{ "info": { "author": "Zulko", "author_email": "", "bugtrack_url": null, "classifiers": [], "description": "DNA Chisel\n==========\n\nDNA Chisel is a Python library to optimize the nucleotides of DNA sequences with respect to a set of constraints and optimization objectives. It can be used for codon-optimizing the genes of a sequence for a particular organism, modifying a sequence to meet the constraints of a DNA provider while preserving genes, and much more.\n\n\nDNA Chisel comes with more than 15 types of optimizations and constraints and allows users to define new specifications in Python, making the library suitable for a large range of automated sequence design applications, or complex custom design projects.\n\nExample of use\n---------------\n\n.. code:: python\n\n from dnachisel import *\n\n # DEFINE THE OPTIMIZATION PROBLEM\n\n random_sequence = random_dna_sequence(10000)\n problem = DnaOptimizationProblem(\n sequence=random_sequence,\n constraints=[AvoidPattern(\"BsaI_site\"),\n EnforceGCContent(mini=0.3, maxi=0.7, window=50)],\n objectives=[CodonOptimize(species='e_coli', location=(500, 1300))]\n )\n\n # SOLVE THE CONSTRAINTS, OPTIMIZE WITH RESPECT TO THE OBJECTIVE\n\n problem.resolve_constraints()\n problem.optimize()\n\n # PRINT SUMMARIES TO CHECK THAT CONSTRAINTS PASS\n\n print(problem.constraints_text_summary())\n print(problem.objectives_text_summary())\n\nSee `this page `_\nfor an overview of available specifications.\n\nInfos\n-----\n\n**PIP installation:**\n\n.. code:: bash\n\n pip install dnachisel[reports]\n\n(you can omit the ``[reports]`` suffix if you intend to use dnachisel only\nfor sequence optimization, without generating figures or PDF reports)\n\n**Web documentation:**\n\n``_\n\n**Github Page**\n\n``_\n\n**Live demo**\n\n``_\n\n**License:** MIT, Copyright Edinburgh Genome Foundry\n\nMore biology software\n-----------------------\n\n.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png\n :target: https://edinburgh-genome-foundry.github.io/\n\nDNA Chisel is part of the `EGF Codons `_ synthetic biology software suite for DNA design, manufacturing and validation.\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/Edinburgh-Genome-Foundry/DnaChisel", "keywords": "DNA optimization constraints synthetic biology", "license": "MIT", "maintainer": "", "maintainer_email": "", "name": "dnachisel", "package_url": "https://pypi.org/project/dnachisel/", "platform": "", "project_url": "https://pypi.org/project/dnachisel/", "project_urls": { "Homepage": "https://github.com/Edinburgh-Genome-Foundry/DnaChisel" }, "release_url": "https://pypi.org/project/dnachisel/2.1.0/", "requires_dist": null, "requires_python": "", "summary": "Optimize DNA sequences under constraints.", "version": "2.1.0" }, "last_serial": 5909450, "releases": { "0.1.0": [ { "comment_text": "", "digests": { "md5": "e1d632492717ccba2b89789542d18dda", "sha256": "3e29be2c321e7ae621b34793426ab8b71280d00de23e94187f838b48aab77f71" }, "downloads": -1, "filename": "dnachisel-0.1.0.tar.gz", "has_sig": false, "md5_digest": "e1d632492717ccba2b89789542d18dda", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 