{ "info": { "author": "Kai Blin", "author_email": "kblin@biosustain.dtu.dk", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: Apache Software License", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Merge multiple GenBank records using a defined spacer sequence\n==============================================================\n\n| A small script to turn a multiple GenBank records (either in multiple\n files or a\n| single multi-record file) into a single record.\n\n| Sequences are merged by concatenating them in order, and putting a\n spacer\n| sequence between them. Spacer sequence length can be given in kbp. It\n is\n| possible to pick an all-N spacer, or using a spacer consisting of\n all-frame stop\n| codons.\n\nInstallation\n------------\n\n::\n\n pip install merge-gbk-records\n\nAlternatively, clone this repository from GitHub, then run (in a python\nvirtual environment)\n\n::\n\n pip install .\n\nIf this fails on older versions of Python, try updating your ``pip``\ntool first:\n\n::\n\n pip install --upgrade pip\n\nand then rerun the ``merge-gbk-records`` install.\n\n| ``merge-gbk-records`` is only developed and tested on Python releases\n still under active\n| support by the Python project. At the moment, this means versions 2.7,\n 3.3, 3.4, 3.5 and 3.6.\n| Specifically, no attempt at testing under Python versions older than\n 2.7 or 3.3 is being made.\n\n| If your system is stuck on an older version of Python, consider using\n a tool like\n| `Homebrew `__ or `Linuxbrew `__\n to obtain a more up-to-date\n| version.\n\nUsage\n-----\n\n| By default, ``merge-gbk-records`` will add a 20 kbp spacer of all\n ``N``\\ s and output\n| the merged record on the terminal.\n\n::\n\n merge-gbk-records first.gbk second.gbk > merged.gbk\n\nYou can set different lengths using ``-l`` or ``--length``. To use a 5\nkbp spacer, use:\n\n::\n\n merge-gbk-records --length 5 first.gbk second.gbk > merged.gbk\n\nYou can select an all-frame stop codon spacer instead using ``-s stop``\nor ``--spacer stop``:\n\n::\n\n merge-gbk-records --spacer stop first.gbk second.gbk > merged.gbk\n\nInstead of writing to stdout, you can also write to a file using ``-o``\nor ``--outfile``:\n\n::\n\n merge-gbk-records --outfile merged.gbk first.gbk second.gbk\n\nTo print help about the command, just run it with ``-h`` or ``--help``:\n\n::\n\n merge-gbk-records --help\n\nLicense\n-------\n\n| All code is available under the Apache License version 2, see the\n| ```LICENSE`` `__ file for details.\n\n\n", "description_content_type": null, "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/kblin/merge-gbk-records/", "keywords": "", "license": "Apache Software License", "maintainer": "", "maintainer_email": "", "name": "merge-gbk-records", "package_url": "https://pypi.org/project/merge-gbk-records/", "platform": "", "project_url": "https://pypi.org/project/merge-gbk-records/", "project_urls": { "Homepage": "https://github.com/kblin/merge-gbk-records/" }, "release_url": "https://pypi.org/project/merge-gbk-records/0.1.1/", "requires_dist": [ "biopython" ], "requires_python": "", "summary": "Merge multiple GenBank files using a spacer sequence", "version": "0.1.1" }, "last_serial": 3253959, "releases": { "0.1.0": [ { "comment_text": "", "digests": { "md5": "157dab3beccdd21d160d814918fce547", "sha256": "5ca7af39c28c91c51da511ac938a0a09210d4b75bcb39b66a80455bc5b446f98" }, "downloads": -1, "filename": "merge_gbk_records-0.1.0-py3-none-any.whl", "has_sig": false, "md5_digest": "157dab3beccdd21d160d814918fce547", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 5585, "upload_time": "2017-10-16T15:16:40", "url": "https://files.pythonhosted.org/packages/a2/ed/1c2514fe34d029ff6d32d105a4ee6a6ee30d67d32d52576f4f152f5c63bd/merge_gbk_records-0.1.0-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "1407be8e94340809d2d341c5ef2cfe91", "sha256": "0865ae8f8bb2657183c97ccde5fb8b00d16881679b4f9b7c1e2b6fe727fddaf4" }, "downloads": -1, "filename": "merge-gbk-records-0.1.0.tar.gz", "has_sig": false, "md5_digest": "1407be8e94340809d2d341c5ef2cfe91", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 3723, "upload_time": "2017-10-16T15:16:41", "url": "https://files.pythonhosted.org/packages/ba/c7/4c0f84443551783c03d62be07e37313cc93e1509b28f3575384d8fa2a903/merge-gbk-records-0.1.0.tar.gz" } ], "0.1.1": [ { "comment_text": "", "digests": { "md5": "18dbb6dc3951d210bcd9c626e0300840", "sha256": "3fca3662a380f082aea451b005bd8bb17c859ef0c3c383bc1ab2ab2e7e103c80" }, "downloads": -1, "filename": "merge_gbk_records-0.1.1-py3-none-any.whl", "has_sig": false, "md5_digest": "18dbb6dc3951d210bcd9c626e0300840", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 6331, "upload_time": "2017-10-16T15:33:58", "url": "https://files.pythonhosted.org/packages/c8/e0/8bb8515602b83b2c6cd4b01762d30b49d6f273bc4520abd49af516925b90/merge_gbk_records-0.1.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "fcad3fd7f22b97ae181420cfe64e3287", "sha256": "37cc241e7cbc2430b02ef2d290f3e07cd0ea39fa8ddec46d8ad80713ee95520c" }, "downloads": -1, "filename": "merge-gbk-records-0.1.1.tar.gz", "has_sig": false, "md5_digest": "fcad3fd7f22b97ae181420cfe64e3287", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4231, "upload_time": "2017-10-16T15:34:00", "url": "https://files.pythonhosted.org/packages/a8/bb/cb2e47338e0c032b887a5b7595593e83e94e935d7327ae55552ae97f28dc/merge-gbk-records-0.1.1.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "18dbb6dc3951d210bcd9c626e0300840", "sha256": "3fca3662a380f082aea451b005bd8bb17c859ef0c3c383bc1ab2ab2e7e103c80" }, "downloads": -1, "filename": "merge_gbk_records-0.1.1-py3-none-any.whl", "has_sig": false, "md5_digest": "18dbb6dc3951d210bcd9c626e0300840", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 6331, "upload_time": "2017-10-16T15:33:58", "url": "https://files.pythonhosted.org/packages/c8/e0/8bb8515602b83b2c6cd4b01762d30b49d6f273bc4520abd49af516925b90/merge_gbk_records-0.1.1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "fcad3fd7f22b97ae181420cfe64e3287", "sha256": "37cc241e7cbc2430b02ef2d290f3e07cd0ea39fa8ddec46d8ad80713ee95520c" }, "downloads": -1, "filename": "merge-gbk-records-0.1.1.tar.gz", "has_sig": false, "md5_digest": "fcad3fd7f22b97ae181420cfe64e3287", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 4231, "upload_time": "2017-10-16T15:34:00", "url": "https://files.pythonhosted.org/packages/a8/bb/cb2e47338e0c032b887a5b7595593e83e94e935d7327ae55552ae97f28dc/merge-gbk-records-0.1.1.tar.gz" } ] }