diff --git a/glyphs/goldenPICS.key b/glyphs/goldenPICS.key new file mode 100644 index 0000000..3f06667 Binary files /dev/null and b/glyphs/goldenPICS.key differ diff --git a/index.html b/index.html index 882ab38..3313ecb 100644 --- a/index.html +++ b/index.html @@ -19,7 +19,7 @@

📋 How to Use This Form 📋

  1. 📑 Prepare the files following + href="https://github.com/OpenCloning/OpenCloning-submission/blob/master/docs/index.md"> these instructions.
  2. 📂 Submit the .xlsx spreadsheet file and all the images using the form.
    3. diff --git a/poetry.lock b/poetry.lock index adb8ea1..5501703 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.0.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. [[package]] name = "annotated-types" @@ -7,7 +7,6 @@ description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, @@ -20,7 +19,6 @@ description = "High level compatibility layer for multiple asynchronous event lo optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "anyio-4.9.0-py3-none-any.whl", hash = "sha256:9f76d541cad6e36af7beb62e978876f3b41e3e04f2c1fbf0884604c0a9c4d93c"}, {file = "anyio-4.9.0.tar.gz", hash = "sha256:673c0c244e15788651a4ff38710fea9675823028a6f08a5eda409e0c9840a028"}, @@ -33,7 +31,7 @@ typing_extensions = {version = ">=4.5", markers = "python_version < \"3.13\""} [package.extras] doc = ["Sphinx (>=8.2,<9.0)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx_rtd_theme"] -test = ["anyio[trio]", "blockbuster (>=1.5.23)", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1)", "uvloop (>=0.21)"] +test = ["anyio[trio]", "blockbuster (>=1.5.23)", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "trustme", "truststore (>=0.9.1) ; python_version >= \"3.10\"", "uvloop (>=0.21) ; platform_python_implementation == \"CPython\" and platform_system != \"Windows\" and python_version < \"3.14\""] trio = ["trio (>=0.26.1)"] [[package]] @@ -43,12 +41,34 @@ description = "A small Python module for determining appropriate platform-specif optional = false python-versions = "*" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, ] +[[package]] +name = "beautifulsoup4" +version = "4.13.4" +description = "Screen-scraping library" +optional = false +python-versions = ">=3.7.0" +groups = ["main"] +files = [ + {file = "beautifulsoup4-4.13.4-py3-none-any.whl", hash = "sha256:9bbbb14bfde9d79f38b8cd5f8c7c85f4b8f2523190ebed90e950a8dea4cb1c4b"}, + {file = "beautifulsoup4-4.13.4.tar.gz", hash = "sha256:dbb3c4e1ceae6aefebdaf2423247260cd062430a410e38c66f2baa50a8437195"}, +] + +[package.dependencies] +soupsieve = ">1.2" +typing-extensions = ">=4.0.0" + +[package.extras] +cchardet = ["cchardet"] +chardet = ["chardet"] +charset-normalizer = ["charset-normalizer"] +html5lib = ["html5lib"] +lxml = ["lxml"] + [[package]] name = "biopython" version = "1.85" @@ -56,7 +76,6 @@ description = "Freely available tools for computational molecular biology." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "biopython-1.85-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:a6308053a61f3bdbb11504ece4cf24e264c6f1d6fad278f7e59e6b84b0d9a7b4"}, {file = "biopython-1.85-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:434dd23e972b0c89e128f2ebbd16b38075d609184f4f1fd16368035f923019c2"}, @@ -102,7 +121,6 @@ description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "certifi-2025.6.15-py3-none-any.whl", hash = "sha256:2e0c7ce7cb5d8f8634ca55d2ba7e6ec2689a2fd6537d8dec1296a477a4910057"}, {file = "certifi-2025.6.15.tar.gz", hash = "sha256:d747aa5a8b9bbbb1bb8c22bb13e22bd1f18e9796defa16bab421f7f7a317323b"}, @@ -115,7 +133,6 @@ description = "Foreign Function Interface for Python calling C code." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "cffi-1.17.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:df8b1c11f177bc2313ec4b2d46baec87a5f3e71fc8b45dab2ee7cae86d9aba14"}, {file = "cffi-1.17.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8f2cdc858323644ab277e9bb925ad72ae0e67f69e804f4898c070998d50b1a67"}, @@ -196,7 +213,6 @@ description = "The Real First Universal Charset Detector. Open, modern and activ optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "charset_normalizer-3.4.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7c48ed483eb946e6c04ccbe02c6b4d1d48e51944b6db70f697e089c193404941"}, {file = "charset_normalizer-3.4.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b2d318c11350e10662026ad0eb71bb51c7812fc8590825304ae0bdd4ac283acd"}, @@ -299,7 +315,6 @@ description = "Composable command line interface toolkit" optional = false python-versions = ">=3.10" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "click-8.2.1-py3-none-any.whl", hash = "sha256:61a3265b914e850b85317d0b3109c7f8cd35a670f963866005d6ef1d5175a12b"}, {file = "click-8.2.1.tar.gz", hash = "sha256:27c491cc05d968d271d5a1db13e3b5a184636d9d930f148c50b038f0d0646202"}, @@ -319,7 +334,7 @@ files = [ {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"}, {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"}, ] -markers = {main = "(platform_system == \"Windows\" or sys_platform == \"win32\") and (python_version == \"3.11\" or python_version >= \"3.12\")", test = "(python_version == \"3.11\" or python_version >= \"3.12\") and sys_platform == \"win32\""} +markers = {main = "platform_system == \"Windows\" or sys_platform == \"win32\"", test = "sys_platform == \"win32\""} [[package]] name = "cryptography" @@ -328,7 +343,6 @@ description = "cryptography is a package which provides cryptographic recipes an optional = false python-versions = "!