163549, "upload_time": "2017-10-05T12:12:23", "url": "https://files.pythonhosted.org/packages/05/47/a96748f3a5b7244f0831e226d5e41739a4d5e9ce407bbc8a2780a75aaff9/dnachisel-0.1.0.tar.gz" } ], "0.1.1": [ { "comment_text": "", "digests": { "md5": "30b86ae51c63ecb69112e0c05000afbd", "sha256": "e690b1f009fa9e425a2fd27682b07ebdc1b961f24c1e281ed3932ef1fb22f615" }, "downloads": -1, "filename": "dnachisel-0.1.1.tar.gz", "has_sig": false, "md5_digest": "30b86ae51c63ecb69112e0c05000afbd", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 165365, "upload_time": "2018-02-17T20:26:44", "url": "https://files.pythonhosted.org/packages/f1/47/a7e5698b69ef6ccff6f92c2114b5d4274fafd847309180e643a0463c71ad/dnachisel-0.1.1.tar.gz" } ], "0.1.2": [ { "comment_text": "", "digests": { "md5": "f1f6118d4cb2073d6c500a19252ba149", "sha256": "305dc43d68e82de30009b53b9092064e6dfbcc65878209ab77a20d7ca79c52b9" }, "downloads": -1, "filename": "dnachisel-0.1.2.tar.gz", "has_sig": false, "md5_digest": "f1f6118d4cb2073d6c500a19252ba149", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 166960, "upload_time": "2018-04-13T17:07:49", "url": "https://files.pythonhosted.org/packages/44/f2/2ca105de7874b06905dca1ce5889c8523a2c76bc940383cd41ea5e63384a/dnachisel-0.1.2.tar.gz" } ], "0.1.3": [ { "comment_text": "", "digests": { "md5": "3bdc46cf4ea04d580ed40ecca6411182", "sha256": "2e0871c16a4bacf9a929d592aef721c48ab47a46abff979102b4399b3587d2db" }, "downloads": -1, "filename": "dnachisel-0.1.3.tar.gz", "has_sig": false, "md5_digest": "3bdc46cf4ea04d580ed40ecca6411182", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 991283, "upload_time": "2018-07-03T14:49:00", "url": "https://files.pythonhosted.org/packages/a2/41/df1ebdb209906aa5339e4e07844efd206cdeb535ed3d158d247ee183346b/dnachisel-0.1.3.tar.gz" } ], "0.1.4": [ { "comment_text": "", "digests": { "md5": "9695ec2dc7f9b7643b755c869df14212", "sha256": "6c91dc8d757493f824ad5a876caed7bc61a41d04556e653d05889e2cef8180b0" }, "downloads": -1, "filename": "dnachisel-0.1.4.tar.gz", "has_sig": false, "md5_digest": "9695ec2dc7f9b7643b755c869df14212", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1017575, "upload_time": "2018-07-30T15:33:49", "url": "https://files.pythonhosted.org/packages/05/8d/6fa334dd787e19a6c059b8b40435c0a92041ecdd350f4d3a3729a0b15380/dnachisel-0.1.4.tar.gz" } ], "0.1.5": [ { "comment_text": "", "digests": { "md5": "f3d20d9454a80344c6819e29aac62d3c", "sha256": "d4ff87e073de5d8a6d119f6ef5e26b40244896f3d1b6a3655a0377e4d45863bd" }, "downloads": -1, "filename": "dnachisel-0.1.5.tar.gz", "has_sig": false, "md5_digest": "f3d20d9454a80344c6819e29aac62d3c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1017587, "upload_time": "2018-08-10T14:43:29", "url": "https://files.pythonhosted.org/packages/9d/a3/b300e0794e4d26492d5bb17f48d4acb9f5e9ad5a09393ae21e126e2cc38a/dnachisel-0.1.5.tar.gz" } ], "0.1.6": [ { "comment_text": "", "digests": { "md5": "c2996f73f064ab70ea355a49ca87769a", "sha256": "545fa808b2ac8124b1685ef00fd709b6cf9ffdd6a55f1bcdae376e3072d741aa" }, "downloads": -1, "filename": "dnachisel-0.1.6.tar.gz", "has_sig": false, "md5_digest": "c2996f73f064ab70ea355a49ca87769a", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1018004, "upload_time": "2018-10-02T20:50:22", "url": "https://files.pythonhosted.org/packages/31/58/e3c107bbfceb08be5b2e7d67c24a4cb779e59300e0591a795ddc53e8eeab/dnachisel-0.1.6.tar.gz" } ], "0.1.7": [ { "comment_text": "", "digests": { "md5": "f330ced87fcdb4d432526ee452051377", "sha256": "a897f0b55420e8203484a2abaf8c8e229423e22647b773bf5139d35bd8835c93" }, "downloads": -1, "filename": "dnachisel-0.1.7.tar.gz", "has_sig": false, "md5_digest": "f330ced87fcdb4d432526ee452051377", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1019837, "upload_time": "2019-02-08T16:15:08", "url": "https://files.pythonhosted.org/packages/a3/23/47c02344131eaeb270e89ca4e38226a0dc7e1b0c156a8b6d92c4a1645c5a/dnachisel-0.1.7.tar.gz" } ], "0.1.8": [ { "comment_text": "", "digests": { "md5": "7e1ba8fe6ac4acefbb8ee960293675f5", "sha256": "d296343ebf70ae8d20b187a34025f9712fa72ea4f1c5fbc2844db2a6a73d7962" }, "downloads": -1, "filename": "dnachisel-0.1.8.tar.gz", "has_sig": false, "md5_digest": "7e1ba8fe6ac4acefbb8ee960293675f5", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1019830, "upload_time": "2019-02-08T16:44:21", "url": "https://files.pythonhosted.org/packages/92/7c/7d2bc5e0742106a515fe2355493b8c923c8f47dd7c5de84592c9337cbd89/dnachisel-0.1.8.tar.gz" } ], "0.1.9": [ { "comment_text": "", "digests": { "md5": "fd00cb0c95e27ab9113bbffa63c2ccc2", "sha256": "58b0c11c1ecbdfad9d425cb43c935e694d5e9da345b2990aa319e25d782df92c" }, "downloads": -1, "filename": "dnachisel-0.1.9.tar.gz", "has_sig": false, "md5_digest": "fd00cb0c95e27ab9113bbffa63c2ccc2", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1019834, "upload_time": "2019-02-08T17:07:21", "url": "https://files.pythonhosted.org/packages/c0/c1/7970faf4a8eec61766eb311ee586a70fe838f9e4c58ab812b83276d61f0c/dnachisel-0.1.9.tar.gz" } ], "0.2.0": [ { "comment_text": "", "digests": { "md5": "19856e10109072c214d4fa70e3826510", "sha256": "63d07c7f4b26ffe76fe10f3e099c80403bddc49a094b669415c26b19464bdae6" }, "downloads": -1, "filename": "dnachisel-0.2.0.tar.gz", "has_sig": false, "md5_digest": "19856e10109072c214d4fa70e3826510", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1094185, "upload_time": "2019-02-11T19:55:40", "url": "https://files.pythonhosted.org/packages/a0/0b/85ee2c0625a40c535e6a33413d5f523edb5c6546917929ba2e7c03828ab6/dnachisel-0.2.0.tar.gz" } ], "0.3.0": [ { "comment_text": "", "digests": { "md5": "efcdfdd49bc2c7272437cf085e2ca02d", "sha256": "bf4c08128d2e7807b2cdb22cfcb957df9c48130ecf3914984dbb5f048e556188" }, "downloads": -1, "filename": "dnachisel-0.3.0.tar.gz", "has_sig": false, "md5_digest": "efcdfdd49bc2c7272437cf085e2ca02d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1296802, "upload_time": "2019-02-28T19:44:14", "url": "https://files.pythonhosted.org/packages/c0/29/db1c95f8e340101f9332b267e2995935f2f62bb5ff11393180ffd096549e/dnachisel-0.3.0.tar.gz" } ], "0.3.1": [ { "comment_text": "", "digests": { "md5": "118243b46d5341708bb19d7cdc52b1d4", "sha256": "f8c3dd2c2d91630052e8f4c3ccb8a8219d395aedbf3d0a012564e96dda869440" }, "downloads": -1, "filename": "dnachisel-0.3.1.tar.gz", "has_sig": false, "md5_digest": "118243b46d5341708bb19d7cdc52b1d4", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1296833, "upload_time": "2019-03-11T21:38:10", "url": "https://files.pythonhosted.org/packages/a5/36/fdfbf8e7b94c4bac0c1accae5fc84acac47f3cce59fee55e2d67e2b3a8d0/dnachisel-0.3.1.tar.gz" } ], "1.0.0": [ { "comment_text": "", "digests": { "md5": "e6d836555338ad15af2304e7792c8156", "sha256": "0fab12cc56bf43748c06e42ef5b461d94a798dcee4698fcc12d1a3f63301e3f0" }, "downloads": -1, "filename": "dnachisel-1.0.0.tar.gz", "has_sig": false, "md5_digest": "e6d836555338ad15af2304e7792c8156", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1297131, "upload_time": "2019-03-21T21:20:01", "url": "https://files.pythonhosted.org/packages/29/2c/05743f061b8604c700ced74c2c036f2e02d5bcc179f96670739019d539fb/dnachisel-1.0.0.tar.gz" } ], "1.0.1": [ { "comment_text": "", "digests": { "md5": "3bb03a77f5e358e640ebb64af430dad6", "sha256": "9c017af8ae3c4918a9c4b6e85c1b527e42831bc4ba8a4f4f9af054e6ddea70f1" }, "downloads": -1, "filename": "dnachisel-1.0.1.tar.gz", "has_sig": false, "md5_digest": "3bb03a77f5e358e640ebb64af430dad6", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1297152, "upload_time": "2019-03-22T20:12:33", "url": "https://files.pythonhosted.org/packages/6b/0b/bba0d5cebcba782549cf8b551b97e57b9e9ec0724b010321133f05fc48fe/dnachisel-1.0.1.tar.gz" } ], "1.0.2": [ { "comment_text": "", "digests": { "md5": "10944e6c5c7aaed709e46438b8f7f7f6", "sha256": "f8f805476cec966398d7ca4b9fdcc6b23dbbb84ae8a82d8d6b946d80046587e8" }, "downloads": -1, "filename": "dnachisel-1.0.2.tar.gz", "has_sig": false, "md5_digest": "10944e6c5c7aaed709e46438b8f7f7f6", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1297145, "upload_time": "2019-03-22T21:29:10", "url": "https://files.pythonhosted.org/packages/49/d5/8531e5002b8953c1f00bd3ca8160c61860d1e5694af793ac9db1932d530c/dnachisel-1.0.2.tar.gz" } ], "1.1": [ { "comment_text": "", "digests": { "md5": "6fa0eed4fa5bec6ebfdeb4758498a84a", "sha256": "4e51dd8334bffcbeb8b496bb0aaa54bdf25824308724a0feaf2f0767d57d1098" }, "downloads": -1, "filename": "dnachisel-1.1.tar.gz", "has_sig": false, "md5_digest": "6fa0eed4fa5bec6ebfdeb4758498a84a", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1296971, "upload_time": "2019-03-25T16:14:10", "url": "https://files.pythonhosted.org/packages/1a/9f/e3a23a2eb761313cbedf0a6eb5eb4839dcd097a2e0f048caf00a0960a875/dnachisel-1.1.tar.gz" } ], "1.2": [ { "comment_text": "", "digests": { "md5": "2150363297c11952a82bdc5162e3cf7c", "sha256": "3919b87c2b52cb3b68610dfbe22b5e49ecf7ad47fdfea9b30d1581e2e2d79a4a" }, "downloads": -1, "filename": "dnachisel-1.2.tar.gz", "has_sig": false, "md5_digest": "2150363297c11952a82bdc5162e3cf7c", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1297483, "upload_time": "2019-05-15T20:35:20", "url": "https://files.pythonhosted.org/packages/28/3a/90c1c8c66ac4d1855e68d84f5ac4b02725b66269fa1e5f3ad659e8aee5ce/dnachisel-1.2.tar.gz" } ], "1.3": [ { "comment_text": "", "digests": { "md5": "69b723c088a52086e639a197da37ba91", "sha256": "565d1babb633c25a717cf6bf512a2dd9fc78ec1cde14604bb5ffd4c99a7f0e0c" }, "downloads": -1, "filename": "dnachisel-1.3.tar.gz", "has_sig": false, "md5_digest": "69b723c088a52086e639a197da37ba91", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1298486, "upload_time": "2019-08-01T19:25:05", "url": "https://files.pythonhosted.org/packages/17/72/010b47cc62d2106d185010311b30fd8befd2da3b63d824f1f2a14f0acece/dnachisel-1.3.tar.gz" } ], "1.4": [ { "comment_text": "", "digests": { "md5": "4e0c7e581eac5b8cca4a9d6fdb74b236", "sha256": "c242997b4b867d337d21cfa24eab78a94b3f5e5f659ab48e9fa2055150540a5e" }, "downloads": -1, "filename": "dnachisel-1.4.tar.gz", "has_sig": false, "md5_digest": "4e0c7e581eac5b8cca4a9d6fdb74b236", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1298902, "upload_time": "2019-09-03T17:58:06", "url": "https://files.pythonhosted.org/packages/17/a4/2d692becb5bb3b9e8cae803bde47b606c26e58b86149c52d13c320150a92/dnachisel-1.4.tar.gz" } ], "1.4.1": [ { "comment_text": "", "digests": { "md5": "771e48cd64c5a64ee697a97307e69c31", "sha256": "87033eaee8ceccbe5c2363706d0a04516f82049a2ad51e713440a1efef98b370" }, "downloads": -1, "filename": "dnachisel-1.4.1.tar.gz", "has_sig": false, "md5_digest": "771e48cd64c5a64ee697a97307e69c31", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1299189, "upload_time": "2019-09-03T20:40:47", "url": "https://files.pythonhosted.org/packages/81/f0/c45e6358561f83b95cd1910cb4fdd4158238abed56cc6ece1013b7b88eee/dnachisel-1.4.1.tar.gz" } ], "2.0.0": [ { "comment_text": "", "digests": { "md5": "7327ea2e6b54aad714c29ed0e821798b", "sha256": "e48f31c5779bfed9f23bf41a6689f8c2909a5d1e75b93260bb3b73adbc1e2058" }, "downloads": -1, "filename": "dnachisel-2.0.0.tar.gz", "has_sig": false, "md5_digest": "7327ea2e6b54aad714c29ed0e821798b", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1633439, "upload_time": "2019-09-24T20:25:35", "url": "https://files.pythonhosted.org/packages/66/d8/866a7025c8125864ec06e29d23be478f50a38470fa30ef189b5b9445f12e/dnachisel-2.0.0.tar.gz" } ], "2.1.0": [ { "comment_text": "", "digests": { "md5": "c62c066d7833e912f72c6b996e68506d", "sha256": "216f7f75912ccdd2b51eca2ad6062fa77a756f4c41859706968b3c87bf890c67" }, "downloads": -1, "filename": "dnachisel-2.1.0.tar.gz", "has_sig": false, "md5_digest": "c62c066d7833e912f72c6b996e68506d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1633752, "upload_time": "2019-09-30T23:02:13", "url": "https://files.pythonhosted.org/packages/79/c2/8d534725f459a631034e367ae792ea8eecfb6a6a9ce5f24aab857a10244b/dnachisel-2.1.0.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "c62c066d7833e912f72c6b996e68506d", "sha256": "216f7f75912ccdd2b51eca2ad6062fa77a756f4c41859706968b3c87bf890c67" }, "downloads": -1, "filename": "dnachisel-2.1.0.tar.gz", "has_sig": false, "md5_digest": "c62c066d7833e912f72c6b996e68506d", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 1633752, "upload_time": "2019-09-30T23:02:13", "url": "https://files.pythonhosted.org/packages/79/c2/8d534725f459a631034e367ae792ea8eecfb6a6a9ce5f24aab857a10244b/dnachisel-2.1.0.tar.gz" } ] }