fwd_primer, rvs_primer, 3)[0].seq + Dseq(-5) + ATGGC + ACCG + + Multiple values can be returned: + + >>> rvs_primer2 = Primer("GCCATaaGCCAT") + >>> oligonucleotide_hybridization(fwd_primer, rvs_primer2, 3)[0].seq + Dseq(-12) + ATGGC + TACCGaaTACCG + >>> oligonucleotide_hybridization(fwd_primer, rvs_primer2, 3)[1].seq + Dseq(-12) + ATGGC + TACCGaaTACCG + + If no possible overhangs are found, it returns an empty list. + + >>> oligonucleotide_hybridization(fwd_primer, rvs_primer, 100) + [] + + If there are mismatches given the minimal annealing length, it raises an error. + + >>> fwd_primer3 = Primer("cATGGC") + >>> rvs_primer3 = Primer("GCCATa") + >>> oligonucleotide_hybridization(fwd_primer3, rvs_primer3, 5) + Traceback (most recent call last): + ... + ValueError: The oligonucleotides can anneal with mismatches + """ + possible_overhangs = oligonucleotide_hybridization_overhangs( + str(fwd_primer.seq), str(rvs_primer.seq), minimal_annealing + ) + sources = [ + OligoHybridizationSource( + overhang_crick_3prime=pos, + input=[SourceInput(sequence=fwd_primer), SourceInput(sequence=rvs_primer)], + ) + for pos in possible_overhangs + ] + return [ + Dseqrecord( + Dseq( + str(fwd_primer.seq), + str(rvs_primer.seq), + ovhg=source.overhang_crick_3prime, + ), + source=source, + ) + for source in sources + ] diff --git a/src/pydna/opencloning_models.py b/src/pydna/opencloning_models.py index 327c813c..a3708dbf 100644 --- a/src/pydna/opencloning_models.py +++ b/src/pydna/opencloning_models.py @@ -24,10 +24,11 @@ from contextlib import contextmanager from threading import local -from pydantic import BaseModel, ConfigDict, Field, field_validator +from pydantic import BaseModel, ConfigDict, Field, field_serializer, field_validator from opencloning_linkml.datamodel import ( CloningStrategy as _BaseCloningStrategy, + DatabaseSource as _DatabaseSource, Primer as _PrimerModel, Source as _Source, TextFileSequence as _TextFileSequence, @@ -47,14 +48,32 @@ LigationSource as _LigationSource, GatewaySource as _GatewaySource, GatewayReactionType, + AnnotationTool, HomologousRecombinationSource as _HomologousRecombinationSource, CreLoxRecombinationSource as _CreLoxRecombinationSource, PCRSource as _PCRSource, CRISPRSource as _CRISPRSource, - RepositoryIdSource as _RepositoryIdSource, # here! + RepositoryIdSource as _RepositoryIdSource, UploadedFileSource as _UploadedFileSource, + AddgeneIdSource as _AddgeneIdSource, + AddgeneSequenceType, + BenchlingUrlSource as _BenchlingUrlSource, + SnapGenePlasmidSource as _SnapGenePlasmidSource, + EuroscarfSource as _EuroscarfSource, + WekWikGeneIdSource as _WekWikGeneIdSource, + SEVASource as _SEVASource, + IGEMSource as _IGEMSource, + OpenDNACollectionsSource as _OpenDNACollectionsSource, + GenomeCoordinatesSource as _GenomeCoordinatesSource, + OligoHybridizationSource as _OligoHybridizationSource, + PolymeraseExtensionSource as _PolymeraseExtensionSource, + AnnotationSource as _AnnotationSource, + AnnotationReport as _AnnotationReport, + PlannotateAnnotationReport as _PlannotateAnnotationReport, + ReverseComplementSource as _ReverseComplementSource, + NCBISequenceSource as _NCBISequenceSource, ) -from Bio.SeqFeature import Location, LocationParserError +from Bio.SeqFeature import Location, LocationParserError, SimpleLocation from Bio.Restriction.Restriction import AbstractCut import networkx as nx from typing import List @@ -80,8 +99,9 @@ def id_mode(use_python_internal_id: bool = True): mapping them to the OpenCloning data model. If ``use_python_internal_id`` is True, the built-in python ``id()`` function is used to assign ids to objects. That function produces a unique integer for each object in python, so it's guaranteed to be unique. - If ``use_python_internal_id`` is False, the object's ``.id`` attribute (must be a string integer) - is used to assign ids to objects. This is useful when the objects already