=3.9.0,!=3.9.1,>=3.7" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "cryptography-45.0.4-cp311-abi3-macosx_10_9_universal2.whl", hash = "sha256:425a9a6ac2823ee6e46a76a21a4e8342d8fa5c01e08b823c1f19a8b74f096069"}, {file = "cryptography-45.0.4-cp311-abi3-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:680806cf63baa0039b920f4976f5f31b10e772de42f16310a6839d9f21a26b0d"}, @@ -373,10 +387,10 @@ files = [ cffi = {version = ">=1.14", markers = "platform_python_implementation != \"PyPy\""} [package.extras] -docs = ["sphinx (>=5.3.0)", "sphinx-inline-tabs", "sphinx-rtd-theme (>=3.0.0)"] +docs = ["sphinx (>=5.3.0)", "sphinx-inline-tabs ; python_full_version >= \"3.8.0\"", "sphinx-rtd-theme (>=3.0.0) ; python_full_version >= \"3.8.0\""] docstest = ["pyenchant (>=3)", "readme-renderer (>=30.0)", "sphinxcontrib-spelling (>=7.3.1)"] -nox = ["nox (>=2024.4.15)", "nox[uv] (>=2024.3.2)"] -pep8test = ["check-sdist", "click (>=8.0.1)", "mypy (>=1.4)", "ruff (>=0.3.6)"] +nox = ["nox (>=2024.4.15)", "nox[uv] (>=2024.3.2) ; python_full_version >= \"3.8.0\""] +pep8test = ["check-sdist ; python_full_version >= \"3.8.0\"", "click (>=8.0.1)", "mypy (>=1.4)", "ruff (>=0.3.6)"] sdist = ["build (>=1.0.0)"] ssh = ["bcrypt (>=3.1.5)"] test = ["certifi (>=2024)", "cryptography-vectors (==45.0.4)", "pretend (>=0.7)", "pytest (>=7.4.0)", "pytest-benchmark (>=4.0)", "pytest-cov (>=2.10.1)", "pytest-xdist (>=3.5.0)"] @@ -389,7 +403,6 @@ description = "Python @deprecated decorator to deprecate old python classes, fun optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "Deprecated-1.2.18-py2.py3-none-any.whl", hash = "sha256:bd5011788200372a32418f888e326a09ff80d0214bd961147cfed01b5c018eec"}, {file = "deprecated-1.2.18.tar.gz", hash = "sha256:422b6f6d859da6f2ef57857761bfb392480502a64c3028ca9bbe86085d72115d"}, @@ -399,7 +412,7 @@ files = [ wrapt = ">=1.10,<2" [package.extras] -dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools", "tox"] +dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "setuptools ; python_version >= \"3.12\"", "tox"] [[package]] name = "dnspython" @@ -408,7 +421,6 @@ description = "DNS toolkit" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "dnspython-2.7.0-py3-none-any.whl", hash = "sha256:b4c34b7d10b51bcc3a5071e7b8dee77939f1e878477eeecc965e9835f63c6c86"}, {file = "dnspython-2.7.0.tar.gz", hash = "sha256:ce9c432eda0dc91cf618a5cedf1a4e142651196bbcd2c80e89ed5a907e5cfaf1"}, @@ -430,7 +442,6 @@ description = "A robust email address syntax and deliverability validation libra optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "email_validator-2.2.0-py3-none-any.whl", hash = "sha256:561977c2d73ce3611850a06fa56b414621e0c8faa9d66f2611407d87465da631"}, {file = "email_validator-2.2.0.tar.gz", hash = "sha256:cb690f344c617a714f22e66ae771445a1ceb46821152df8e165c5f9a364582b7"}, @@ -447,7 +458,6 @@ description = "An implementation of lxml.xmlfile for the standard library" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "et_xmlfile-2.0.0-py3-none-any.whl", hash = "sha256:7a91720bc756843502c3b7504c77b8fe44217c85c537d85037f0f536151b2caa"}, {file = "et_xmlfile-2.0.0.tar.gz", hash = "sha256:dab3f4764309081ce75662649be815c4c9081e88f0837825f90fd28317d4da54"}, @@ -460,7 +470,6 @@ description = "FastAPI framework, high performance, easy to learn, fast to code, optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "fastapi-0.111.1-py3-none-any.whl", hash = "sha256:4f51cfa25d72f9fbc3280832e84b32494cf186f50158d364a8765aabf22587bf"}, {file = "fastapi-0.111.1.tar.gz", hash = "sha256:ddd1ac34cb1f76c2e2d7f8545a4bcb5463bce4834e81abf0b189e0c359ab2413"}, @@ -487,7 +496,6 @@ description = "Run and manage FastAPI apps from the command line with FastAPI CL optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "fastapi_cli-0.0.7-py3-none-any.whl", hash = "sha256:d549368ff584b2804336c61f192d86ddea080c11255f375959627911944804f4"}, {file = "fastapi_cli-0.0.7.tar.gz", hash = "sha256:02b3b65956f526412515907a0793c9094abd4bfb5457b389f645b0ea6ba3605e"}, @@ -508,7 +516,6 @@ description = "Lightweight in-process concurrent programming" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "greenlet-3.2.3-cp310-cp310-macosx_11_0_universal2.whl", hash = "sha256:1afd685acd5597349ee6d7a88a8bec83ce13c106ac78c196ee9dde7c04fe87be"}, {file = "greenlet-3.2.3-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:761917cac215c61e9dc7324b2606107b3b292a8349bdebb31503ab4de3f559ac"}, @@ -577,7 +584,6 @@ description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "h11-0.16.0-py3-none-any.whl", hash = "sha256:63cf8bbe7522de3bf65932fda1d9c2772064ffb3dae62d55932da54b31cb6c86"}, {file = "h11-0.16.0.tar.gz", hash = "sha256:4e35b956cf45792e4caa5885e69fba00bdbc6ffafbfa020300e549b208ee5ff1"}, @@ -590,7 +596,6 @@ description = "A minimal low-level HTTP client." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "httpcore-1.0.9-py3-none-any.whl", hash = "sha256:2d400746a40668fc9dec9810239072b40b4484b640a8c38fd654a024c7a1bf55"}, {file = "httpcore-1.0.9.tar.gz", hash = "sha256:6e34463af53fd2ab5d807f399a9b45ea31c3dfa2276f15a2c3f00afff6e176e8"}, @@ -613,7 +618,6 @@ description = "A collection of framework independent HTTP protocol utils." optional = false python-versions = ">=3.8.0" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "httptools-0.6.4-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3c73ce323711a6ffb0d247dcd5a550b8babf0f757e86a52558fe5b86d6fefcc0"}, {file = "httptools-0.6.4-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:345c288418f0944a6fe67be8e6afa9262b18c7626c3ef3c28adc5eabc06a68da"}, @@ -670,7 +674,6 @@ description = "The next generation HTTP client." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad"}, {file = "httpx-0.28.1.tar.gz", hash = "sha256:75e98c5f16b0f35b567856f597f06ff2270a374470a5c2392242528e3e3e42fc"}, @@ -683,7 +686,7 @@ httpcore = "==1.*" idna = "*" [package.extras] -brotli = ["brotli", "brotlicffi"] +brotli = ["brotli ; platform_python_implementation == \"CPython\"", "brotlicffi ; platform_python_implementation != \"CPython\""] cli = ["click (==8.*)", "pygments (==2.*)", "rich (>=10,<14)"] http2 = ["h2 (>=3,<5)"] socks = ["socksio (==1.*)"] @@ -696,7 +699,6 @@ description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.6" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"}, {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"}, @@ -712,7 +714,6 @@ description = "brain-dead simple config-ini parsing" optional = false python-versions = ">=3.8" groups = ["test"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"}, {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"}, @@ -725,7 +726,6 @@ description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"}, {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"}, @@ -744,7 +744,6 @@ description = "Python port of markdown-it. Markdown parsing, done right!" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"}, {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"}, @@ -770,7 +769,6 @@ description = "Safely add untrusted strings to HTML/XML markup." optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7e94c425039cde14257288fd61dcfb01963e658efbc0ff54f5306b06054700f8"}, {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9e2d922824181480953426608b81967de705c3cef4d1af983af849d7bd619158"}, @@ -842,7 +840,6 @@ description = "Markdown URL utilities" optional = false python-versions = ">=3.7" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"}, {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"}, @@ -855,7 +852,6 @@ description = "Python package for creating and manipulating graphs and networks" optional = false python-versions = ">=3.11" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "networkx-3.5-py3-none-any.whl", hash = "sha256:0030d386a9a06dee3565298b4a734b68589749a544acbb6c412dc9e2489ec6ec"}, {file = "networkx-3.5.tar.gz", hash = "sha256:d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037"}, @@ -877,7 +873,6 @@ description = "Fundamental package for array computing in Python" optional = false python-versions = ">=3.11" 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"uvloop-0.21.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ec7e6b09a6fdded42403182ab6b832b71f4edaf7f37a9a0e371a01db5f0cb45f"}, {file = "uvloop-0.21.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:196274f2adb9689a289ad7d65700d37df0c0930fd8e4e743fa4834e850d7719d"}, @@ -1919,7 +2069,6 @@ description = "Simple, modern and high performance file watching and code reload optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "watchfiles-1.1.0-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:27f30e14aa1c1e91cb653f03a63445739919aef84c8d2517997a83155e7a2fcc"}, {file = "watchfiles-1.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:3366f56c272232860ab45c77c3ca7b74ee819c8e1f6f35a7125556b198bbc6df"}, @@ -2039,7 +2188,6 @@ description = "Measures the displayed width of unicode strings in a terminal" optional = false python-versions = "*" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, @@ -2052,7 +2200,6 @@ description = "An implementation of the WebSocket Protocol (RFC 6455 & 7692)" optional = false python-versions = ">=3.9" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "websockets-15.0.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:d63efaa0cd96cf0c5fe4d581521d9fa87744540d4bc999ae6e08595a1014b45b"}, {file = "websockets-15.0.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ac60e3b188ec7574cb761b08d50fcedf9d77f1530352db4eef1707fe9dee7205"}, @@ -2132,7 +2279,6 @@ description = "A built-package format for Python" optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "wheel-0.45.1-py3-none-any.whl", hash = "sha256:708e7481cc80179af0e556bbf0cc00b8444c7321e2700b8d8580231d13017248"}, {file = "wheel-0.45.1.tar.gz", hash = "sha256:661e1abd9198507b1409a20c02106d9670b2576e916d58f520316666abca6729"}, @@ -2148,7 +2294,6 @@ description = "Module for decorators, wrappers and monkey patching." optional = false python-versions = ">=3.8" groups = ["main"] -markers = "python_version == \"3.11\" or python_version >= \"3.12\"" files = [ {file = "wrapt-1.17.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3d57c572081fed831ad2d26fd430d565b76aa277ed1d30ff4d40670b1c0dd984"}, {file = "wrapt-1.17.