├── .buildinfo ├── .coveragerc ├── .flake8 ├── .gitattributes ├── .github ├── dependabot.yml └── workflows │ ├── publish-docs.yml │ ├── pydna_pypi_build_workflow.yml │ ├── pydna_test_and_coverage_workflow.yml │ └── pydna_test_pypi_build_workflow.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── .vscode ├── extensions.json └── settings.json ├── CODE_OF_CONDUCT.md ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── codecov.yml ├── dependabot.yml ├── docs ├── .gitignore ├── CHANGELOG.md ├── README.md ├── _static │ ├── 458010537-a5b66c97-7101-4586-b32d-681caf6afb70.png │ ├── BMC.png │ ├── BMC_resized.png │ ├── BMC_resized_old.png │ ├── assembly_fragment_slide_circular.png │ ├── assembly_fragment_slide_linear.png │ ├── banner.png │ ├── cloning_strategy.png │ ├── custom.css │ ├── favicon.ico │ ├── gel.png │ ├── pydna-web.png │ ├── pydna.png │ ├── pydna.resized.png │ ├── pydna240x240.png │ ├── pydna_512x512.png │ ├── pydna_512x512_trsp.png │ ├── pydna_logo_769x1057.png │ ├── pydna_logo_resized.png │ ├── pydna_transparent.png │ └── snake.png ├── build_docs.sh ├── colored.png ├── conf.py ├── cookbook │ ├── 2389.fasta │ ├── 2577.fasta │ ├── 5681.fasta │ ├── GUP1_locus.gb │ ├── GUP1rec1sens.txt │ ├── GUP1rec2AS.txt │ ├── XKS1_orf.txt │ ├── YEp24PGK.txt │ ├── YEp24PGK_XK.gb │ ├── YEp24PGK_XK_manually_assembled.txt │ ├── YEp24PGK_XK_vector.gb │ ├── cookbook.ipynb │ ├── figure1.gif │ ├── figure1.odp │ ├── figure1.png │ ├── figure2.png │ ├── logo.png │ ├── pGREG505.gb │ ├── pGREG505.png │ ├── pGUP1.gb │ ├── pGUP1_NEW.gb │ ├── pGUP1_OLD.gb │ ├── pGUP1_vector.gb │ ├── primer1.txt │ ├── primer3.txt │ ├── pydna_cookbook_0-6-0.docx │ ├── pydna_cookbook_0-6-0.odt │ ├── pydna_cookbook_0-6-0.pdf │ └── seqs.fas ├── docs regarding PCR programs for enzymes with sso7 domains │ ├── Finnzymes Reagents - Optimizing Tm and annealing.pdf │ ├── Optimizing Tm and Annealing _ Thermo Fisher Scientific.pdf │ └── PCR Protocol for Phusion High-Fidelity DNA Polymerase (M0530) _ NEB.pdf ├── example.png ├── example_gallery.rst ├── example_old.png ├── future_release_names.md ├── getting_started.rst ├── how_pydna_works.rst ├── index.rst ├── installation.rst ├── notebooks │ ├── .gitignore │ ├── CRISPR.ipynb │ ├── CU329670.gb │ ├── Dseq.ipynb │ ├── Dseq_Features.ipynb │ ├── Example_CRISPR.ipynb │ ├── Example_Gibson.ipynb │ ├── Example_Restriction.ipynb │ ├── Gibson.ipynb │ ├── Importing_Seqs.ipynb │ ├── PCR.ipynb │ ├── Restrict_Ligate_Cloning.ipynb │ ├── U49845.fasta │ ├── U49845.gb │ ├── gibson_eg.gb │ ├── hackathon_copenhagen_2025.ipynb │ ├── history.ipynb │ ├── images │ │ ├── assembly.png │ │ ├── snapgene_screenshot.png │ │ ├── snapgene_screenshot2.png │ │ └── weird_assembly.png │ ├── new_assemblies.ipynb │ ├── pCC1BAC.gb │ ├── pDONRtm201.dna │ ├── pFA6a-kanMX6.gb │ ├── primer_design.ipynb │ ├── readme_example.ipynb │ └── sample_seq.gb ├── pydna_cheat_sheet.odt ├── pydna_cheat_sheet.pdf └── pydna_session.py ├── gpl.txt ├── objects.inv ├── poetry.lock ├── poetry.toml ├── pyproject.toml ├── run_test.py ├── src └── pydna │ ├── __init__.py │ ├── _pretty.py │ ├── _thermodynamic_data.py │ ├── all.py │ ├── amplicon.py │ ├── amplify.py │ ├── assembly.py │ ├── assembly2.py │ ├── codon.py │ ├── common_sub_strings.py │ ├── conftest.py │ ├── contig.py │ ├── cre_lox.py │ ├── crispr.py │ ├── design.py │ ├── download.py │ ├── dseq.py │ ├── dseqrecord.py │ ├── fakeseq.py │ ├── fusionpcr.py │ ├── gateway.py │ ├── gel.py │ ├── genbank.py │ ├── genbankfile.py │ ├── genbankfixer.py │ ├── genbankrecord.py │ ├── goldengate.py │ ├── ladders.py │ ├── ligate.py │ ├── opencloning_models.py │ ├── parsers.py │ ├── primer.py │ ├── readers.py │ ├── seq.py │ ├── seqrecord.py │ ├── sequence_picker.py │ ├── sequence_regex.py │ ├── threading_timer_decorator_exit.py │ ├── tm.py │ ├── types.py │ ├── user_cloning.py │ └── utils.py └── tests ├── .coveragerc ├── 02-G1_B01_013.ab1 ├── 1362_6.ape ├── 15405_2.ape ├── 28-1rev_D04_026.ab1 ├── 32-3rev_H04_018.ab1 ├── 36-5rev_D05_041.ab1 ├── 8054_2.ape ├── AAA_OLD.gb ├── ABI01.abi ├── AJ515744.gb ├── AJ515746.gb ├── AJ580803.gb ├── AJ580804.gb ├── AM086621.gb ├── AX023560.gb ├── E05006.gb ├── G.txt ├── GIN11M86.gb ├── GUP1_locus.gb ├── GUP1rec1sens.txt ├── GUP1rec2AS.txt ├── Ggatcc (copy).gb ├── Ggatcc.gb ├── KlLEU2tt.fas ├── KlLEU2tt.gb ├── New_DNA.gb ├── New_DNA__________________.gb ├── RefDataBjorn.fas ├── SYNPUC19CV.gb ├── X06035.ape ├── X60065-100-110.gb ├── X60065.gb ├── XKS1_orf.txt ├── YEp24PGK.txt ├── YEp24PGK_.txt ├── YEp24PGK_XK_manually_assembled.txt ├── YLACC1_locus.gb ├── _.gb ├── __getenv.txt ├── _test_module_genbank2.py_ ├── all_cre_lox.gb ├── broken_genbank_files ├── ApE_example.gb ├── Author sequence.gb ├── NCBI_example.gb ├── P30350%20(2013-10-11%2013_49_14).dna.txt ├── VectorNTI_example.gb ├── YEplac181.txt ├── fakeGenBankFile.gb ├── hej.txt ├── pGADT7-Rec.gb ├── pGreenLantern1.gb └── sequence.gb ├── conftest.py ├── dna2943.gb ├── dna2943_mod.gb ├── example.ipynb ├── figures.odt ├── foo ├── format_sequences.ipynb ├── gateway_manual_cloning ├── entry-attP1_1-attP2_1.dna ├── entry-attP1_2-attP2_2.dna ├── entry-attP2_1-attP1_3.dna ├── entry-attP2_3-attP3_2.dna ├── entry-attP3_1-attP2_1.dna ├── entry-attP4_2-attP1_4.dna ├── example_valerie │ ├── 483_P4-P1r_EC1.2EC1.1p.dna │ ├── 484_pDONR221_(Cas9_NLS_rbcS_E9t_U6_29p.dna │ ├── P2RP3 test SYC.dna │ ├── addgene-plasmid-133748-sequence-271264.dna │ ├── output.gb │ └── output2.gb ├── expression-attP1_1-attP2_1.dna ├── expression-attP1_2-attP2_2.dna ├── expression-attP2_1-attP1_3.dna ├── pBAD-DEST49.dna ├── pDONRtm201.dna ├── pDONRtm221 P3-P2.dna ├── pDONRtm221.dna ├── pDONRtmP2r-P3.dna ├── pDONRtmP4-P1r.dna ├── pDONRtm_Zeo.dna ├── pET-53-DESTtm.dna ├── pairing.tsv ├── pcDNAtm-DEST53.dna ├── pcr_product-attP1_1-attP2_1.dna ├── pcr_product-attP1_2-attP2_2.dna ├── pcr_product-attP2_1-attP1_3.dna ├── pcr_product-attP2_3-attP3_2.dna ├── pcr_product-attP3_1-attP2_1.dna └── pcr_product-attP4_2-attP1_4.dna ├── jupyter_test_repr (copy).ipynb________ ├── jupyter_test_repr.ipynb ├── lambda.gb ├── my_test_enzymes.txt ├── myseq.gb ├── nucleotide1.xml ├── output.file ├── pAG25.gb ├── pAG32.gb ├── pCAPs-AjiI.gb ├── pCAPs-pSU0.gb ├── pCAPs.gb ├── pCAPs_fasta (copy).txt ├── pCAPs_fasta.txt ├── pCAPs_lowgc.gb ├── pCR_MCT1_HA46.gb ├── pGREG505.gb ├── pGSHU 7180bp.gb ├── pGSKU 6961bp.gb ├── pGUP1_correct.gb ├── pGUP1_not_synced.gb ├── pKT127______.ape ├── pMEC1135.gb ├── pMX4blaster2_old.gb ├── pUC19-BamHI-a-rc.gb ├── pUC19-BamHI-a.gb ├── pUC19-EcoRI_PstI-d-rc.gb ├── pUC19-SmaI-a.gb ├── pUC19.gb ├── pUC19_M77789.gb ├── pUC19_MarkBudde.gb ├── pUC19_fasta.txt ├── pUC19_small_gene.gb ├── pUC_LAC4.gb ├── pUC_LAC4_correct_rotation.gb ├── pYPK0_TDH3_GAL2_PGI1.gb ├── pYPK7_TDH3_GAL2_PGI1.gb ├── pYPKa.gb ├── pYPKp7.gb ├── primer1.txt ├── primer3.txt ├── primers.fas ├── primers_linux_line_endings.txt ├── primers_linux_line_endings_not_unique.txt ├── profile.pstat ├── pth1.txt ├── pth2.txt ├── pthx.txt ├── pydna_gel.png ├── pydna_gel2.png ├── pydna_read_test.txt ├── pydna_read_test2.txt ├── pydna_read_test3.txt ├── read1.gb ├── read2.gb ├── read3.fasta ├── read4.fasta ├── run_pytest_with_coverage.sh ├── save_changed_seq.ipynb ├── sequence.gb ├── subfolder └── sequence.gb ├── test ├── test_USERcloning.py ├── test_extra_cut_features.py ├── test_extra_markbudde.py ├── test_extra_santirdnd_bug_spanning_features.py ├── test_longerlocus_name_gives_dseq.py ├── test_module___init__.py ├── test_module__pretty.py ├── test_module__thermodynamic_data.py ├── test_module_all.py ├── test_module_amplicon.py ├── test_module_amplify.py ├── test_module_assembly.py ├── test_module_assembly2.py ├── test_module_common_sub_strings.py ├── test_module_contig.py ├── test_module_cre_lox.py ├── test_module_crispr.py ├── test_module_design.py ├── test_module_download.py ├── test_module_dseq.py ├── test_module_dseqrecord.py ├── test_module_fakeseq.py ├── test_module_fusionpcr.py ├── test_module_gateway.py ├── test_module_gel.py ├── test_module_genbank.py ├── test_module_genbankfile.py ├── test_module_genbankfixer.py ├── test_module_genbankrecord.py ├── test_module_ligate.py ├── test_module_opencloning_models.py ├── test_module_parsers.py ├── test_module_primer.py ├── test_module_readers.py ├── test_module_seq.py ├── test_module_seqrecord.py ├── test_module_tm.py └── test_module_utils.py /.buildinfo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.buildinfo -------------------------------------------------------------------------------- /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.coveragerc -------------------------------------------------------------------------------- /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.flake8 -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/workflows/publish-docs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.github/workflows/publish-docs.yml -------------------------------------------------------------------------------- /.github/workflows/pydna_pypi_build_workflow.