{ "info": { "author": "Jaroslaw Surkont", "author_email": "jarek.surkont@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Natural Language :: English", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.4", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Rabifier\n========\n\n.. image:: https://img.shields.io/pypi/v/rabifier.svg\n :target: https://pypi.python.org/pypi/rabifier\n\nRabifier is an automated bioinformatic pipeline for prediction and classification of Rab GTPases. \nFor more detailed description of the pipeline check the references. \nIf you prefer just to browse Rab GTPases in all sequenced Eukaryotic genomes visit `rabdb.org `_.\n\nRabifier is freely distributed under the GNU General Public License, check the LICENCE file for details.\n\nPlease cite our papers if you use Rabifier in your projects.\n\n* Rabifier2: an improved bioinformatic classifier of Rab GTPases. Surkont J, et al.\n* Thousands of Rab GTPases for the Cell Biologist. Diekmann Y, et al. PLoS Comput Biol 7(10): e1002217.\n `doi:10.1371/journal.pcbi.1002217 `_\n\nInstallation\n------------\n\nTo install Rabifier simply run\n\n.. code-block:: bash\n\n pip install rabifier\n\nPython requirements, third party packages and other dependencies\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nRabifier supports Python 2.7 and Python 3.4.\nRabifier was tested only on a GNU/Linux operating system, we are not planning to support other platforms.\n\nRabifier depends on third-party Python libraries:\n\n* biopython (>=1.66)\n* numpy (>=1.10.1)\n* scipy (>=0.16.1)\n\nRabifier uses several bioinformatic tools, which are required for most of the classification stages. \nEnsure that the following programs (or links pointing to them) are available in the system path.\n\n* `HMMER `_ (3.1b1): ``phmmer``, ``hmmbuild``, ``hmmpress``, ``hmmscan``\n* `BLAST+ `_ (2.2.30): ``blastp``\n* `MEME4 `_ (4.10.2): ``meme``, ``mast``\n* `Superfamily `_ (>=1.75): ``superfamily``\n (NOTE: this is a folder containing several Superfamily database files and scripts, see below)\n\nIf you have cloned this repository you need to compile the HMMs of Rab subfamilies using ``hmmpress``, i.e. run\n``hmmpress rabifier/data/rab_subfamily.hmm``\n\nRabifier requires a seed database for Rab classification. A precomputed database is a part of this repository.\nYou can also create the database using ``rabifier-mkdb`` on the raw, manually curated data sets, available in\na seperate repository https://github.com/evocell/rabifier-data.\nThe build process requires additional software.\n\n* `CD-HIT `_ (v4.6.4): ``cd-hit``\n* `PRANK `_ (v.150803): ``prank``\n* `MAFFT `_ (v7.221): ``mafft``\n* `matplotlib `_ (>=1.4.3) (optional)\n\nTo install Superfamily database follow the instructions below (based on the\n`Superfamily website `_).\n\n.. code-block:: bash\n\n # Register at the Superfamily website to get your username and password\n\n # Download files\n mkdir superfamily\n cd superfamily\n wget --http-user USERNAME --http-password PASSWORD -r -np -nd -e robots=off \\\n -R 'index.html*' 'http://supfam.org/SUPERFAMILY/downloads/license/supfam-local-1.75/'\n wget http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.75 -O dir.cla.scop.txt\n wget http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.75 -O dir.des.scop.txt\n\n # Uncompress files\n gzip -d *.gz\n mv hmmlib_1.75 hmmblib\n\n # Make Perl scripts executable\n chmod u+x *.pl\n \n # Build the HMM library\n hmmpress hmmlib\n\n # Create a symbolic link pointing to the database directory e.g. ln -s superfamily $HOME/bin/\n\nUsage\n-----\n\nTo run Rab prediction on protein sequences, save sequences in the\n`FASTA format `_ and run:\n\n.. code-block:: bash\n\n rabifier sequences.fa\n \nFor more options controlling Rabifier behaviour type:\n\n.. code-block:: bash\n\n rabifier -h\n\nBug reports and contributing\n----------------------------\n\nPlease use the `issue tracker `_ to report bugs and suggest improvements.", "description_content_type": null, "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/evocell/rabifier", "keywords": "Rab,classifier,bioinformatics", "license": "GPLv3", 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