have meaningful ids, + If ``use_python_internal_id`` is False, the object's ``.id`` attribute + (must be a string integer) is used to assign ids to objects. This is useful + when the objects already have meaningful ids, and you want to keep references to them in ``SourceInput`` objects (which sequences and primers are used in a particular source). @@ -180,6 +200,14 @@ def from_start_and_end( ): return cls.from_biopython_location(create_location(start, end, seq_len, strand)) + def get_ncbi_format_coordinates(self) -> str: + """Return start, end, strand in the same format as the NCBI eutils API (1-based, inclusive)""" + return ( + self.to_biopython_location().start + 1, + self.to_biopython_location().end, + self.to_biopython_location().strand, + ) + class ConfiguredBaseModel(BaseModel): model_config = ConfigDict( @@ -263,18 +291,23 @@ class Source(ConfiguredBaseModel): input: list[Union[SourceInput, AssemblyFragment]] = Field(default_factory=list) TARGET_MODEL: ClassVar[Type[_Source]] = _Source - def input_models(self): - return [fragment.to_pydantic_model() for fragment in self.input] - - def _kwargs(self, seq_id: int) -> dict: - return { - "id": seq_id, - "input": self.input_models(), - } + @field_serializer("input") + def serialize_input( + self, input: list[Union[SourceInput, AssemblyFragment]] + ) -> list[_SourceInput | _AssemblyFragment]: + return [fragment.to_pydantic_model() for fragment in input] def to_pydantic_model(self, seq_id: int): - kwargs = self._kwargs(seq_id) - return self.TARGET_MODEL(**kwargs) + model_dict = self.model_dump() + model_dict["id"] = seq_id + return self.TARGET_MODEL(**model_dict) + + def to_unserialized_dict(self): + """ + Converts into a dictionary without serializing the fields. + This is used to be able to recast. + """ + return {field: getattr(self, field) for field in self.__pydantic_fields__} def add_to_history_graph(self, history_graph: nx.DiGraph, seq: "Dseqrecord"): """ @@ -317,15 +350,6 @@ class AssemblySource(Source): TARGET_MODEL: ClassVar[Type[_AssemblySource]] = _AssemblySource - def _kwargs(self, seq_id: int) -> dict: - return { - **super()._kwargs(seq_id), - "circular": self.circular, - } - - def to_pydantic_model(self, seq_id: int): - return self.TARGET_MODEL(**self._kwargs(seq_id)) - @classmethod def from_subfragment_representation( cls, @@ -348,6 +372,12 @@ def from_subfragment_representation( return AssemblySource(input=input_list, circular=is_circular) +class DatabaseSource(Source): + TARGET_MODEL: ClassVar[Type[_DatabaseSource]] = _DatabaseSource + + database_id: int + + class UploadedFileSource(Source): TARGET_MODEL: ClassVar[Type[_UploadedFileSource]] = _UploadedFileSource @@ -356,48 +386,74 @@ class UploadedFileSource(Source): index_in_file: int sequence_file_format: str - # "id": 1, - # "type": "UploadedFileSource", - # "output_name": null, - # "database_id": null, - # "input": [], - # "sequence_file_format": "fasta", - # "file_name": "seq2.fasta", - # "index_in_file": 0, - # "circularize": false, - # "coordinates": null, - # "output": 1 - - def _kwargs(self, seq_id: int) -> dict: - return { - **super()._kwargs(seq_id), - "file_name": self.file_name, - "index_in_file": self.index_in_file, - "sequence_file_format": self.sequence_file_format, - } - class RepositoryIdSource(Source): TARGET_MODEL: ClassVar[Type[_RepositoryIdSource]] = _RepositoryIdSource + repository_id: str - repository_name: str - location: Location + # location: Location + + +class RepositoryIdSourceWithSequenceFileUrl(RepositoryIdSource): + """ + Auxiliary class to avoid code duplication in the sources that have + a sequence file url. + """ + + sequence_file_url: Optional[str] = None + + +class AddgeneIdSource(RepositoryIdSourceWithSequenceFileUrl): + TARGET_MODEL: ClassVar[Type[_AddgeneIdSource]] = _AddgeneIdSource + + addgene_sequence_type: Optional[AddgeneSequenceType] = None + + +class