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.github/workflows/pydna_pypi_build_workflow.yml -------------------------------------------------------------------------------- /.github/workflows/pydna_test_and_coverage_workflow.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.github/workflows/pydna_test_and_coverage_workflow.yml -------------------------------------------------------------------------------- /.github/workflows/pydna_test_pypi_build_workflow.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.github/workflows/pydna_test_pypi_build_workflow.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /.vscode/extensions.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.vscode/extensions.json -------------------------------------------------------------------------------- /.vscode/settings.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/.vscode/settings.json -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/README.md -------------------------------------------------------------------------------- /codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/codecov.yml -------------------------------------------------------------------------------- /dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/dependabot.yml -------------------------------------------------------------------------------- /docs/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/.gitignore -------------------------------------------------------------------------------- /docs/CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/CHANGELOG.md -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/_static/458010537-a5b66c97-7101-4586-b32d-681caf6afb70.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/458010537-a5b66c97-7101-4586-b32d-681caf6afb70.png -------------------------------------------------------------------------------- /docs/_static/BMC.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/BMC.png -------------------------------------------------------------------------------- /docs/_static/BMC_resized.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/BMC_resized.png -------------------------------------------------------------------------------- /docs/_static/BMC_resized_old.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/BMC_resized_old.png -------------------------------------------------------------------------------- /docs/_static/assembly_fragment_slide_circular.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/assembly_fragment_slide_circular.png -------------------------------------------------------------------------------- /docs/_static/assembly_fragment_slide_linear.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/assembly_fragment_slide_linear.png -------------------------------------------------------------------------------- /docs/_static/banner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/banner.png -------------------------------------------------------------------------------- /docs/_static/cloning_strategy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/cloning_strategy.png -------------------------------------------------------------------------------- /docs/_static/custom.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/custom.css -------------------------------------------------------------------------------- /docs/_static/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/favicon.ico -------------------------------------------------------------------------------- /docs/_static/gel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/gel.png -------------------------------------------------------------------------------- /docs/_static/pydna-web.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna-web.png -------------------------------------------------------------------------------- /docs/_static/pydna.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna.png -------------------------------------------------------------------------------- /docs/_static/pydna.resized.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna.resized.png -------------------------------------------------------------------------------- /docs/_static/pydna240x240.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna240x240.png -------------------------------------------------------------------------------- /docs/_static/pydna_512x512.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna_512x512.png -------------------------------------------------------------------------------- /docs/_static/pydna_512x512_trsp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna_512x512_trsp.png -------------------------------------------------------------------------------- /docs/_static/pydna_logo_769x1057.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna_logo_769x1057.png -------------------------------------------------------------------------------- /docs/_static/pydna_logo_resized.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna_logo_resized.png -------------------------------------------------------------------------------- /docs/_static/pydna_transparent.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/pydna_transparent.png -------------------------------------------------------------------------------- /docs/_static/snake.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/_static/snake.png -------------------------------------------------------------------------------- /docs/build_docs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/build_docs.sh -------------------------------------------------------------------------------- /docs/colored.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/colored.png -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/cookbook/2389.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/2389.fasta -------------------------------------------------------------------------------- /docs/cookbook/2577.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/2577.fasta -------------------------------------------------------------------------------- /docs/cookbook/5681.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/5681.fasta -------------------------------------------------------------------------------- /docs/cookbook/GUP1_locus.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/GUP1_locus.gb -------------------------------------------------------------------------------- /docs/cookbook/GUP1rec1sens.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/GUP1rec1sens.txt -------------------------------------------------------------------------------- /docs/cookbook/GUP1rec2AS.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/GUP1rec2AS.txt -------------------------------------------------------------------------------- /docs/cookbook/XKS1_orf.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/XKS1_orf.txt -------------------------------------------------------------------------------- /docs/cookbook/YEp24PGK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/YEp24PGK.txt -------------------------------------------------------------------------------- /docs/cookbook/YEp24PGK_XK.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/YEp24PGK_XK.gb -------------------------------------------------------------------------------- /docs/cookbook/YEp24PGK_XK_manually_assembled.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/YEp24PGK_XK_manually_assembled.txt -------------------------------------------------------------------------------- /docs/cookbook/YEp24PGK_XK_vector.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/YEp24PGK_XK_vector.gb -------------------------------------------------------------------------------- /docs/cookbook/cookbook.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/cookbook.ipynb -------------------------------------------------------------------------------- /docs/cookbook/figure1.