{ "info": { "author": "Guanliang Meng", "author_email": "mengguanliang@genomics.cn", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# polish_genbank\n\n## 1 Introduction\n\nsee `https://github.com/linzhi2013/polish_genbank`.\n\nThis package is to check for the internal stop codon in Genbank or FASTA file (CDS), then\n substitute the internal stop codon with NNN. \n\n## 2 Installation\n\n pip3 install polish_genbank\n\nThere will be a command `polish_genbank` created under the same directory as your `pip3` command.\n\n## 3 Usage\nrun `polish_genbank`\n\n\n usage: polish_genbank.py [-h] --in [--format {gb,fa}] [--table ]\n [--ntNs ] [--aaNs ] --out \n\n Check for the internal stop codon, then substitute the internal stop codon\n with NNN. By mengguanliang [] genomics.cn, where [] == @. See\n https://github.com/linzhi2013/polish_genbank\n\n optional arguments:\n -h, --help show this help message and exit\n --in input genbank file or CDS file (fasta format)\n --format {gb,fa} the input file format. For fasta file, all sequences are\n assumed to be forward strand, coding from +1 position [gb]\n --table The genetic code table used for translation, for fasta\n input only [2]\n --ntNs the chars used for substituting an internal stop codon in\n CDS sequence. [NNN]\n --aaNs the chars used for substituting an internal stop codon in\n protein sequence. [X]\n --out output filename\n\n\n\n## 4 Used in scripts\n\n In [1]: from polish_genbank import polish_gb, polish_fasta\n\n In [2]: polish_gb?\n Signature: polish_gb(ingb=None, NewInternalStopCodonNT='NNN', NewInternalStopCodonAA='X', logger=None)\n Docstring:\n Replace the internal stop codon with NNNs on Genbank nt sequence,\n and replace the '*' in 'translation' tag (protein sequence) with 'X'\n\n Return:\n An generator.\n\n Usage:\n\n >>> records = polish_gb(ingb='in.gb', NewInternalStopCodonNT='NNN',\n NewInternalStopCodonAA='X')\n >>> for rec in records:\n >>> print(rec.id, rec.seq)\n\n\n In [3]: polish_fasta?\n Signature: polish_fasta(infasta=None, NewInternalStopCodonNT='NNN', table=2, logger=None)\n Docstring:\n Replace the internal stop codon with NNNs.\n\n The infasta file is assumed to be CDS sequences, and coding from +1\n position.\n\n Return:\n An generator.\n\n Usage:\n\n >>> records = polish_fasta(infasta='myfile', NewInternalStopCodonNT='NNN', table=2)\n >>> for rec in records:\n >>> print(rec.id, rec.seq)\n\n## 5 Citation\nCurrently I have no plan to publish `polish_genbank`.\n\nHowever, since `polish_genbank` makes use of `Biopython`, you should also cite it if you use `breakSeqInNs_then_translate` in your work:\n\n Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: \u201cBiopython: freely available Python tools for computational molecular biology and bioinformatics\u201d. Bioinformatics 25 (11), 1422\u20131423 (2009). https://doi.org/10.1093/bioinformatics/btp163\n\nPlease go to `http://www.biopython.org/` for more details.", "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/linzhi2013/polish_genbank", "keywords": "", "license": "", "maintainer": "", "maintainer_email": "", "name": "polish-genbank", "package_url": "https://pypi.org/project/polish-genbank/", "platform": "", "project_url": "https://pypi.org/project/polish-genbank/", "project_urls": { "Homepage": "https://github.com/linzhi2013/polish_genbank" }, "release_url": "https://pypi.org/project/polish-genbank/0.0.2/", "requires_dist": null, "requires_python": ">=3.4", "summary": "To check for the internal stop codon in Genbank or FASTA file (CDS), then substitute the internal stop codon with NNN.", "version": "0.0.2" }, "last_serial": 4292038, "releases": { "0.0.1": [ { "comment_text": "", "digests": { "md5": "601a65c6916d7f1527162efafec03f95", "sha256": "1709524c96512512bfa64003154b1465f3cbb5a2ae6a028714229658f987af0f" }, "downloads": -1, "filename": "polish_genbank-0.0.1.tar.gz", "has_sig": false, "md5_digest": "601a65c6916d7f1527162efafec03f95", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.4", "size": 18703, "upload_time": "2018-09-20T09:10:00", "url": "https://files.pythonhosted.org/packages/6c/b9/d2edb406731080138c91d6a45e6dea77e88d60b9e89f34d6c4076b42874a/polish_genbank-0.0.1.tar.gz" } ], "0.0.2": [ { "comment_text": "", "digests": { "md5": "b4d3b9bdc4efe12f4ce90f24d8df7e6f", "sha256": "5b6b019867690d7b7bb7b9b1fc30f7c577de852651f9128df827fccb24d630aa" }, "downloads": -1, "filename": "polish_genbank-0.0.2.tar.gz", "has_sig": false, "md5_digest": "b4d3b9bdc4efe12f4ce90f24d8df7e6f", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.4", "size": 18703, "upload_time": "2018-09-20T09:44:31", "url": "https://files.pythonhosted.org/packages/01/81/1a6d94ebf6c612af13712f2c7c567d953e7b47722d1c8dc2052a1029ed7e/polish_genbank-0.0.2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "b4d3b9bdc4efe12f4ce90f24d8df7e6f", "sha256": "5b6b019867690d7b7bb7b9b1fc30f7c577de852651f9128df827fccb24d630aa" }, "downloads": -1, "filename": "polish_genbank-0.0.2.tar.gz", "has_sig": false, "md5_digest": "b4d3b9bdc4efe12f4ce90f24d8df7e6f", "packagetype": "sdist", "python_version": "source", "requires_python": ">=3.4", "size": 18703, "upload_time": "2018-09-20T09:44:31", "url": "https://files.pythonhosted.org/packages/01/81/1a6d94ebf6c612af13712f2c7c567d953e7b47722d1c8dc2052a1029ed7e/polish_genbank-0.0.2.tar.gz" } ] }