Metadata-Version: 1.1
Name: genecoder
Version: 1.1.1
Summary: code analysis for genes
Home-page: https://github.com/kerug/genecoder
Author: kerug
Author-email: keru.work@gmail.com
License: MIT
Description: ==========================================================
        genecoder: Code analyzer for the coding region of a gene.
        ==========================================================
        
        .. image:: https://travis-ci.org/kerug/genecoder.svg
            :target: https://travis-ci.org/kerug/genecoder
        
        
        Requirements
        ============
        
        - Qt4
        
        Qt4 (Mac OS X)
        --------------
        
        Install Qt4 via Homebrew is recommended. Install Homebrew_ is as follows:
        
        ::
        
            $ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
        
        .. _Homebrew: http://brew.sh/
        
        
        Install Qt4 is as follows:
        
        ::
        
            $ brew install qt
        
        Qt4 (Ubuntu)
        ------------
        
        ::
        
            $ sudo apt-get install libqt4-dev
        
        How to install
        ==============
        
        The genecoder can be installed via pip_.
        
        .. _pip: https://pip.pypa.io/en/latest/installing.html
        
        ::
        
            $ pip install genecoder
            $ pyside_postinstall.py -install
        
        Usage examples
        ==============
        
        Calculate RC distance:
        
        
        ::
        
            $ genecoder distance --coder n3_1 --coder n3_2 -gf4 ATGC --seq label1:ATGCATGCATGC --output [result]
            $ genecoder --all --gf4all --input [FASTA]
        
        Survival analysis:
        
        ::
        
            $ genecoder stat --graph --coder n3_1 --outdir [result_dir] --input [tp53 database file]
        
        
        The results are stored in ``result_dir`` folder.
        
        
        Generate FASTA file from csv database:
        
        ::
        
            $ genecoder csv2fasta <idx_name> <idx_seq> [<length>] [--input=<csv>] [--output=<output>]
        
        Use GUI:
        
        ::
        
            $ genecoder gui
        
        Show help:
        
        ::
        
            $ genecoder -h
        
        Show support coders:
        
        ::
        
            $ genecoder list
        
        
        TP53 database file format
        =========================
        
        TP53 database is a CSV(Comma-Separated Values) format file.
        Columns should be the followings:
        
        - mutation_id
        - seq_category
        - region_name
        - seq_na
        - RFS(months)
        - RFS(event)
        - OS(months)
        - OS(event)
        
        
        How to develop
        ==============
        
        Developers should use pyenv_ and `pyenv-virtualenv`_.
        
        .. _pyenv: https://github.com/yyuu/pyenv
        .. _pyenv-virtualenv: https://github.com/yyuu/pyenv-virtualenv
        
        Mac OS X users can be installed via Homebrew:
        
        ::
        
            $ brew install pyenv-virtualenv
        
        
        How to construct an environment:
        
        ::
        
            $ git clone https://github.com/kerug/genecoder.git
            $ cd genecoder
        
            $ pyenv install 2.7.5
            $ pyenv install 3.4.1
            $ pyenv virtualenv 2.7.5 genecoder-2.7.5
            $ pyenv virtualenv 3.4.1 genecoder-3.4.1
            $ pyenv local genecoder-2.7.5 genecoder-3.4.1
        
            $ pip install -r test-requirements.txt
            $ pip3 install -r test-requirements.txt
        
        
        Tests for Python 2 & 3:
        
        ::
        
            $ tox
        
        
        Alternatively,
        
        ::
        
            $ python setup.py test
        
        
        Sometimes, the following commands are needed:
        
        ::
        
            $ pyside_postinstall.py -install
            $ pyenv rehash
        
        
        Qt creator's user-interface (\*.ui) can be converted to python code as follows:
        
        ::
        
            $ pyside-uic -o mainwindow.py mainwindow.ui
        
        
        References
        ==========
        
        - Sato Keiko, Toshihide Hara, and Masanori Ohya. "The code structure of the p53 DNA-binding domain
          and the prognosis of breast cancer patients." Bioinformatics 29.22 (2013): 2822-2825. [Link_]
        - http://theory.cs.uvic.ca/gen/poly.html
        
        .. _Link: http://www.ncbi.nlm.nih.gov/pubmed/23986567
        
        Changes
        =======
        1.1.1
        -----
        add auto ext recognition
        
        1.1.0
        -----
        add --compress option
        
        1.0.5
        -----
        change results-header of distance mode
        
        1.0.4
        -----
        fix csv2fasta mode
        
        1.0.3
        -----
        fix csv2fasta mode
        
        1.0.2
        -----
        update support coders
        
        1.0.1
        -----
        fix list mode
        
        1.0.0
        -----
        first version
        
Keywords: analyze gene
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