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/figure1.gif -------------------------------------------------------------------------------- /docs/cookbook/figure1.odp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/figure1.odp -------------------------------------------------------------------------------- /docs/cookbook/figure1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/figure1.png -------------------------------------------------------------------------------- /docs/cookbook/figure2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/figure2.png -------------------------------------------------------------------------------- /docs/cookbook/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/logo.png -------------------------------------------------------------------------------- /docs/cookbook/pGREG505.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pGREG505.gb -------------------------------------------------------------------------------- /docs/cookbook/pGREG505.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pGREG505.png -------------------------------------------------------------------------------- /docs/cookbook/pGUP1.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pGUP1.gb -------------------------------------------------------------------------------- /docs/cookbook/pGUP1_NEW.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pGUP1_NEW.gb -------------------------------------------------------------------------------- /docs/cookbook/pGUP1_OLD.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pGUP1_OLD.gb -------------------------------------------------------------------------------- /docs/cookbook/pGUP1_vector.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pGUP1_vector.gb -------------------------------------------------------------------------------- /docs/cookbook/primer1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/primer1.txt -------------------------------------------------------------------------------- /docs/cookbook/primer3.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/primer3.txt -------------------------------------------------------------------------------- /docs/cookbook/pydna_cookbook_0-6-0.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pydna_cookbook_0-6-0.docx -------------------------------------------------------------------------------- /docs/cookbook/pydna_cookbook_0-6-0.odt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pydna_cookbook_0-6-0.odt -------------------------------------------------------------------------------- /docs/cookbook/pydna_cookbook_0-6-0.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/pydna_cookbook_0-6-0.pdf -------------------------------------------------------------------------------- /docs/cookbook/seqs.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/cookbook/seqs.fas -------------------------------------------------------------------------------- /docs/docs regarding PCR programs for enzymes with sso7 domains/Finnzymes Reagents - Optimizing Tm and annealing.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/docs regarding PCR programs for enzymes with sso7 domains/Finnzymes Reagents - Optimizing Tm and annealing.pdf -------------------------------------------------------------------------------- /docs/docs regarding PCR programs for enzymes with sso7 domains/Optimizing Tm and Annealing _ Thermo Fisher Scientific.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/docs regarding PCR programs for enzymes with sso7 domains/Optimizing Tm and Annealing _ Thermo Fisher Scientific.pdf -------------------------------------------------------------------------------- /docs/docs regarding PCR programs for enzymes with sso7 domains/PCR Protocol for Phusion High-Fidelity DNA Polymerase (M0530) _ NEB.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/docs regarding PCR programs for enzymes with sso7 domains/PCR Protocol for Phusion High-Fidelity DNA Polymerase (M0530) _ NEB.pdf -------------------------------------------------------------------------------- /docs/example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/example.png -------------------------------------------------------------------------------- /docs/example_gallery.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/example_gallery.rst -------------------------------------------------------------------------------- /docs/example_old.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/example_old.png -------------------------------------------------------------------------------- /docs/future_release_names.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/future_release_names.md -------------------------------------------------------------------------------- /docs/getting_started.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/getting_started.rst -------------------------------------------------------------------------------- /docs/how_pydna_works.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/how_pydna_works.rst -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/installation.rst -------------------------------------------------------------------------------- /docs/notebooks/.gitignore: -------------------------------------------------------------------------------- 1 | *.json 2 | -------------------------------------------------------------------------------- /docs/notebooks/CRISPR.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/CRISPR.ipynb -------------------------------------------------------------------------------- /docs/notebooks/CU329670.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/CU329670.gb -------------------------------------------------------------------------------- /docs/notebooks/Dseq.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/Dseq.ipynb -------------------------------------------------------------------------------- /docs/notebooks/Dseq_Features.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/Dseq_Features.ipynb -------------------------------------------------------------------------------- /docs/notebooks/Example_CRISPR.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/Example_CRISPR.ipynb -------------------------------------------------------------------------------- /docs/notebooks/Example_Gibson.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/Example_Gibson.ipynb -------------------------------------------------------------------------------- /docs/notebooks/Example_Restriction.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/Example_Restriction.ipynb -------------------------------------------------------------------------------- /docs/notebooks/Gibson.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/Gibson.ipynb -------------------------------------------------------------------------------- /docs/notebooks/Importing_Seqs.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/Importing_Seqs.ipynb -------------------------------------------------------------------------------- /docs/notebooks/PCR.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/PCR.ipynb -------------------------------------------------------------------------------- /docs/notebooks/Restrict_Ligate_Cloning.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/Restrict_Ligate_Cloning.ipynb -------------------------------------------------------------------------------- /docs/notebooks/U49845.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/U49845.fasta -------------------------------------------------------------------------------- /docs/notebooks/U49845.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/U49845.gb -------------------------------------------------------------------------------- /docs/notebooks/gibson_eg.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/gibson_eg.gb -------------------------------------------------------------------------------- /docs/notebooks/hackathon_copenhagen_2025.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/hackathon_copenhagen_2025.ipynb -------------------------------------------------------------------------------- /docs/notebooks/history.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/history.ipynb -------------------------------------------------------------------------------- /docs/notebooks/images/assembly.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/images/assembly.png -------------------------------------------------------------------------------- /docs/notebooks/images/snapgene_screenshot.