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        "author": "kerug",
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        "description": "==========================================================\ngenecoder: Code analyzer for the coding region of a gene.\n==========================================================\n\n.. image:: https://travis-ci.org/kerug/genecoder.svg\n    :target: https://travis-ci.org/kerug/genecoder\n\n\nRequirements\n============\n\n- Qt4\n\nQt4 (Mac OS X)\n--------------\n\nInstall Qt4 via Homebrew is recommended. Install Homebrew_ is as follows:\n\n::\n\n    $ ruby -e \"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)\"\n\n.. _Homebrew: http://brew.sh/\n\n\nInstall Qt4 is as follows:\n\n::\n\n    $ brew install qt\n\nQt4 (Ubuntu)\n------------\n\n::\n\n    $ sudo apt-get install libqt4-dev\n\nHow to install\n==============\n\nThe genecoder can be installed via pip_.\n\n.. _pip: https://pip.pypa.io/en/latest/installing.html\n\n::\n\n    $ pip install genecoder\n    $ pyside_postinstall.py -install\n\nUsage examples\n==============\n\nCalculate RC distance:\n\n\n::\n\n    $ genecoder distance --coder n3_1 --coder n3_2 -gf4 ATGC --seq label1:ATGCATGCATGC --output [result]\n    $ genecoder --all --gf4all --input [FASTA]\n\nSurvival analysis:\n\n::\n\n    $ genecoder stat --graph --coder n3_1 --outdir [result_dir] --input [tp53 database file]\n\n\nThe results are stored in ``result_dir`` folder.\n\n\nGenerate FASTA file from csv database:\n\n::\n\n    $ genecoder csv2fasta <idx_name> <idx_seq> [<length>] [--input=<csv>] [--output=<output>]\n\nUse GUI:\n\n::\n\n    $ genecoder gui\n\nShow help:\n\n::\n\n    $ genecoder -h\n\nShow support coders:\n\n::\n\n    $ genecoder list\n\n\nTP53 database file format\n=========================\n\nTP53 database is a CSV(Comma-Separated Values) format file.\nColumns should be the followings:\n\n- mutation_id\n- seq_category\n- region_name\n- seq_na\n- RFS(months)\n- RFS(event)\n- OS(months)\n- OS(event)\n\n\nHow to develop\n==============\n\nDevelopers should use pyenv_ and `pyenv-virtualenv`_.\n\n.. _pyenv: https://github.com/yyuu/pyenv\n.. _pyenv-virtualenv: https://github.com/yyuu/pyenv-virtualenv\n\nMac OS X users can be installed via Homebrew:\n\n::\n\n    $ brew install pyenv-virtualenv\n\n\nHow to construct an environment:\n\n::\n\n    $ git clone https://github.com/kerug/genecoder.git\n    $ cd genecoder\n\n    $ pyenv install 2.7.5\n    $ pyenv install 3.4.1\n    $ pyenv virtualenv 2.7.5 genecoder-2.7.5\n    $ pyenv virtualenv 3.4.1 genecoder-3.4.1\n    $ pyenv local genecoder-2.7.5 genecoder-3.4.1\n\n    $ pip install -r test-requirements.txt\n    $ pip3 install -r test-requirements.txt\n\n\nTests for Python 2 & 3:\n\n::\n\n    $ tox\n\n\nAlternatively,\n\n::\n\n    $ python setup.py test\n\n\nSometimes, the following commands are needed:\n\n::\n\n    $ pyside_postinstall.py -install\n    $ pyenv rehash\n\n\nQt creator's user-interface (\\*.ui) can be converted to python code as follows:\n\n::\n\n    $ pyside-uic -o mainwindow.py mainwindow.ui\n\n\nReferences\n==========\n\n- Sato Keiko, Toshihide Hara, and Masanori Ohya. \"The code structure of the p53 DNA-binding domain\n  and the prognosis of breast cancer patients.\" Bioinformatics 29.22 (2013): 2822-2825. [Link_]\n- http://theory.cs.uvic.ca/gen/poly.html\n\n.. _Link: http://www.ncbi.nlm.nih.gov/pubmed/23986567\n\nChanges\n=======\n1.1.1\n-----\nadd auto ext recognition\n\n1.1.0\n-----\nadd --compress option\n\n1.0.5\n-----\nchange results-header of distance mode\n\n1.0.4\n-----\nfix csv2fasta mode\n\n1.0.3\n-----\nfix csv2fasta mode\n\n1.0.2\n-----\nupdate support coders\n\n1.0.1\n-----\nfix list mode\n\n1.0.0\n-----\nfirst version",
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