├── .bumpversion.cfg ├── .flake8 ├── .gitignore ├── .pylintrc ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── data ├── cloning │ ├── pdsred2.gb │ ├── pdusk-dsred2.gb │ └── pdusk.gb ├── features │ ├── dna.db │ ├── dna.id.pickle │ ├── dna.kmermap.pickle │ ├── protein.db │ ├── protein.id.pickle │ └── protein.kmermap.pickle ├── gibson │ ├── BBa_K1085023.fa │ ├── BBa_K1649003.fa │ ├── pDusk.fa │ └── pdsred2.fa └── goldengate │ ├── B0015_DE.gb │ ├── B0015_DE_utr.gb │ ├── B0015_DF.gb │ ├── B0015_DG.gb │ ├── B0015_DH.gb │ ├── B0032m_BC.gb │ ├── B0033m_BC.gb │ ├── B0034m_BC.gb │ ├── BCD12_BC.gb │ ├── BCD2_BC.gb │ ├── BCD8_BC.gb │ ├── C0012m_CD.gb │ ├── C0040_CD.gb │ ├── C0062_CD.gb │ ├── C0080_CD.gb │ ├── DVA.gb │ ├── DVA_AB.gb │ ├── DVA_AE.gb │ ├── DVA_AF.gb │ ├── DVA_AG.gb │ ├── DVA_AH.gb │ ├── DVA_BC.gb │ ├── DVA_CD.gb │ ├── DVA_DE.gb │ ├── DVA_DF.gb │ ├── DVA_DG.gb │ ├── DVA_DH.gb │ ├── DVA_EB.gb │ ├── DVA_EF.gb │ ├── DVA_EG.gb │ ├── DVA_EH.gb │ ├── DVA_FB.gb │ ├── DVA_GB.gb │ ├── DVK.gb │ ├── DVK_AE.gb │ ├── DVK_AF.gb │ ├── DVK_EF.gb │ ├── DVK_FG.gb │ ├── DVK_GH.gb │ ├── E0030_CD.gb │ ├── E0040m_CD.gb │ ├── E1010m_CD.gb │ ├── I13453_AB.gb │ ├── I13453_EB.gb │ ├── I13453_FB.gb │ ├── I13453_GB.gb │ ├── J23100_AB.gb │ ├── J23100_EB.gb │ ├── J23100_FB.gb │ ├── J23100_GB.gb │ ├── J23102_AB.gb │ ├── J23102_EB.gb │ ├── J23102_FB.gb │ ├── J23102_GB.gb │ ├── J23103_AB.gb │ ├── J23103_EB.gb │ ├── J23103_FB.gb │ ├── J23103_GB.gb │ ├── J23106_AB.gb │ ├── J23106_EB.gb │ ├── J23106_FB.gb │ ├── J23106_GB.gb │ ├── J23107_AB.gb │ ├── J23107_EB.gb │ ├── J23107_FB.gb │ ├── J23107_GB.gb │ ├── J23116_AB.gb │ ├── J23116_EB.gb │ ├── J23116_FB.gb │ ├── J23116_GB.gb │ ├── R0010_AB.gb │ ├── R0010_EB.gb │ ├── R0010_FB.gb │ ├── R0010_GB.gb │ ├── R0040_AB.gb │ ├── R0040_EB.gb │ ├── R0040_FB.gb │ ├── R0040_GB.gb │ ├── R0063_AB.gb │ ├── R0063_EB.gb │ ├── R0063_FB.gb │ ├── R0063_GB.gb │ ├── cre_CD.gb │ ├── eBFP2_CD.gb │ ├── lincoln │ ├── ar_pNBU2_erm_bla_2508-4651_new.fa │ ├── brep_pIP417_1965-3636_new.fa │ ├── brep_pNBU2_612-2507_new.fa │ ├── erep_pBAM1_R6K_ori_4-392_new.fa │ ├── orit_Tn4399_new.fa │ ├── orit_pBUN24_2656-5039_new.fa │ ├── reporter_pBf_glow_new.fa │ └── reporter_pBtTetO_glow_TetR_new.fa │ ├── pJ02B2GmRm_AF.gb │ ├── pJ02B2Gm_AE(A).gb │ ├── pJ02B2Gm_AE.gb │ ├── pJ02B2Gm_EF(A).gb │ ├── pJ02B2Gm_EF.gb │ ├── pJ02B2RmGm_AF.gb │ ├── pJ02B2Rm_AE(A).gb │ ├── pJ02B2Rm_AE.gb │ ├── pJ02B2Rm_EF(A).gb │ └── pJ02B2Rm_EF.gb ├── docs ├── .nojekyll ├── Makefile ├── annotate.py ├── clone_assembly.py ├── conf.py ├── doctrees │ ├── environment.pickle │ ├── example.doctree │ ├── examples.doctree │ ├── index.doctree │ └── ref │ │ ├── designs.doctree │ │ ├── protocols.doctree │ │ ├── ref.doctree │ │ └── steps.doctree ├── examples.rst ├── gibson_assembly.py ├── gibson_library.py ├── gibson_plasmid.py ├── goldengate_combinatorial.py ├── goldengate_combinatorial_bins.py ├── goldengate_plasmid.py ├── html │ ├── .buildinfo │ ├── .nojekyll │ ├── _sources │ │ ├── examples.rst.txt │ │ ├── index.rst.txt │ │ └── ref │ │ │ ├── designs.rst.txt │ │ │ ├── protocols.rst.txt │ │ │ ├── ref.rst.txt │ │ │ └── steps.rst.txt │ ├── _static │ │ ├── basic.css │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Inconsolata.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ │ ├── jquery-3.2.1.js │ │ ├── jquery-3.4.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ ├── examples.html │ ├── genindex.html │ ├── index.html │ ├── objects.inv │ ├── py-modindex.html │ ├── ref │ │ ├── designs.html │ │ ├── protocols.html │ │ ├── ref.html │ │ └── steps.html │ ├── search.html │ └── searchindex.js ├── index.html ├── index.rst ├── make.bat └── ref │ ├── designs.rst │ ├── protocols.rst │ ├── ref.rst │ └── steps.rst ├── examples ├── README.md ├── annotate.py ├── clone_assembly.py ├── gibson_assembly.py ├── gibson_library.py ├── gibson_plasmid.py ├── goldengate_combinatorial.py ├── goldengate_combinatorial_bins.py └── goldengate_plasmid.py ├── requirements.txt ├── setup.py ├── synbio ├── __init__.py ├── assembly │ ├── __init__.py │ ├── clone.py │ └── gibson.py ├── containers.py ├── designs.py ├── features │ ├── __init__.py │ ├── annotate.py │ ├── cluster.py │ ├── config.py │ ├── seed.py │ └── snapgene.py ├── instructions.py ├── mix.py ├── picklists │ ├── __init__.py │ ├── hamilton.py │ ├── labcyte.py │ ├── opentrons.py │ └── tecan.py ├── primers.py ├── protocol.py ├── protocols │ ├── __init__.py │ ├── clone.py │ ├── gibson.py │ └── goldengate.py ├── reagents.py ├── species.py └── steps.py └── tests ├── __init__.py ├── assembly ├── __init__.py ├── clone_test.py ├── gibson_test.py ├── seq_records.fasta └── strict_test.py ├── containers_test.py ├── designs_test.py ├── features ├── __init__.py ├── annotate_test.py └── cluster_test.py ├── instructions_test.py ├── mix_test.py ├── picklists ├── __init__.py ├── labcyte_test.py └── tecan_test.py ├── primers_test.py ├── protocol_test.py ├── protocols ├── __init__.py ├── clone_test.py ├── gibson_test.py └── goldengate_test.py ├── reagents_test.py ├── species_test.py └── steps_test.py /.bumpversion.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Lattice-Automation/synbio/HEAD/.bumpversion.cfg -------------------------------------------------------------------------------- /.flake8: -------------------------------------------------------------------------------- 1 | [flake8] 2 | min-public-methods=0 3 | max-line-length=88 4 | ignore=E252 5 | 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