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/images/snapgene_screenshot.png -------------------------------------------------------------------------------- /docs/notebooks/images/snapgene_screenshot2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/images/snapgene_screenshot2.png -------------------------------------------------------------------------------- /docs/notebooks/images/weird_assembly.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/images/weird_assembly.png -------------------------------------------------------------------------------- /docs/notebooks/new_assemblies.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/new_assemblies.ipynb -------------------------------------------------------------------------------- /docs/notebooks/pCC1BAC.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/pCC1BAC.gb -------------------------------------------------------------------------------- /docs/notebooks/pDONRtm201.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/pDONRtm201.dna -------------------------------------------------------------------------------- /docs/notebooks/pFA6a-kanMX6.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/pFA6a-kanMX6.gb -------------------------------------------------------------------------------- /docs/notebooks/primer_design.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/primer_design.ipynb -------------------------------------------------------------------------------- /docs/notebooks/readme_example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/readme_example.ipynb -------------------------------------------------------------------------------- /docs/notebooks/sample_seq.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/notebooks/sample_seq.gb -------------------------------------------------------------------------------- /docs/pydna_cheat_sheet.odt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/pydna_cheat_sheet.odt -------------------------------------------------------------------------------- /docs/pydna_cheat_sheet.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/pydna_cheat_sheet.pdf -------------------------------------------------------------------------------- /docs/pydna_session.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/docs/pydna_session.py -------------------------------------------------------------------------------- /gpl.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/gpl.txt -------------------------------------------------------------------------------- /objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/objects.inv -------------------------------------------------------------------------------- /poetry.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/poetry.lock -------------------------------------------------------------------------------- /poetry.toml: -------------------------------------------------------------------------------- 1 | [virtualenvs] 2 | in-project = true 3 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/pyproject.toml -------------------------------------------------------------------------------- /run_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/run_test.py -------------------------------------------------------------------------------- /src/pydna/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/__init__.py -------------------------------------------------------------------------------- /src/pydna/_pretty.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/_pretty.py -------------------------------------------------------------------------------- /src/pydna/_thermodynamic_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/_thermodynamic_data.py -------------------------------------------------------------------------------- /src/pydna/all.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/all.py -------------------------------------------------------------------------------- /src/pydna/amplicon.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/amplicon.py -------------------------------------------------------------------------------- /src/pydna/amplify.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/amplify.py -------------------------------------------------------------------------------- /src/pydna/assembly.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/assembly.py -------------------------------------------------------------------------------- /src/pydna/assembly2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/assembly2.py -------------------------------------------------------------------------------- /src/pydna/codon.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/codon.py -------------------------------------------------------------------------------- /src/pydna/common_sub_strings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/common_sub_strings.py -------------------------------------------------------------------------------- /src/pydna/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/conftest.py -------------------------------------------------------------------------------- /src/pydna/contig.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/contig.py -------------------------------------------------------------------------------- /src/pydna/cre_lox.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/cre_lox.py -------------------------------------------------------------------------------- /src/pydna/crispr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/crispr.py -------------------------------------------------------------------------------- /src/pydna/design.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/design.py -------------------------------------------------------------------------------- /src/pydna/download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/download.py -------------------------------------------------------------------------------- /src/pydna/dseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/dseq.py -------------------------------------------------------------------------------- /src/pydna/dseqrecord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/dseqrecord.py -------------------------------------------------------------------------------- /src/pydna/fakeseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/fakeseq.py -------------------------------------------------------------------------------- /src/pydna/fusionpcr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/fusionpcr.py -------------------------------------------------------------------------------- /src/pydna/gateway.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/gateway.py -------------------------------------------------------------------------------- /src/pydna/gel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/gel.py -------------------------------------------------------------------------------- /src/pydna/genbank.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/genbank.py -------------------------------------------------------------------------------- /src/pydna/genbankfile.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/genbankfile.py -------------------------------------------------------------------------------- /src/pydna/genbankfixer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/genbankfixer.py -------------------------------------------------------------------------------- /src/pydna/genbankrecord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/genbankrecord.py -------------------------------------------------------------------------------- /src/pydna/goldengate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/goldengate.py -------------------------------------------------------------------------------- /src/pydna/ladders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/ladders.py -------------------------------------------------------------------------------- /src/pydna/ligate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/ligate.py -------------------------------------------------------------------------------- /src/pydna/opencloning_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/opencloning_models.py -------------------------------------------------------------------------------- /src/pydna/parsers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/parsers.py -------------------------------------------------------------------------------- /src/pydna/primer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/primer.py -------------------------------------------------------------------------------- /src/pydna/readers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/readers.py -------------------------------------------------------------------------------- /src/pydna/seq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/seq.py -------------------------------------------------------------------------------- /src/pydna/seqrecord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/seqrecord.py -------------------------------------------------------------------------------- /src/pydna/sequence_picker.