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b5e251054542ae57ac7f3fba5d10bfff615b6c2fb09abeb37d2f1463f841ae22"}, @@ -2234,4 +2379,4 @@ files = [ [metadata] lock-version = "2.1" python-versions = "^3.11" -content-hash = "5164ec8d159536980c5d92ec4ef842c7f0377b71a10be64f6c60551188ff8167" +content-hash = "35fe6eec19535ab62a7bbea1e7771d5775c3b5964e12a40d867b3a067ceb053f" diff --git a/processed/kits-gasser-goldenpics/submission.json b/processed/kits-gasser-goldenpics/submission.json new file mode 100644 index 0000000..fd0e827 --- /dev/null +++ b/processed/kits-gasser-goldenpics/submission.json @@ -0,0 +1,652 @@ +{ + "submitters": [ + { + "full_name": "Manuel Lera-Ramirez", + "orcid": "0000-0002-8666-9746", + "github_username": "manulera" + } + ], + "kit": { + "pmid": "PMID:29221460", + "addgene_url": "https://www.addgene.org/kits/gasser-goldenpics", + "title": "GoldenPiCS", + "description": "Flexible modular system for advanced strain engineering in P. pastoris / K. phaffii" + }, + "sequences": [ + { + "name": "BB1_12", + "category": "recipient BB1", + "description": "promoter cloning", + "type": "AddgenePlasmid", + "addgene_id": "98495", + "resistance": "Kanamycin", + "well": "A / 1" + }, + { + "name": "BB1_23", + "category": "recipient BB1", + "description": "cds cloning", + "type": "AddgenePlasmid", + "addgene_id": "98496", + "resistance": "Kanamycin", + "well": "A / 2" + }, + { + "name": "BB1_34", + "category": "recipient BB1", + "description": "terminator cloning", + "type": "AddgenePlasmid", + "addgene_id": "98497", + "resistance": "Kanamycin", + "well": "A / 3" + }, + { + "name": "BB1_12_pGAP", + "category": "promoter", + "description": "PGAP", + "type": "AddgenePlasmid", + "addgene_id": "98498", + "resistance": "Kanamycin", + "well": "A / 4" + }, + { + "name": "BB1_12_pGPM1", + "category": "promoter", + "description": "PGPM1", + "type": "AddgenePlasmid", + "addgene_id": "98499", + "resistance": "Kanamycin", + "well": "A / 5" + }, + { + "name": "BB1_12_pRPP1B", + "category": "promoter", + "description": "PRPP1B", + "type": "AddgenePlasmid", + "addgene_id": "98500", + "resistance": "Kanamycin", + "well": "A / 6" + }, + { + "name": "BB1_12_pPDC1", + "category": "promoter", + "description": "PPDC1", + "type": "AddgenePlasmid", + "addgene_id": "98501", + "resistance": "Kanamycin", + "well": "A / 7" + }, + { + "name": "BB1_12_pPOR1", + "category": "promoter", + "description": "PPOR1", + "type": "AddgenePlasmid", + "addgene_id": "98502", + "resistance": "Kanamycin", + "well": "A / 8" + }, + { + "name": "BB1_12_pMDH3", + "category": "promoter", + "description": "PMDH3", + "type": "AddgenePlasmid", + "addgene_id": "98503", + "resistance": "Kanamycin", + "well": "A / 9" + }, + { + "name": "BB1_12_pADH2", + "category": "promoter", + "description": "PADH2", + "type": "AddgenePlasmid", + "addgene_id": "98504", + "resistance": "Kanamycin", + "well": "A / 10" + }, + { + "name": "BB1_12_pFBA1-1", + "category": "promoter", + "description": "PFBA1-1", + "type": "AddgenePlasmid", + "addgene_id": "98505", + "resistance": "Kanamycin", + "well": "A / 11" + }, + { + "name": "BB1_12_pSHB17", + "category": "promoter", + "description": "PSHB17", + "type": "AddgenePlasmid", + "addgene_id": "98506", + "resistance": "Kanamycin", + "well": "A / 12" + }, + { + "name": "BB1_12_pTEF2", + "category": "promoter", + "description": "PTEF2", + "type": "AddgenePlasmid", + "addgene_id": "98507", + "resistance": "Kanamycin", + "well": "B / 1" + }, + { + "name": "BB1_12_pRPL2A", + "category": "promoter", + "description": "PRPL2A", + "type": "AddgenePlasmid", + "addgene_id": "98508", + "resistance": "Kanamycin", + "well": "B / 2" + }, + { + "name": "BB1_12_pLAT1", + "category": "promoter", + "description": "PLAT1", + "type": "AddgenePlasmid", + "addgene_id": "98509", + "resistance": "Kanamycin", + "well": "B / 3" + }, + { + "name": "BB1_12_pPFK300", + "category": "promoter", + "description": "PPpPfk", + "type": "AddgenePlasmid", + "addgene_id": "98510", + "resistance": "Kanamycin", + "well": "B / 4" + }, + { + "name": "BB1_12_pGUT1", + "category": "promoter", + "description": "PGUT1", + "type": "AddgenePlasmid", + "addgene_id": "98511", + "resistance": "Kanamycin", + "well": "B / 5" + }, + { + "name": "BB1_12_pTHI11", + "category": "promoter", + "description": "PTHI11", + "type": "AddgenePlasmid", + "addgene_id": "98512", + "resistance": "Kanamycin", + "well": "B / 6" + }, + { + "name": "BB1_12_pDAS2", + "category": "promoter", + "description": "PDAS2", + "type": "AddgenePlasmid", + "addgene_id": "98513", + "resistance": "Kanamycin", + "well": "B / 7" + }, + { + "name": "BB1_12_pAOX1", + "category": "promoter", + "description": "PAOX1", + "type": "AddgenePlasmid", + "addgene_id": "98514", + "resistance": "Kanamycin", + "well": "B / 8" + }, + { + "name": "BB1_12_pDAS1", + "category": "promoter", + "description": "PDAS1", + "type": "AddgenePlasmid", + "addgene_id": "98515", + "resistance": "Kanamycin", + "well": "B / 9" + }, + { + "name": "BB1_12_pFDH1", + "category": "promoter", + "description": "PFDH1", + "type": "AddgenePlasmid", + "addgene_id": "98516", + "resistance": "Kanamycin", + "well": "B / 10" + }, + { + "name": "BB1_23_eGFP", + "category": "coding sequence", + "description": "eGFP", + "type": "AddgenePlasmid", + "addgene_id": "98518", + "resistance": "Kanamycin", + "well": "B / 12" + }, + { + "name": "BB1_34_ScCYC1tt", + "category": "terminator", + "description": "ScCYC1tt", + "type": "AddgenePlasmid", + "addgene_id": "98519", + "resistance": "Kanamycin", + "well": "C / 1" + }, + { + "name": "BB1_34_TDH3tt", + "category": "terminator", + "description": "TDH3tt", + "type": "AddgenePlasmid", + "addgene_id": "98520", + "resistance": "Kanamycin", + "well": "C / 2" + }, + { + "name": "BB1_34_RPS2tt", + "category": "terminator", + "description": "RPS2tt", + "type": "AddgenePlasmid", + "addgene_id": "98521", + "resistance": "Kanamycin", + "well": "C / 3" + }, + { + "name": "BB1_34_RPP1Btt", + "category": "terminator", + "description": "RPP1Btt", + "type": "AddgenePlasmid", + "addgene_id": "98522", + "resistance": "Kanamycin", + "well": "C / 4" + }, + { + "name": "BB1_34_RPS17Btt", + "category": "terminator", + "description": "RPS17Btt", + "type": "AddgenePlasmid", + "addgene_id": "98523", + "resistance": "Kanamycin", + "well": "C / 5" + }, + { + "name": "BB1_34_chr4_0883tt", + "category": "terminator", + "description": "chr4_0883tt", + "type": "AddgenePlasmid", + "addgene_id": "98524", + "resistance": "Kanamycin", + "well": "C / 6" + }, + { + "name": "BB1_34_IDP1tt", + "category": "terminator", + "description": "IDP1tt", + "type": "AddgenePlasmid", + "addgene_id": "98525", + "resistance": "Kanamycin", + "well": "C / 7" + }, + { + "name": "BB1_34_RPS25Att", + "category": "terminator", + "description": "RPS25Att", + "type": "AddgenePlasmid", + "addgene_id": "98526", + "resistance": "Kanamycin", + "well": "C / 8" + }, + { + "name": "BB1_34_RPS3tt", + "category": "terminator", + "description": "RPS3tt", + "type": "AddgenePlasmid", + "addgene_id": "98527", + "resistance": "Kanamycin", + "well": "C / 9" + }, + { + "name": "BB1_34_RPL2Att", + "category": "terminator", + "description": "RPL2Att", + "type": "AddgenePlasmid", + "addgene_id": "98528", + "resistance": "Kanamycin", + "well": "C / 10" + }, + { + "name": "BB3aK_14*", + "category": "recipient BB3 - single", + "description": "1 TU (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "addgene_id": "98529", + "resistance": "Kanamycin", + "well": "C / 11" + }, + { + "name": "BB3aK_AC", + "category": "recipient BB3", + "description": "2 TUs (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "addgene_id": "98530", + "resistance": "Kanamycin", + "well": "C / 12" + }, + { + "name": "BB3aK_AD", + "category": "recipient BB3", + "description": "3 TUs (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "addgene_id": "98531", + "resistance": "Kanamycin", + "well": "D / 1" + }, + { + "name": "BB3aK_AE", + "category": "recipient BB3", + "description": "4 TUs (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "addgene_id": "98532", + "resistance": "Kanamycin", + "well": "D / 2" + }, + { + "name": "BB3aK_AF", + "category": "recipient BB3", + "description": "5 TUs (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "addgene_id": "98533", + "resistance": "Kanamycin", + "well": "D / 3" + }, + { + "name": "BB2_AB", + "category": "recipient BB2", + "description": "Transcription unit 1 (AB)", + "type": "AddgenePlasmid", + "addgene_id": "98534", + "resistance": "Ampicillin", + "well": "D / 4" + }, + { + "name": "BB2_BC", + "category": "recipient BB2", + "description": "Transcription unit 2 (BC)", + "type": "AddgenePlasmid", + "addgene_id": "98535", + "resistance": "Ampicillin", + "well": "D / 5" + }, + { + "name": "BB2_CD", + "category": "recipient BB2", + "description": "Transcription unit 3 (CD)", + "type": "AddgenePlasmid", + "addgene_id": "98536", + "resistance": "Ampicillin", + "well": "D / 6" + }, + { + "name": "BB2_DE", + "category": "recipient BB2", + "description": "Transcription unit 4 (DE)", + "type": "AddgenePlasmid", + "addgene_id": "98537", + "resistance": "Ampicillin", + "well": "D / 7" + }, + { + "name": "BB2_EF", + "category": "recipient BB2", + "description": "Transcription unit 5 (EF)", + "type": "AddgenePlasmid", + "addgene_id": "98538", + "resistance": "Ampicillin", + "well": "D / 8" + }, + { + "name": "BB2_FG", + "category": "recipient BB2", + "description": "Transcription unit 6 (FG)", + "type": "AddgenePlasmid", + "addgene_id": "98539", + "resistance": "Ampicillin", + "well": "D / 9" + }, + { + "name": "BB2_GH", + "category": "recipient BB2", + "description": "Transcription unit 7 (GH)", + "type": "AddgenePlasmid", + "addgene_id": "98540", + "resistance": "Ampicillin", + "well": "D / 10" + }, + { + "name": "BB2_HI", + "category": "recipient BB2", + "description": "Transcription unit 8 (HI)", + "type": "AddgenePlasmid", + "addgene_id": "98541", + "resistance": "Ampicillin", + "well": "D / 11" + }, + { + "name": "BB3aZ_14*", + "category": "recipient BB3 - single", + "description": "1 TU (locus AOX1tt, Zeocin) ", + "type": "AddgenePlasmid", + "addgene_id": "98542", + "resistance": "Bleocin (Zeocin)", + "well": "D / 12" + }, + { + "name": "BB3eH_14*", + "category": "recipient BB3 - single", + "description": "1 TU (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "addgene_id": "98543", + "resistance": "Hygromycin", + "well": "E / 1" + }, + { + "name": "BB3eH_AC", + "category": "recipient BB3", + "description": "2 TUs (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "addgene_id": "98544", + "resistance": "Hygromycin", + "well": "E / 2" + }, + { + "name": "BB3eH_AD", + "category": "recipient BB3", + "description": "3 TUs (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "addgene_id": "98545", + "resistance": "Hygromycin", + "well": "E / 3" + }, + { + "name": "BB3eH_AE", + "category": "recipient BB3", + "description": "4 TUs (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "addgene_id": "98546", + "resistance": "Hygromycin", + "well": "E / 4" + }, + { + "name": "BB3eH_AF", + "category": "recipient BB3", + "description": "5 TUs (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "addgene_id": "98547", + "resistance": "Hygromycin", + "well": "E / 5" + }, + { + "name": "BB3aN_14*", + "category": "recipient BB3 - single", + "description": "1 TU (locus AOX1tt, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98548", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 6" + }, + { + "name": "BB3eN_14*", + "category": "recipient BB3 - single", + "description": "1 TU (locus ENO1, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98549", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 7" + }, + { + "name": "BB3rN_14*", + "category": "recipient BB3 - single", + "description": "1 TU (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98550", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 8" + }, + { + "name": "BB3rN_AC", + "category": "recipient BB3", + "description": "2 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98551", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 9" + }, + { + "name": "BB3rN_AD", + "category": "recipient BB3", + "description": "3 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98552", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 10" + }, + { + "name": "BB3rN_AE", + "category": "recipient BB3", + "description": "4 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98553", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 11" + }, + { + "name": "BB3rN_AF", + "category": "recipient BB3", + "description": "5 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98554", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 12" + }, + { + "name": "BB3rN_AG", + "category": "recipient BB3", + "description": "6 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98555", + "resistance": "Nourseothricin (clonNat)", + "well": "F / 1" + }, + { + "name": "BB3rN_AH", + "category": "recipient BB3", + "description": "7 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98556", + "resistance": "Nourseothricin (clonNat)", + "well": "F / 2" + }, + { + "name": "BB3rN_AI", + "category": "recipient BB3", + "description": "8 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "addgene_id": "98557", + "resistance": "Nourseothricin (clonNat)", + "well": "F / 3" + } + ], + "categories": [ + { + "id": "recipient BB1", + "title": "Recipient BB1", + "description": "To domesticate parts ", + "image": null + }, + { + "id": "promoter", + "title": "Promoter", + "description": "BB1 plasmid with promoter", + "image": "promoter.png" + }, + { + "id": "coding sequence", + "title": "Coding Sequence", + "description": "BB1 plasmid with coding sequence", + "image": "cds.png" + }, + { + "id": "terminator", + "title": "Terminator", + "description": "BB1 plasmid with terminator", + "image": "terminator.png" + }, + { + "id": "recipient BB3 - single", + "title": "Recipient BB3 - single TU", + "description": "To clone a single TU directly from 3 BB1", + "image": "backbone.png" + }, + { + "id": "recipient BB3", + "title": "Recipient BB3", + "description": "To clone multiple TUs from BB2 plasmids", + "image": null + }, + { + "id": "recipient BB2", + "title": "Recipient BB2", + "description": "To combine several BB1 plasmids into a TU", + "image": "backbone.png" + } + ], + "assemblies": [ + { + "title": "Single TU BB3 plasmid", + "description": "Overexpression of a single TU, direct cloning from BB1 into a special BB3", + "fragment_order": [ + "promoter", + "coding sequence", + "terminator", + "recipient BB3 - single" + ], + "template_file": "assembly_template_001.json" + }, + { + "title": "TU cloning into BB2", + "description": "Cloning of a TU into a BB2 plasmid, for eventual multi-TU assembly into a BB3 plasmid", + "fragment_order": [ + "promoter", + "coding sequence", + "terminator", + "recipient BB2" + ], + "template_file": "assembly_template_002.json" + }, + 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null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB2_DE", + "description": "Transcription unit 4 (DE)", + "type": "AddgenePlasmid", + "resistance": "Ampicillin", + "well": "D / 7" + } + }, + { + "name": "BB2_EF - Transcription unit 5 (EF)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98538", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB2_EF", + "description": "Transcription unit 5 (EF)", + "type": "AddgenePlasmid", + "resistance": "Ampicillin", + "well": "D / 8" + } + }, + { + "name": "BB2_FG - Transcription unit 6 (FG)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98539", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB2_FG", + "description": "Transcription unit 6 (FG)", + "type": "AddgenePlasmid", + "resistance": "Ampicillin", + "well": "D / 9" + } + }, + { + "name": "BB2_GH - Transcription unit 7 (GH)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98540", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB2_GH", + "description": "Transcription unit 7 (GH)", + "type": "AddgenePlasmid", + "resistance": "Ampicillin", + "well": "D / 10" + } + }, + { + "name": "BB2_HI - Transcription unit 8 (HI)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98541", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB2_HI", + "description": "Transcription unit 8 (HI)", + "type": "AddgenePlasmid", + "resistance": "Ampicillin", + "well": "D / 11" + } + } + ] + }, + { + "id": 5, + "type": "RestrictionAndLigationSource", + "output_name": null, + "database_id": null, + "input": [ + { + "type": "SourceInput", + "sequence": 1 + }, + { + "type": "SourceInput", + "sequence": 2 + }, + { + "type": "SourceInput", + "sequence": 3 + }, + { + "type": "SourceInput", + "sequence": 4 + } + ], + "circular": null, + "restriction_enzymes": [ + "BsaI" + ] + } + ], + "primers": [], + "description": "TU cloning into BB2\n\nCloning of a TU into a BB2 plasmid, for eventual multi-TU assembly into a BB3 plasmid", + "files": null, + "schema_version": "0.4.3", + "backend_version": null, + "frontend_version": null +} \ No newline at end of file diff --git a/processed/kits-gasser-goldenpics/templates/assembly_template_003.json b/processed/kits-gasser-goldenpics/templates/assembly_template_003.json new file mode 100644 index 0000000..81c85c3 --- /dev/null +++ b/processed/kits-gasser-goldenpics/templates/assembly_template_003.json @@ -0,0 +1,411 @@ +{ + "sequences": [ + { + "id": 1, + "type": "TemplateSequence", + "circular": null, + "primer_design": null + }, + { + "id": 2, + "type": "TemplateSequence", + "circular": null, + "primer_design": null + }, + { + "id": 3, + "type": "TemplateSequence", + "circular": false, + "primer_design": null + }, + { + "id": 4, + "type": "TemplateSequence", + "circular": false, + "primer_design": null + } + ], + "sources": [ + { + "id": 1, + "type": "CollectionSource", + "output_name": null, + "database_id": null, + "input": [], + "category_id": "recipient BB3", + "title": "Recipient BB3", + "description": "To clone multiple TUs from BB2 plasmids", + "image": null, + "options": [ + { + "name": "BB3aK_AC - 2 TUs (locus AOX1tt, Kanamycin)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98530", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3aK_AC", + "description": "2 TUs (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "resistance": "Kanamycin", + "well": "C / 12" + } + }, + { + "name": "BB3aK_AD - 3 TUs (locus AOX1tt, Kanamycin)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98531", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3aK_AD", + "description": "3 TUs (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "resistance": "Kanamycin", + "well": "D / 1" + } + }, + { + "name": "BB3aK_AE - 4 TUs (locus AOX1tt, Kanamycin)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98532", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3aK_AE", + "description": "4 TUs (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "resistance": "Kanamycin", + "well": "D / 2" + } + }, + { + "name": "BB3aK_AF - 5 TUs (locus AOX1tt, Kanamycin)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98533", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3aK_AF", + "description": "5 TUs (locus AOX1tt, Kanamycin)", + "type": "AddgenePlasmid", + "resistance": "Kanamycin", + "well": "D / 3" + } + }, + { + "name": "BB3eH_AC - 2 TUs (locus ENO1, Hygromycin)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98544", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3eH_AC", + "description": "2 TUs (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "resistance": "Hygromycin", + "well": "E / 2" + } + }, + { + "name": "BB3eH_AD - 3 TUs (locus ENO1, Hygromycin)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98545", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3eH_AD", + "description": "3 TUs (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "resistance": "Hygromycin", + "well": "E / 3" + } + }, + { + "name": "BB3eH_AE - 4 TUs (locus ENO1, Hygromycin)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98546", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3eH_AE", + "description": "4 TUs (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "resistance": "Hygromycin", + "well": "E / 4" + } + }, + { + "name": "BB3eH_AF - 5 TUs (locus ENO1, Hygromycin)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98547", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3eH_AF", + "description": "5 TUs (locus ENO1, Hygromycin)", + "type": "AddgenePlasmid", + "resistance": "Hygromycin", + "well": "E / 5" + } + }, + { + "name": "BB3rN_AC - 2 TUs (locus RGI2, clonNat)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98551", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3rN_AC", + "description": "2 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 9" + } + }, + { + "name": "BB3rN_AD - 3 TUs (locus RGI2, clonNat)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98552", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3rN_AD", + "description": "3 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 10" + } + }, + { + "name": "BB3rN_AE - 4 TUs (locus RGI2, clonNat)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98553", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3rN_AE", + "description": "4 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 11" + } + }, + { + "name": "BB3rN_AF - 5 TUs (locus