{ "info": { "author": "Benjamin Lee", "author_email": "benjamindlee@me.com", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: Apache Software License", "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: Implementation :: CPython", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "\n# Freqgen\n\n

\n\n

\n\n[![Build Status](https://travis-ci.org/Lab41/freqgen.svg?branch=master)](https://travis-ci.org/Lab41/freqgen) [![Documentation Status](https://readthedocs.org/projects/freqgen/badge/?version=latest)](https://freqgen.readthedocs.io/en/latest/?badge=latest) [![CodeFactor](https://www.codefactor.io/repository/github/lab41/freqgen/badge)](https://www.codefactor.io/repository/github/lab41/freqgen)\n\n\nFreqgen is a tool to generate coding DNA sequences with specified amino acid\nusage frequencies or sequence, GC content, codon usage bias, and/or *k*-mer\nusage bias. To accomplish this, Freqgen uses genetic algorithms to efficiently\nsearch the solution space of possible DNA sequences to find ones that most\nclosely match the desired parameters.\n\n## Features\n\n- CLI and Python API\n- Can simultaneously match multiple DNA statistics\n- Built-in visualization utility\n- Supports several fitness metrics (and you can bring your own!)\n\n## Installation\n\nSimply run:\n\n $ pip install freqgen\n\nOr, to get the latest (but not necessarily stable) development version:\n\n $ pip install git+https://github.com/Lab41/freqgen.git\n\n## Five-second CLI tutorial\n\nThe basic flow of Freqgen can be summarized in three steps:\n\n1. Generate a new amino acid sequence based on the amino acid usage profile of\nreference sequences. If you already have a specific amino acid sequence in mind\n(*i.e.* for synthetic biology uses), skip this step:\n\n $ freqgen aa reference_sequences.fna -o new_sequence.faa -l LENGTH\n\n2. Create a YAML file containing *k*-mer frequencies for the amino acid\nsequence's DNA to have:\n\n $ freqgen featurize reference_sequences.fna -k INT -o reference_freqs.yaml\n\n3. Generate the DNA sequence coding for the amino acid sequence:\n\n $ freqgen -t reference_freqs.yaml -s new_sequence.faa -v -o optimized.fna\n\n4. Visualize the results of the optimization (*optional*):\n\n $ freqgen visualize --target reference_freqs.yaml --optimized optimized.fna\n\n## Documentation\n\nRead the full docs over at\n[freqgen.readthedocs.io](http://freqgen.readthedocs.io).\n\n## Citation\n\nTo be determined!\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/Lab41/freqgen", "keywords": "", "license": "MIT", "maintainer": "", "maintainer_email": "", "name": "freqgen", "package_url": "https://pypi.org/project/freqgen/", "platform": "", "project_url": "https://pypi.org/project/freqgen/", "project_urls": { "Homepage": "https://github.com/Lab41/freqgen" }, "release_url": "https://pypi.org/project/freqgen/0.1.0/", "requires_dist": [ "numpy", "click (<=6.7)", "biopython", "pyyaml", "click-default-group", "dit", "bokeh", "colorama" ], "requires_python": ">=3.5.0", "summary": "Generate DNA sequences with specified amino acid, codon, and k-mer frequencies.", "version": "0.1.0" }, "last_serial": 4539861, "releases": { "0.1.0": [ { "comment_text": "", "digests": { "md5": "bc559fe2eb643b52f61bbc795498e06c", "sha256": "cfa069ee6e03ff10abbdd8f351fadbfbdc785d76dc56554fa2b7a946ddaf7574" }, "downloads": -1, "filename": "freqgen-0.1.0-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "bc559fe2eb643b52f61bbc795498e06c", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=3.5.0", "size": 23905, "upload_time": "2018-11-28T19:00:03", "url": "https://files.pythonhosted.org/packages/eb/fd/9810d4eb162cffd77dfa095c1ae285ba073d7cdc4579de31dce78767cf74/freqgen-0.1.0-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "3deb680f27a31dd35f1cb11bd2f06140", "sha256": "d495eff2fd91c5ef274e339640ab794930650a1c8e920acc23fc8cf865378d67" }, "downloads": -1, "filename": "freqgen-0.1.0.tar.gz", "has_sig": false, "md5_digest": "3deb680f27a31dd35f1cb11bd2f06140", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.5.0", "size": 17800, "upload_time": "2018-11-28T19:00:05", "url": "https://files.pythonhosted.org/packages/61/81/1306b2f17ee524b988cf007a446250765b311a5409d686d8f2326e95bb4a/freqgen-0.1.0.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "bc559fe2eb643b52f61bbc795498e06c", "sha256": "cfa069ee6e03ff10abbdd8f351fadbfbdc785d76dc56554fa2b7a946ddaf7574" }, "downloads": -1, "filename": "freqgen-0.1.0-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "bc559fe2eb643b52f61bbc795498e06c", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=3.5.0", "size": 23905, "upload_time": "2018-11-28T19:00:03", "url": "https://files.pythonhosted.org/packages/eb/fd/9810d4eb162cffd77dfa095c1ae285ba073d7cdc4579de31dce78767cf74/freqgen-0.1.0-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "3deb680f27a31dd35f1cb11bd2f06140", "sha256": "d495eff2fd91c5ef274e339640ab794930650a1c8e920acc23fc8cf865378d67" }, "downloads": -1, "filename": "freqgen-0.1.0.tar.gz", "has_sig": false, "md5_digest": "3deb680f27a31dd35f1cb11bd2f06140", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.5.0", "size": 17800, "upload_time": "2018-11-28T19:00:05", "url": "https://files.pythonhosted.org/packages/61/81/1306b2f17ee524b988cf007a446250765b311a5409d686d8f2326e95bb4a/freqgen-0.1.0.tar.gz" } ] }