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/sequence_picker.py -------------------------------------------------------------------------------- /src/pydna/sequence_regex.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/sequence_regex.py -------------------------------------------------------------------------------- /src/pydna/threading_timer_decorator_exit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/threading_timer_decorator_exit.py -------------------------------------------------------------------------------- /src/pydna/tm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/tm.py -------------------------------------------------------------------------------- /src/pydna/types.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/types.py -------------------------------------------------------------------------------- /src/pydna/user_cloning.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/user_cloning.py -------------------------------------------------------------------------------- /src/pydna/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/src/pydna/utils.py -------------------------------------------------------------------------------- /tests/.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/.coveragerc -------------------------------------------------------------------------------- /tests/02-G1_B01_013.ab1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/02-G1_B01_013.ab1 -------------------------------------------------------------------------------- /tests/1362_6.ape: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/1362_6.ape -------------------------------------------------------------------------------- /tests/15405_2.ape: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/15405_2.ape -------------------------------------------------------------------------------- /tests/28-1rev_D04_026.ab1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/28-1rev_D04_026.ab1 -------------------------------------------------------------------------------- /tests/32-3rev_H04_018.ab1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/32-3rev_H04_018.ab1 -------------------------------------------------------------------------------- /tests/36-5rev_D05_041.ab1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/36-5rev_D05_041.ab1 -------------------------------------------------------------------------------- /tests/8054_2.ape: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/8054_2.ape -------------------------------------------------------------------------------- /tests/AAA_OLD.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/AAA_OLD.gb -------------------------------------------------------------------------------- /tests/ABI01.abi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/ABI01.abi -------------------------------------------------------------------------------- /tests/AJ515744.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/AJ515744.gb -------------------------------------------------------------------------------- /tests/AJ515746.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/AJ515746.gb -------------------------------------------------------------------------------- /tests/AJ580803.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/AJ580803.gb -------------------------------------------------------------------------------- /tests/AJ580804.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/AJ580804.gb -------------------------------------------------------------------------------- /tests/AM086621.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/AM086621.gb -------------------------------------------------------------------------------- /tests/AX023560.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/AX023560.gb -------------------------------------------------------------------------------- /tests/E05006.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/E05006.gb -------------------------------------------------------------------------------- /tests/G.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/GIN11M86.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/GIN11M86.gb -------------------------------------------------------------------------------- /tests/GUP1_locus.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/GUP1_locus.gb -------------------------------------------------------------------------------- /tests/GUP1rec1sens.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/GUP1rec1sens.txt -------------------------------------------------------------------------------- /tests/GUP1rec2AS.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/GUP1rec2AS.txt -------------------------------------------------------------------------------- /tests/Ggatcc (copy).gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/Ggatcc (copy).gb -------------------------------------------------------------------------------- /tests/Ggatcc.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/Ggatcc.gb -------------------------------------------------------------------------------- /tests/KlLEU2tt.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/KlLEU2tt.fas -------------------------------------------------------------------------------- /tests/KlLEU2tt.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/KlLEU2tt.gb -------------------------------------------------------------------------------- /tests/New_DNA.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/New_DNA.gb -------------------------------------------------------------------------------- /tests/New_DNA__________________.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/New_DNA__________________.gb -------------------------------------------------------------------------------- /tests/RefDataBjorn.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/RefDataBjorn.fas -------------------------------------------------------------------------------- /tests/SYNPUC19CV.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/SYNPUC19CV.gb -------------------------------------------------------------------------------- /tests/X06035.ape: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/X06035.ape -------------------------------------------------------------------------------- /tests/X60065-100-110.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/X60065-100-110.gb -------------------------------------------------------------------------------- /tests/X60065.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/X60065.gb -------------------------------------------------------------------------------- /tests/XKS1_orf.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/XKS1_orf.txt -------------------------------------------------------------------------------- /tests/YEp24PGK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/YEp24PGK.txt -------------------------------------------------------------------------------- /tests/YEp24PGK_.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/YEp24PGK_.txt -------------------------------------------------------------------------------- /tests/YEp24PGK_XK_manually_assembled.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/YEp24PGK_XK_manually_assembled.txt -------------------------------------------------------------------------------- /tests/YLACC1_locus.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/YLACC1_locus.gb -------------------------------------------------------------------------------- /tests/_.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/_.gb -------------------------------------------------------------------------------- /tests/__getenv.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/__getenv.txt -------------------------------------------------------------------------------- /tests/_test_module_genbank2.py_: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/_test_module_genbank2.py_ -------------------------------------------------------------------------------- /tests/all_cre_lox.