RGI2, clonNat)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98554", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3rN_AF", + "description": "5 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "resistance": "Nourseothricin (clonNat)", + "well": "E / 12" + } + }, + { + "name": "BB3rN_AG - 6 TUs (locus RGI2, clonNat)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98555", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3rN_AG", + "description": "6 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "resistance": "Nourseothricin (clonNat)", + "well": "F / 1" + } + }, + { + "name": "BB3rN_AH - 7 TUs (locus RGI2, clonNat)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98556", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3rN_AH", + "description": "7 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "resistance": "Nourseothricin (clonNat)", + "well": "F / 2" + } + }, + { + "name": "BB3rN_AI - 8 TUs (locus RGI2, clonNat)", + "source": { + "id": 0, + "type": "AddgeneIdSource", + "output_name": null, + "database_id": null, + "input": [], + "repository_id": "98557", + "repository_name": "addgene", + "sequence_file_url": null, + "addgene_sequence_type": null + }, + "info": { + "name": "BB3rN_AI", + "description": "8 TUs (locus RGI2, clonNat)", + "type": "AddgenePlasmid", + "resistance": "Nourseothricin (clonNat)", + "well": "F / 3" + } + } + ] + }, + { + "id": 2, + "type": "RestrictionAndLigationSource", + "output_name": null, + "database_id": null, + "input": [ + { + "type": "SourceInput", + "sequence": 1 + } + ], + "circular": null, + "restriction_enzymes": [ + "BsaI" + ] + }, + { + "id": 3, + "type": "GenomeCoordinatesSource", + "output_name": null, + "database_id": null, + "input": [], + "assembly_accession": "GCA_900235035.2", + "sequence_accession": "LT962479.2", + "locus_tag": "BQ9382_C4-0695", + "gene_id": null, + "start": 1237975, + "end": 241966, + "strand": 1 + }, + { + "id": 4, + "type": "HomologousRecombinationSource", + "output_name": null, + "database_id": null, + "input": [ + { + "type": "SourceInput", + "sequence": 3 + }, + { + "type": "SourceInput", + "sequence": 2 + } + ], + "circular": null + } + ], + "primers": [], + "description": "Multiple BB2 into BB3\n\nCloning of several TUs from BB2 plasmids into a BB3", + "files": null, + "schema_version": "0.4.3", + "backend_version": null, + "frontend_version": null +} \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 8a6ab26..c3fa192 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,6 +16,7 @@ openpyxl = "^3.1.3" jinja2 = "^3.1.4" pydna = "^5.2.0" opencloning-linkml = "0.4.3" +opencloning = "^0.4.2" [tool.poetry.group.test.dependencies] diff --git a/re_process.py b/re_process.py index 2e6cab6..7e8c06d 100644 --- a/re_process.py +++ b/re_process.py @@ -3,6 +3,13 @@ import os import json from copy import deepcopy +from opencloning.pydantic_models import ( + BaseCloningStrategy as CloningStrategy, + HomologousRecombinationSource, + GenomeCoordinatesSource, + SourceInput, +) +from opencloning_linkml.datamodel.models import TemplateSequence submission_folders = [d for d in glob.glob("submissions/*") if os.path.isdir(d)] @@ -47,5 +54,44 @@ option["info"]["well"] = "Base CIDAR Kit " + option["info"]["well"] source_new["options"].extend(old_options) + +## Add Homologous Recombination to K. phaffi kit +files = [ + "processed/kits-gasser-goldenpics/templates/assembly_template_001.json", + "processed/kits-gasser-goldenpics/templates/assembly_template_003.json", +] + +for file in files: + with open(file, "r") as f: + template = json.load(f) + cs = CloningStrategy.model_validate(template) + restriction_source = next( + s for s in cs.sources if s.type == "RestrictionAndLigationSource" + ) + + genome_source = GenomeCoordinatesSource( + id=0, + assembly_accession="GCA_900235035.2", + sequence_accession="LT962479.2", + locus_tag="BQ9382_C4-0695", + start=1237975, + end=241966, + strand=1, + ) + + cs.add_source_and_sequence(genome_source, TemplateSequence(circular=False, id=0)) + + hom_rec = HomologousRecombinationSource( + id=0, + input=[ + SourceInput(sequence=genome_source.id), + SourceInput(sequence=restriction_source.id), + ], + ) + cs.add_source_and_sequence(hom_rec, TemplateSequence(circular=False, id=0)) + + with open(file, "w") as f: + json.dump(cs.model_dump(), f, indent=2) + with open(extension_path, "w") as f: json.dump(template_extension, f, indent=2) diff --git a/submissions/kits-gasser-goldenpics/backbone.png b/submissions/kits-gasser-goldenpics/backbone.png new file mode 100644 index 0000000..1fc6999 Binary files /dev/null and b/submissions/kits-gasser-goldenpics/backbone.png differ diff --git a/submissions/kits-gasser-goldenpics/cds.png b/submissions/kits-gasser-goldenpics/cds.png new file mode 100644 index 0000000..b45dd3f Binary files /dev/null and b/submissions/kits-gasser-goldenpics/cds.png differ diff --git a/submissions/kits-gasser-goldenpics/promoter.png b/submissions/kits-gasser-goldenpics/promoter.png new file mode 100644 index 0000000..bd46ad3 Binary files /dev/null and b/submissions/kits-gasser-goldenpics/promoter.png differ diff --git a/submissions/kits-gasser-goldenpics/submission.xlsx b/submissions/kits-gasser-goldenpics/submission.xlsx new file mode 100644 index 0000000..0ef604e Binary files /dev/null and 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