BenchlingUrlSource(RepositoryIdSource): + TARGET_MODEL: ClassVar[Type[_BenchlingUrlSource]] = _BenchlingUrlSource + + +class SnapGenePlasmidSource(RepositoryIdSource): + TARGET_MODEL: ClassVar[Type[_SnapGenePlasmidSource]] = _SnapGenePlasmidSource + + +class EuroscarfSource(RepositoryIdSource): + TARGET_MODEL: ClassVar[Type[_EuroscarfSource]] = _EuroscarfSource - # "id": 2, - # "type": "RepositoryIdSource", - # "output_name": null, - # "database_id": null, - # "input": [], - # "repository_id": "NM_001018957.2", - # "repository_name": "genbank" - def _kwargs(self, seq_id: int) -> dict: - return { - **super()._kwargs(seq_id), - "repository_id": self.repository_id, - "repository_name": self.repository_name, - } +class WekWikGeneIdSource(RepositoryIdSourceWithSequenceFileUrl): + TARGET_MODEL: ClassVar[Type[_WekWikGeneIdSource]] = _WekWikGeneIdSource + + +class SEVASource(RepositoryIdSourceWithSequenceFileUrl): + TARGET_MODEL: ClassVar[Type[_SEVASource]] = _SEVASource + + +class IGEMSource(RepositoryIdSourceWithSequenceFileUrl): + TARGET_MODEL: ClassVar[Type[_IGEMSource]] = _IGEMSource + + +class OpenDNACollectionsSource(RepositoryIdSourceWithSequenceFileUrl): + TARGET_MODEL: ClassVar[Type[_OpenDNACollectionsSource]] = _OpenDNACollectionsSource + + +class NCBISequenceSource(RepositoryIdSource): + TARGET_MODEL: ClassVar[Type[_NCBISequenceSource]] = _NCBISequenceSource + coordinates: SimpleLocation | None = None + + +class GenomeCoordinatesSource(NCBISequenceSource): + TARGET_MODEL: ClassVar[Type[_GenomeCoordinatesSource]] = _GenomeCoordinatesSource + + assembly_accession: Optional[str] = None + locus_tag: Optional[str] = None + gene_id: Optional[int] = None + coordinates: SimpleLocation + + @field_serializer("coordinates") + def serialize_coordinates(self, coordinates: SimpleLocation) -> str: + return SequenceLocationStr.from_biopython_location(coordinates) class RestrictionAndLigationSource(AssemblySource): @@ -407,11 +463,11 @@ class RestrictionAndLigationSource(AssemblySource): _RestrictionAndLigationSource ) - def _kwargs(self, seq_id: int) -> dict: - return { - **super()._kwargs(seq_id), - "restriction_enzymes": [str(enzyme) for enzyme in self.restriction_enzymes], - } + @field_serializer("restriction_enzymes") + def serialize_restriction_enzymes( + self, restriction_enzymes: list[AbstractCut] + ) -> list[str]: + return [str(enzyme) for enzyme in restriction_enzymes] class GibsonAssemblySource(AssemblySource): @@ -441,13 +497,6 @@ class GatewaySource(AssemblySource): reaction_type: GatewayReactionType greedy: bool = Field(default=False) - def _kwargs(self, seq_id: int) -> dict: - return { - **super()._kwargs(seq_id), - "reaction_type": self.reaction_type, - "greedy": self.greedy, - } - class HomologousRecombinationSource(AssemblySource): TARGET_MODEL: ClassVar[Type[_HomologousRecombinationSource]] = ( @@ -469,21 +518,24 @@ class PCRSource(AssemblySource): TARGET_MODEL: ClassVar[Type[_PCRSource]] = _PCRSource add_primer_features: bool = Field(default=False) - def _kwargs(self, seq_id: int) -> dict: - return { - **super()._kwargs(seq_id), - "add_primer_features": self.add_primer_features, - } - class SequenceCutSource(Source): left_edge: CutSiteType | None right_edge: CutSiteType | None - BASE_MODEL: ClassVar[Type[_SequenceCutSource]] = _SequenceCutSource - ENZYME_MODEL: ClassVar[Type[_RestrictionEnzymeDigestionSource]] = ( - _RestrictionEnzymeDigestionSource - ) + @property + def TARGET_MODEL(self): + return ( + _RestrictionEnzymeDigestionSource + if self._has_enzyme() + else _SequenceCutSource + ) + + @field_serializer("left_edge", "right_edge") + def serialize_cut_site( + self, cut_site: CutSiteType | None + ) -> _RestrictionSequenceCut | _SequenceCut | None: + return self._cutsite_to_model(cut_site) @staticmethod def _cutsite_to_model(cut_site: CutSiteType | None): @@ -515,18 +567,31 @@ def has_enzyme(edge): return