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/all_cre_lox.gb -------------------------------------------------------------------------------- /tests/broken_genbank_files/ApE_example.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/ApE_example.gb -------------------------------------------------------------------------------- /tests/broken_genbank_files/Author sequence.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/Author sequence.gb -------------------------------------------------------------------------------- /tests/broken_genbank_files/NCBI_example.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/NCBI_example.gb -------------------------------------------------------------------------------- /tests/broken_genbank_files/P30350%20(2013-10-11%2013_49_14).dna.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/P30350%20(2013-10-11%2013_49_14).dna.txt -------------------------------------------------------------------------------- /tests/broken_genbank_files/VectorNTI_example.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/VectorNTI_example.gb -------------------------------------------------------------------------------- /tests/broken_genbank_files/YEplac181.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/YEplac181.txt -------------------------------------------------------------------------------- /tests/broken_genbank_files/fakeGenBankFile.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/fakeGenBankFile.gb -------------------------------------------------------------------------------- /tests/broken_genbank_files/hej.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/hej.txt -------------------------------------------------------------------------------- /tests/broken_genbank_files/pGADT7-Rec.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/pGADT7-Rec.gb -------------------------------------------------------------------------------- /tests/broken_genbank_files/pGreenLantern1.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/pGreenLantern1.gb -------------------------------------------------------------------------------- /tests/broken_genbank_files/sequence.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/broken_genbank_files/sequence.gb -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/dna2943.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/dna2943.gb -------------------------------------------------------------------------------- /tests/dna2943_mod.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/dna2943_mod.gb -------------------------------------------------------------------------------- /tests/example.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/example.ipynb -------------------------------------------------------------------------------- /tests/figures.odt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/figures.odt -------------------------------------------------------------------------------- /tests/foo: -------------------------------------------------------------------------------- 1 | some stuff 2 | -------------------------------------------------------------------------------- /tests/format_sequences.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/format_sequences.ipynb -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/entry-attP1_1-attP2_1.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/entry-attP1_1-attP2_1.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/entry-attP1_2-attP2_2.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/entry-attP1_2-attP2_2.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/entry-attP2_1-attP1_3.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/entry-attP2_1-attP1_3.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/entry-attP2_3-attP3_2.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/entry-attP2_3-attP3_2.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/entry-attP3_1-attP2_1.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/entry-attP3_1-attP2_1.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/entry-attP4_2-attP1_4.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/entry-attP4_2-attP1_4.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/example_valerie/483_P4-P1r_EC1.2EC1.1p.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/example_valerie/483_P4-P1r_EC1.2EC1.1p.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/example_valerie/484_pDONR221_(Cas9_NLS_rbcS_E9t_U6_29p.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/example_valerie/484_pDONR221_(Cas9_NLS_rbcS_E9t_U6_29p.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/example_valerie/P2RP3 test SYC.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/example_valerie/P2RP3 test SYC.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/example_valerie/addgene-plasmid-133748-sequence-271264.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/example_valerie/addgene-plasmid-133748-sequence-271264.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/example_valerie/output.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/example_valerie/output.gb -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/example_valerie/output2.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/example_valerie/output2.gb -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/expression-attP1_1-attP2_1.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/expression-attP1_1-attP2_1.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/expression-attP1_2-attP2_2.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/expression-attP1_2-attP2_2.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/expression-attP2_1-attP1_3.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/expression-attP2_1-attP1_3.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pBAD-DEST49.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pBAD-DEST49.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pDONRtm201.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pDONRtm201.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pDONRtm221 P3-P2.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pDONRtm221 P3-P2.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pDONRtm221.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pDONRtm221.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pDONRtmP2r-P3.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pDONRtmP2r-P3.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pDONRtmP4-P1r.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pDONRtmP4-P1r.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pDONRtm_Zeo.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pDONRtm_Zeo.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pET-53-DESTtm.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pET-53-DESTtm.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pairing.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pairing.tsv -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pcDNAtm-DEST53.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pcDNAtm-DEST53.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pcr_product-attP1_1-attP2_1.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pcr_product-attP1_1-attP2_1.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pcr_product-attP1_2-attP2_2.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pcr_product-attP1_2-attP2_2.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pcr_product-attP2_1-attP1_3.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pcr_product-attP2_1-attP1_3.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pcr_product-attP2_3-attP3_2.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pcr_product-attP2_3-attP3_2.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pcr_product-attP3_1-attP2_1.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pcr_product-attP3_1-attP2_1.dna -------------------------------------------------------------------------------- /tests/gateway_manual_cloning/pcr_product-attP4_2-attP1_4.dna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/gateway_manual_cloning/pcr_product-attP4_2-attP1_4.dna -------------------------------------------------------------------------------- /tests/jupyter_test_repr (copy).ipynb________: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/jupyter_test_repr (copy).ipynb________ -------------------------------------------------------------------------------- /tests/jupyter_test_repr.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/jupyter_test_repr.ipynb -------------------------------------------------------------------------------- /tests/lambda.