{ "info": { "author": "Zachary Sailer", "author_email": "zachsailer@gmail.com", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: MIT License", "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: Implementation :: CPython", "Programming Language :: Python :: Implementation :: PyPy" ], "description": "\n# PyASR\n\n**Ancestral Sequence Reconstruction in Python**\n\nPyASR offers a modern Python interface to [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html) (\"Phylogenetic Analysis by Maximum Likelihood\")--tuned specifically for reconstruction\nancestral protein/DNA sequences.\n\n**NOTE:** PyASR currently only supports protein reconstructions. This is a work in progress.\n\n## Basic Usage\n\n```python\nimport phylopandas as pd\nimport dendropy as d\nimport pyasr\n\n# Use phylopandas to read a set of ancestor.s\ndf_seqs = pd.read_fasta('test.fasta')\n\n# Use dendropy to read in tree.\ntree = d.Tree.get(path='tree.newick', schema='newick')\n\n# Reconstruct nodes in tree.\ntree, df_seqs, df_anc = pyasr.reconstruct(df_seqs, tree, working_dir='test', alpha=1.235)\n\n# Write out ancestor dataframe to a CSV file.\ndf_anc.to_csv('ancestors.csv')\n```\n\nWe can visualize the ancestors side-by-side with the tree using inside of JupyterLab\nthanks to the ToyTree library.\n\n\n\n## Install\n\nThis package is released on PyPi. You can install using pip:\n```\npip install pyasr\n```\n\nTo get the development version:\n```\ngit clone\ncd\npip install -e .\n```\n\n## Dependencies\n\nThe actual reconstruction calculation are done using [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html). This requires PAML to be\ninstalled and the `codeml`/`baseml` executables exported to your `$PATH` environment variable. Directions for installing PAML can be found on the PAML website.\n\nThe following Python dependencies are required for PyASR to work.\n\n- Pandas\n- Biopython\n- PhyloPandas\n- DendroPy\n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/Zsailer/pyasr", "keywords": "", "license": "MIT", "maintainer": "", "maintainer_email": "", "name": "pyasr", "package_url": "https://pypi.org/project/pyasr/", "platform": "", "project_url": "https://pypi.org/project/pyasr/", "project_urls": { "Homepage": "https://github.com/Zsailer/pyasr" }, "release_url": "https://pypi.org/project/pyasr/0.6.1/", "requires_dist": null, "requires_python": ">=3.0.0", "summary": "Ancestral sequence reconstruction using Python", "version": "0.6.1" }, "last_serial": 4051936, "releases": { "0.4": [ { "comment_text": "", "digests": { "md5": "20ecfb7777a1f6845eaae3f663b10834", "sha256": "025b65a0fd678af4684a0c244b6434e4675cce1b41579925a75595c342cb6e7a" }, "downloads": -1, "filename": "pyasr-0.4-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "20ecfb7777a1f6845eaae3f663b10834", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": null, "size": 38740, "upload_time": "2017-10-31T23:48:56", "url": "https://files.pythonhosted.org/packages/36/3a/2702013690d02a5ddb0fc81084dcd0de36f10b97323ff648090781344196/pyasr-0.4-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "d3907e1e139b3032a42bf0d4262cd5f1", "sha256": "c3f75e2c739a0632424b6b3789e26b777ed7ccd1c56d5d7b34ffdc6f3dadfefe" }, "downloads": -1, "filename": "pyasr-0.4.tar.gz", "has_sig": false, "md5_digest": "d3907e1e139b3032a42bf0d4262cd5f1", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 33263, "upload_time": "2017-10-31T23:48:57", "url": "https://files.pythonhosted.org/packages/3f/98/79172e11b53422a3b9b22247c62b03d4059bba01eaa25459bb8800279bca/pyasr-0.4.tar.gz" } ], "0.4.1": [ { "comment_text": "", "digests": { "md5": "921df2c98676f166c2cbfdf1fb7f2fbd", "sha256": "e720fa89784c850fd6ba0f8fd002646272589afb4ff1fad0f561c371c89af85e" }, "downloads": -1, "filename": "pyasr-0.4.1-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "921df2c98676f166c2cbfdf1fb7f2fbd", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": null, "size": 38854, "upload_time": "2017-11-01T17:31:43", "url": "https://files.pythonhosted.org/packages/a2/e8/b7e3b0503bfd681e9db4d59817021a08e8c663e7509e9e33af57cc4f6726/pyasr-0.4.1-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "7c1d7b1776297a1e07eb8d39de6d1940", "sha256": "b75daef04eee6f663da6638856da7b767e878b0358b6cfc1e3d382d910a9e055" }, "downloads": -1, "filename": "pyasr-0.4.1.tar.gz", "has_sig": false, "md5_digest": "7c1d7b1776297a1e07eb8d39de6d1940", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 