has_enzyme(self.left_edge) or has_enzyme(self.right_edge) - def _target_model(self): - return self.ENZYME_MODEL if self._has_enzyme() else self.BASE_MODEL - def _kwargs(self, seq_id: int) -> dict: - return { - **super()._kwargs(seq_id), - "left_edge": self._cutsite_to_model(self.left_edge), - "right_edge": self._cutsite_to_model(self.right_edge), - } +class OligoHybridizationSource(Source): + TARGET_MODEL: ClassVar[Type[_OligoHybridizationSource]] = _OligoHybridizationSource - def to_pydantic_model(self, seq_id: int): - return self._target_model()(**self._kwargs(seq_id)) + overhang_crick_3prime: Optional[int] = None + + +class PolymeraseExtensionSource(Source): + TARGET_MODEL: ClassVar[Type[_PolymeraseExtensionSource]] = ( + _PolymeraseExtensionSource + ) + + +class AnnotationSource(Source): + TARGET_MODEL: ClassVar[Type[_AnnotationSource]] = _AnnotationSource + + annotation_tool: AnnotationTool + annotation_tool_version: Optional[str] = None + annotation_report: Optional[ + list[_AnnotationReport | _PlannotateAnnotationReport] + ] = None + + +class ReverseComplementSource(Source): + TARGET_MODEL: ClassVar[Type[_ReverseComplementSource]] = _ReverseComplementSource class CloningStrategy(_BaseCloningStrategy): @@ -564,9 +629,7 @@ def add_dseqrecord(self, dseqr: "Dseqrecord"): else: self.add_primer(source_input.sequence) else: - self.sources.append( - _ManuallyTypedSource(id=get_id(dseqr), input=[], user_input="A") - ) + self.sources.append(_ManuallyTypedSource(id=get_id(dseqr), input=[])) def reassign_ids(self): all_ids = ( diff --git a/src/pydna/parsers.py b/src/pydna/parsers.py index 9d0e7dc7..44af05f2 100644 --- a/src/pydna/parsers.py +++ b/src/pydna/parsers.py @@ -202,7 +202,9 @@ def parse(data, ds=True): result = _Dseqrecord.from_SeqRecord(s) result.source = UploadedFileSource( - file_name=path, sequence_file_format="genbank", index_in_file=0 + file_name=str(path), # we use str to handle PosixPath + sequence_file_format="genbank", + index_in_file=0, ) sequences.append(result) # sequences.append(_GenbankFile.from_SeqRecord(s, path=path)) diff --git a/tests/test_module_assembly2.py b/tests/test_module_assembly2.py index dcdd4605..b8693074 100644 --- a/tests/test_module_assembly2.py +++ b/tests/test_module_assembly2.py @@ -2638,6 +2638,17 @@ def test_crispr_integration(): assert len(products) == 1 +def test_crispr_integration_edge_case(): + homology1 = "ATGCAAACAGTAATGATGGATGACATTCAAAGCACTGATT" + guide = Primer("CATTCAAAGCACTGATTaat") + genome = Dseqrecord(f"aaaaaa{homology1}aattggaa{homology1}tttttttt") + + insert = Dseqrecord(f"{homology1}acaa{homology1}") + + products = assembly.crispr_integration(genome, [insert], [guide], 40) + assert len(products) == 2 + + def test_pcr_assembly(): template = Dseqrecord("TTTTACGTACGTAAAAAAGCGCGCGCTTTTT") diff --git a/tests/test_module_genbank.py b/tests/test_module_genbank.py index 4e9ca824..b92bfe9c 100755 --- a/tests/test_module_genbank.py +++ b/tests/test_module_genbank.py @@ -5,6 +5,7 @@ import pytest from unittest import mock +from Bio.SeqFeature import SimpleLocation def test_set_email(): @@ -105,6 +106,7 @@ def test_pydna_Genbank_fresh_part(monkeypatch): monkeypatch.setenv("pydna_cached_funcs", "") import pytest from unittest import mock + from Bio import SeqIO mock_efetch = mock.MagicMock(name="mock_efetch1") mock_efetch().read.side_effect = open("X60065-100-110.gb", "r").read @@ -113,8 +115,11 @@ def test_pydna_Genbank_fresh_part(monkeypatch): from pydna.genbank import Genbank gb = Genbank("bjornjobb@gmail.com") - result = gb.nucleotide("X60065.1", seq_start=1, seq_stop=10) + result = gb.nucleotide("X60065.1", seq_start=100, seq_stop=110) assert str(result.seq).lower() == "ctgaaacggac" + assert result.source.coordinates == SimpleLocation(99, 110, 1) + full_sequence = SeqIO.read("X60065.gb", "genbank") + assert str(result.source.coordinates.extract(full_sequence.seq)) == str(result.seq) def