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/lambda.gb -------------------------------------------------------------------------------- /tests/my_test_enzymes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/my_test_enzymes.txt -------------------------------------------------------------------------------- /tests/myseq.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/myseq.gb -------------------------------------------------------------------------------- /tests/nucleotide1.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/nucleotide1.xml -------------------------------------------------------------------------------- /tests/output.file: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/output.file -------------------------------------------------------------------------------- /tests/pAG25.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pAG25.gb -------------------------------------------------------------------------------- /tests/pAG32.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pAG32.gb -------------------------------------------------------------------------------- /tests/pCAPs-AjiI.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pCAPs-AjiI.gb -------------------------------------------------------------------------------- /tests/pCAPs-pSU0.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pCAPs-pSU0.gb -------------------------------------------------------------------------------- /tests/pCAPs.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pCAPs.gb -------------------------------------------------------------------------------- /tests/pCAPs_fasta (copy).txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pCAPs_fasta (copy).txt -------------------------------------------------------------------------------- /tests/pCAPs_fasta.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pCAPs_fasta.txt -------------------------------------------------------------------------------- /tests/pCAPs_lowgc.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pCAPs_lowgc.gb -------------------------------------------------------------------------------- /tests/pCR_MCT1_HA46.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pCR_MCT1_HA46.gb -------------------------------------------------------------------------------- /tests/pGREG505.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pGREG505.gb -------------------------------------------------------------------------------- /tests/pGSHU 7180bp.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pGSHU 7180bp.gb -------------------------------------------------------------------------------- /tests/pGSKU 6961bp.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pGSKU 6961bp.gb -------------------------------------------------------------------------------- /tests/pGUP1_correct.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pGUP1_correct.gb -------------------------------------------------------------------------------- /tests/pGUP1_not_synced.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pGUP1_not_synced.gb -------------------------------------------------------------------------------- /tests/pKT127______.ape: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pKT127______.ape -------------------------------------------------------------------------------- /tests/pMEC1135.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pMEC1135.gb -------------------------------------------------------------------------------- /tests/pMX4blaster2_old.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pMX4blaster2_old.gb -------------------------------------------------------------------------------- /tests/pUC19-BamHI-a-rc.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19-BamHI-a-rc.gb -------------------------------------------------------------------------------- /tests/pUC19-BamHI-a.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19-BamHI-a.gb -------------------------------------------------------------------------------- /tests/pUC19-EcoRI_PstI-d-rc.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19-EcoRI_PstI-d-rc.gb -------------------------------------------------------------------------------- /tests/pUC19-SmaI-a.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19-SmaI-a.gb -------------------------------------------------------------------------------- /tests/pUC19.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19.gb -------------------------------------------------------------------------------- /tests/pUC19_M77789.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19_M77789.gb -------------------------------------------------------------------------------- /tests/pUC19_MarkBudde.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19_MarkBudde.gb -------------------------------------------------------------------------------- /tests/pUC19_fasta.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19_fasta.txt -------------------------------------------------------------------------------- /tests/pUC19_small_gene.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC19_small_gene.gb -------------------------------------------------------------------------------- /tests/pUC_LAC4.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC_LAC4.gb -------------------------------------------------------------------------------- /tests/pUC_LAC4_correct_rotation.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pUC_LAC4_correct_rotation.gb -------------------------------------------------------------------------------- /tests/pYPK0_TDH3_GAL2_PGI1.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pYPK0_TDH3_GAL2_PGI1.gb -------------------------------------------------------------------------------- /tests/pYPK7_TDH3_GAL2_PGI1.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pYPK7_TDH3_GAL2_PGI1.gb -------------------------------------------------------------------------------- /tests/pYPKa.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pYPKa.gb -------------------------------------------------------------------------------- /tests/pYPKp7.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pYPKp7.gb -------------------------------------------------------------------------------- /tests/primer1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/primer1.txt -------------------------------------------------------------------------------- /tests/primer3.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/primer3.txt -------------------------------------------------------------------------------- /tests/primers.fas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/primers.fas -------------------------------------------------------------------------------- /tests/primers_linux_line_endings.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/primers_linux_line_endings.txt -------------------------------------------------------------------------------- /tests/primers_linux_line_endings_not_unique.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/primers_linux_line_endings_not_unique.txt -------------------------------------------------------------------------------- /tests/profile.pstat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/profile.pstat -------------------------------------------------------------------------------- /tests/pth1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pth1.txt -------------------------------------------------------------------------------- /tests/pth2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pth2.txt -------------------------------------------------------------------------------- /tests/pthx.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pthx.txt -------------------------------------------------------------------------------- /tests/pydna_gel.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pydna_gel.png -------------------------------------------------------------------------------- /tests/pydna_gel2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pydna_gel2.png -------------------------------------------------------------------------------- /tests/pydna_read_test.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pydna_read_test.txt -------------------------------------------------------------------------------- /tests/pydna_read_test2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pydna_read_test2.txt -------------------------------------------------------------------------------- /tests/pydna_read_test3.