{ "info": { "author": "Bruno F Souza", "author_email": "fsouza.bruno@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.5", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "\ngenial: GENome Interactive Annotation Library\n=============================================\n\n.. image:: https://badge.fury.io/py/genial.png\n :target: https://badge.fury.io/py/genial\n\nThis library provides `InteractiveAnnotation`, a high level representation of genome annotations,\nallowing users to easily extract information, manipulate and reformat commonly used annotation\nfiles such as BED and GFF.\n\nThe package is currently in alpha stage and only runs on `python3`.\n\nSupported formats\n-----------------\n\n* Input: BED, GFF3, GTF\n\n* Output: BED\n\n\nScripts\n-------\nFor convenience, we provide two CLI utilities: `annotParser.py` and `annotMergeSmallGap.py`.\n\n.. code-block::\n\n $ annotParser.py -h\n usage: annotParser.py [-h] [-i INPUT] [-o OUTPUT] [-f {gff3,gtf,bed}]\n [-t {extb,bed}] [-n MIN_EXON_COUNT]\n [-igs IGNORE_GAPS_SMALLER_THAN]\n [-igb IGNORE_GAPS_BIGGER_THAN] [-v]\n\n Parse, filter and convert annotation files\n\n optional arguments:\n -h, --help show this help message and exit\n -i INPUT, --input INPUT\n input file. to read from pipe, use the argument\n 'stdin'\n -o OUTPUT, --output OUTPUT\n output file\n -f {gff3,gtf,bed}, --input_format {gff3,gtf,bed}\n input file format\n -t {extb,bed}, --output_format {extb,bed}\n output file format\n -n MIN_EXON_COUNT, --min_exon_count MIN_EXON_COUNT\n min number of exons\n -igs IGNORE_GAPS_SMALLER_THAN, --ignore_gaps_smaller_than IGNORE_GAPS_SMALLER_THAN\n -igb IGNORE_GAPS_BIGGER_THAN, --ignore_gaps_bigger_than IGNORE_GAPS_BIGGER_THAN\n -v, --invert_match select non matching annotations (similar to grep -v)\n\n\n\n.. code-block::\n\n $ annotMergeSmallGaps.py -h\n usage: annotMergeSmallGaps.py [-h] [-i INPUT] [-o OUTPUT] [-f {gff3,bed,gtf}]\n [-t {extb,bed}] [-s SMALL_GAP_SIZE]\n\n Merge exons separated by small gaps. Can also be used to convert different\n kinds of annotations.\n\n optional arguments:\n -h, --help show this help message and exit\n -i INPUT, --input INPUT\n input file. to read from pipe, use the argument\n 'stdin'\n -o OUTPUT, --output OUTPUT\n output file\n -f {gff3,bed,gtf}, --input_format {gff3,bed,gtf}\n input file format\n -t {extb,bed}, --output_format {extb,bed}\n output file format\n -s SMALL_GAP_SIZE, --small_gap_size SMALL_GAP_SIZE\n gap size.\n\n\n\nBoth the scripts above can also be used to convert from different kinds of annotation files.\nA more advanced usage can be achieved importing the library.\n\nInstalation instructions\n------------------------\n\nfor a systemwide instalation on ubuntu:\n\n.. code-block:: bash\n\n sudo apt-get install python3-pip\n sudo pip3 install genial\n\n\nAcknowledgements\n----------------\n\nI'd like to thank my friends, `Lucas Silva`_ and David Pires, for all the help and encouragement to \nlearn python and software development. Without them, I'd hardly have found so much fun coding and\nthis project would never came to be. I also thank `Marcelo Reis`_ for the help naming this library :D\n\n.. _Marcelo Reis: https://github.com/msreis\n.. _Lucas Silva: https://github.com/LucasSilvaFerreira\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/varnion/genial", "keywords": "", "license": "BSD", "maintainer": "", "maintainer_email": "", "name": "genial", "package_url": "https://pypi.org/project/genial/", "platform": "", "project_url": "https://pypi.org/project/genial/", "project_urls": { "Homepage": "https://github.com/varnion/genial" }, "release_url": "https://pypi.org/project/genial/0.1.0a1/", "requires_dist": [ "numpy", "pandas", "python-magic (>=0.4.12)" ], "requires_python": "", "summary": "GENome Interactive Annotation Library", "version": "0.1.0a1" }, "last_serial": 2510274, "releases": { "0.1.0a1": [ { "comment_text": "", "digests": { "md5": "53793e77dbc3f52c83906d936cf0e000", "sha256": "4efd1c7ee7da3ba496bbf137d41108834f5848078c8b013930487415f3991a25" }, "downloads": -1, "filename": "genial-0.1.0a1-py3-none-any.whl", "has_sig": false, "md5_digest": "53793e77dbc3f52c83906d936cf0e000", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 20305, "upload_time": "2016-12-10T04:23:14", "url": "https://files.pythonhosted.org/packages/4b/50/f994c87b7cbb1ebdc12215f37a35c0599e1d7f47274e83babcf339cc4b01/genial-0.1.0a1-py3-none-any.whl" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "53793e77dbc3f52c83906d936cf0e000", "sha256": "4efd1c7ee7da3ba496bbf137d41108834f5848078c8b013930487415f3991a25" }, "downloads": -1, "filename": "genial-0.1.0a1-py3-none-any.whl", "has_sig": false, "md5_digest": "53793e77dbc3f52c83906d936cf0e000", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 20305, "upload_time": "2016-12-10T04:23:14", "url": "https://files.pythonhosted.org/packages/4b/50/f994c87b7cbb1ebdc12215f37a35c0599e1d7f47274e83babcf339cc4b01/genial-0.1.0a1-py3-none-any.whl" } ] }