test_pydna_Genbank_fresh_partII(monkeypatch): diff --git a/tests/test_module_opencloning_models.py b/tests/test_module_opencloning_models.py index 513b16dc..67667faf 100644 --- a/tests/test_module_opencloning_models.py +++ b/tests/test_module_opencloning_models.py @@ -14,8 +14,11 @@ CloningStrategy, id_mode, get_id, + NCBISequenceSource, + GenomeCoordinatesSource, ) from pydna.primer import Primer +from pydna.oligonucleotide_hybridization import oligonucleotide_hybridization from opencloning_linkml.datamodel import ( AssemblySource as _AssemblySource, AssemblyFragment as _AssemblyFragment, @@ -136,6 +139,17 @@ def get_next_id(self): product_gateway_BP, *_ = gateway_assembly([seq1, seq2], "BP") product_gateway_BP.name = "product_gateway_BP" +## Oligo hybridization + +fwd_primer = Primer("ATGGC", name="fwd_primer") +rvs_primer = Primer("GCCAT", name="rvs_primer") +product_oligo_hybridization, *rest = oligonucleotide_hybridization( + fwd_primer, rvs_primer, 3 +) + +product_oligo_hybridization.name = "product_oligo_hybridization" + + # ======================================================================================== @@ -210,6 +224,15 @@ class DummyModel(BaseModel): DummyModel(location="1..3") DummyModel(location=SequenceLocationStr("1..3")) + def test_get_ncbi_format_coordinates(self): + self.assertEqual( + SequenceLocationStr("1..3").get_ncbi_format_coordinates(), (1, 3, 1) + ) + self.assertEqual( + SequenceLocationStr("complement(1..3)").get_ncbi_format_coordinates(), + (1, 3, -1), + ) + class SourceTest(TestCase): def test_to_pydantic_model(self): @@ -284,13 +307,13 @@ def test_history_string(self): ╙── product (Dseqrecord(-18)) └─╼ LigationSource ├─╼ c (Dseqrecord(-7)) - │ └─╼ Source - │ └─╼ a (Dseqrecord(-18)) ╾ Source, Source + │ └─╼ RestrictionEnzymeDigestionSource + │ └─╼ a (Dseqrecord(-18)) ╾ RestrictionEnzymeDigestionSource, RestrictionEnzymeDigestionSource ├─╼ d (Dseqrecord(-12)) - │ └─╼ Source + │ └─╼ RestrictionEnzymeDigestionSource │ └─╼ ... └─╼ e (Dseqrecord(-7)) - └─╼ Source + └─╼ RestrictionEnzymeDigestionSource └─╼ ... """ ).strip(), @@ -313,7 +336,7 @@ def test_history_string(self): textwrap.dedent( """ ╙── custom_cut_product (Dseqrecord(-7)) - └─╼ Source + └─╼ SequenceCutSource └─╼ name (Dseqrecord(-18)) """ ).strip(), @@ -329,6 +352,17 @@ def test_history_string(self): """ ).strip(), ) + self.assertEqual( + product_oligo_hybridization.history(), + textwrap.dedent( + """ + ╙── product_oligo_hybridization (Dseqrecord(-5)) + └─╼ OligoHybridizationSource + ├─╼ fwd_primer (id 5-mer:5'-ATGGC-3') + └─╼ rvs_primer (id 5-mer:5'-GCCAT-3') + """ + ).strip(), + ) class AssemblySourceTest(TestCase): @@ -546,3 +580,44 @@ def test_id_mode(self): self.assertEqual(get_id(dseqrecord), 456) self.assertRaises(ValueError, get_id, primer_wrong) self.assertRaises(ValueError, get_id, dseqrecord_wrong) + + +class GenomeCoordinatesSourceTest(TestCase): + def test_coordinates_required(self): + with self.assertRaises(ValidationError): + GenomeCoordinatesSource( + coordinates=None, + repository_id="1234567890", + assembly_accession="1234567890", + locus_tag="1234567890", + gene_id=1234567890, + ) + GenomeCoordinatesSource( + coordinates=SimpleLocation(1, 10), + repository_id="1234567890", + assembly_accession="1234567890", + locus_tag="1234567890", + gene_id=1234567890, + ) + + def test_serialize_coordinates(self): + source = GenomeCoordinatesSource( + coordinates=SimpleLocation(0, 10), + repository_id="1234567890", + assembly_accession="1234567890", + locus_tag="1234567890", + gene_id=1234567890, + ) + self.assertEqual(source.model_dump()["coordinates"], "1..10") + + +class NCBISequenceSourceTest(TestCase): + def test_coordinates_not_required(self): + NCBISequenceSource( + coordinates=None, + repository_id="1234567890", + ) + NCBISequenceSource( + coordinates=SimpleLocation(1, 10), + repository_id="1234567890", + )