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/pydna_read_test3.txt -------------------------------------------------------------------------------- /tests/read1.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/read1.gb -------------------------------------------------------------------------------- /tests/read2.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/read2.gb -------------------------------------------------------------------------------- /tests/read3.fasta: -------------------------------------------------------------------------------- 1 | >hej 2 | acgt 3 | -------------------------------------------------------------------------------- /tests/read4.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/read4.fasta -------------------------------------------------------------------------------- /tests/run_pytest_with_coverage.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/run_pytest_with_coverage.sh -------------------------------------------------------------------------------- /tests/save_changed_seq.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/save_changed_seq.ipynb -------------------------------------------------------------------------------- /tests/sequence.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/sequence.gb -------------------------------------------------------------------------------- /tests/subfolder/sequence.gb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/subfolder/sequence.gb -------------------------------------------------------------------------------- /tests/test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test -------------------------------------------------------------------------------- /tests/test_USERcloning.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_USERcloning.py -------------------------------------------------------------------------------- /tests/test_extra_cut_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_extra_cut_features.py -------------------------------------------------------------------------------- /tests/test_extra_markbudde.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_extra_markbudde.py -------------------------------------------------------------------------------- /tests/test_extra_santirdnd_bug_spanning_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_extra_santirdnd_bug_spanning_features.py -------------------------------------------------------------------------------- /tests/test_longerlocus_name_gives_dseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_longerlocus_name_gives_dseq.py -------------------------------------------------------------------------------- /tests/test_module___init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module___init__.py -------------------------------------------------------------------------------- /tests/test_module__pretty.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module__pretty.py -------------------------------------------------------------------------------- /tests/test_module__thermodynamic_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module__thermodynamic_data.py -------------------------------------------------------------------------------- /tests/test_module_all.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_all.py -------------------------------------------------------------------------------- /tests/test_module_amplicon.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_amplicon.py -------------------------------------------------------------------------------- /tests/test_module_amplify.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_amplify.py -------------------------------------------------------------------------------- /tests/test_module_assembly.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_assembly.py -------------------------------------------------------------------------------- /tests/test_module_assembly2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_assembly2.py -------------------------------------------------------------------------------- /tests/test_module_common_sub_strings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_common_sub_strings.py -------------------------------------------------------------------------------- /tests/test_module_contig.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_contig.py -------------------------------------------------------------------------------- /tests/test_module_cre_lox.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_cre_lox.py -------------------------------------------------------------------------------- /tests/test_module_crispr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_crispr.py -------------------------------------------------------------------------------- /tests/test_module_design.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_design.py -------------------------------------------------------------------------------- /tests/test_module_download.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_download.py -------------------------------------------------------------------------------- /tests/test_module_dseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_dseq.py -------------------------------------------------------------------------------- /tests/test_module_dseqrecord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_dseqrecord.py -------------------------------------------------------------------------------- /tests/test_module_fakeseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_fakeseq.py -------------------------------------------------------------------------------- /tests/test_module_fusionpcr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_fusionpcr.py -------------------------------------------------------------------------------- /tests/test_module_gateway.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_gateway.py -------------------------------------------------------------------------------- /tests/test_module_gel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_gel.py -------------------------------------------------------------------------------- /tests/test_module_genbank.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_genbank.py -------------------------------------------------------------------------------- /tests/test_module_genbankfile.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_genbankfile.py -------------------------------------------------------------------------------- /tests/test_module_genbankfixer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_genbankfixer.py -------------------------------------------------------------------------------- /tests/test_module_genbankrecord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_genbankrecord.py -------------------------------------------------------------------------------- /tests/test_module_ligate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_ligate.py -------------------------------------------------------------------------------- /tests/test_module_opencloning_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_opencloning_models.py -------------------------------------------------------------------------------- /tests/test_module_parsers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_parsers.py -------------------------------------------------------------------------------- /tests/test_module_primer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_primer.py -------------------------------------------------------------------------------- /tests/test_module_readers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_readers.py -------------------------------------------------------------------------------- /tests/test_module_seq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_seq.py -------------------------------------------------------------------------------- /tests/test_module_seqrecord.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_seqrecord.py -------------------------------------------------------------------------------- /tests/test_module_tm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_tm.py -------------------------------------------------------------------------------- /tests/test_module_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pydna-group/pydna/HEAD/tests/test_module_utils.py --------------------------------------------------------------------------------