33300, "upload_time": "2017-11-01T17:31:44", "url": "https://files.pythonhosted.org/packages/8e/29/09c1e90e591e92a60f48dadb906c3b990da439ecda2d884f6d09c71b10b9/pyasr-0.4.1.tar.gz" } ], "0.4.2": [ { "comment_text": "", "digests": { "md5": "0d59ca68634f1fb02c4c94e584a4266b", "sha256": "1e0c7bb761fd5d584b9091e6e63eee4d430b24d7eb6b5ae1a7ec595e494b5dc0" }, "downloads": -1, "filename": "pyasr-0.4.2-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "0d59ca68634f1fb02c4c94e584a4266b", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": null, "size": 38870, "upload_time": "2017-11-01T22:37:54", "url": "https://files.pythonhosted.org/packages/5f/9b/7bc72990adf5c63c9663399364d18f74e86b35e2ef828e8ba59aeb860081/pyasr-0.4.2-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "fd524ee3a42497255456061adfe0f941", "sha256": "d204f50bcb96f3cd1581d149261c3bafcd1d8e9db3092024ce276e55e088c8f8" }, "downloads": -1, "filename": "pyasr-0.4.2.tar.gz", "has_sig": false, "md5_digest": "fd524ee3a42497255456061adfe0f941", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 33334, "upload_time": "2017-11-01T22:37:55", "url": "https://files.pythonhosted.org/packages/af/9c/78afca21fd73b24596bba01bcee30a7600a856d6a42ede31393f36d7c66d/pyasr-0.4.2.tar.gz" } ], "0.4.3": [ { "comment_text": "", "digests": { "md5": "4b715d2f49bca88f44b4db879b62258c", "sha256": "5c991585ca3f09337d795a45381c00feeace2119972e8678a2c40690e633dd19" }, "downloads": -1, "filename": "pyasr-0.4.3-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "4b715d2f49bca88f44b4db879b62258c", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": null, "size": 38999, "upload_time": "2017-11-08T18:10:23", "url": "https://files.pythonhosted.org/packages/47/86/163639cf78f1d546f13a6f03e59c62a0f150f461fbb50f76d0137cc9c323/pyasr-0.4.3-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "044aace7954bc4d88d2780b46c8b1951", "sha256": "0f9302d9e0b48690b7d816d49e07c13cf4661049acfce0af98fd1122a8d6b5c0" }, "downloads": -1, "filename": "pyasr-0.4.3.tar.gz", "has_sig": false, "md5_digest": "044aace7954bc4d88d2780b46c8b1951", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 33448, "upload_time": "2017-11-08T18:10:25", "url": "https://files.pythonhosted.org/packages/a5/b8/3b64fe08aad98efd40273bea04289cf4679c946a8926cc8558d43a8f43ec/pyasr-0.4.3.tar.gz" } ], "0.6.1": [ { "comment_text": "", "digests": { "md5": "0818ad50298eb3839377e8d9714063a6", "sha256": "bb4ca3b900abdd8d6d7af4a83bb2cd5ff99d52114f04f052c9cb99c222a54d33" }, "downloads": -1, "filename": "pyasr-0.6.1-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "0818ad50298eb3839377e8d9714063a6", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=3.0.0", "size": 35551, "upload_time": "2018-07-11T18:47:25", "url": "https://files.pythonhosted.org/packages/9b/f8/7d58a42f4f5f6ab308368052607b409d14aff242bed2f35613c233343318/pyasr-0.6.1-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "160d6abbd8f977c05125c3146a957ea1", "sha256": "4d46b42ecfc1089b3f4ee06359fc0561f2b3ceed586c9748614d0ce40a68376c" }, "downloads": -1, "filename": "pyasr-0.6.1.tar.gz", "has_sig": false, "md5_digest": "160d6abbd8f977c05125c3146a957ea1", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.0.0", "size": 31777, "upload_time": "2018-07-11T18:47:27", "url": "https://files.pythonhosted.org/packages/93/84/5d58a2b5aa4ded6328e8143f03dd16df95cde9dfe2fbaf4c9c8e0aef2701/pyasr-0.6.1.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "0818ad50298eb3839377e8d9714063a6", "sha256": "bb4ca3b900abdd8d6d7af4a83bb2cd5ff99d52114f04f052c9cb99c222a54d33" }, "downloads": -1, "filename": "pyasr-0.6.1-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "0818ad50298eb3839377e8d9714063a6", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=3.0.0", "size": 35551, "upload_time": "2018-07-11T18:47:25", "url": "https://files.pythonhosted.org/packages/9b/f8/7d58a42f4f5f6ab308368052607b409d14aff242bed2f35613c233343318/pyasr-0.6.1-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "160d6abbd8f977c05125c3146a957ea1", "sha256": "4d46b42ecfc1089b3f4ee06359fc0561f2b3ceed586c9748614d0ce40a68376c" }, "downloads": -1, "filename": "pyasr-0.6.1.tar.gz", "has_sig": false, "md5_digest": "160d6abbd8f977c05125c3146a957ea1", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.0.0", "size": 31777, "upload_time": "2018-07-11T18:47:27", "url": "https://files.pythonhosted.org/packages/93/84/5d58a2b5aa4ded6328e8143f03dd16df95cde9dfe2fbaf4c9c8e0aef2701/pyasr-0.6.1.tar.gz" } ] }