• Python 2.7 or 3.4
• Qt4

Install Qt4 via Homebrew is recommended. Install Homebrew is as follows:

$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Install Qt4 is as follows:

$ brew install qt

$ sudo apt-get install libqt4-dev

The genecoder can be installed via pip.

$ pip install genecoder
$ pyside_postinstall.py -install

If you meet some PySide error, try the following:

$ pip install --find-links=https://kerug.github.io/python-wheelhouse --use-wheel --no-index --pre PySide

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 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)

We recommend pyenv and pyenv-virtualenv enviroments.

These programs are easily installed by using pyenv-installer:

$ curl -L https://raw.githubusercontent.com/yyuu/pyenv-installer/master/bin/pyenv-installer | bash

How to construct an environment:

$ git clone https://github.com/kerug/genecoder.git
$ cd genecoder

$ pyenv install 2.7.8
$ pyenv install 3.4.2
$ pyenv virtualenv 2.7.8 genecoder-2.7.8
$ pyenv virtualenv 3.4.2 genecoder-3.4.2
$ pyenv local genecoder-2.7.8 genecoder-3.4.2

$ pip install --find-links=https://kerug.github.io/python-wheelhouse --use-wheel --no-index --pre PySide
$ pip3 install --find-links=https://kerug.github.io/python-wheelhouse --use-wheel --no-index --pre PySide
$ pyside_postinstall.py -install

$ pip install -r test-requirements.txt
$ pip3 install -r test-requirements.txt

Tests for Python 2 & 3:

$ tox

Now, the tox test is broken because the PySide 1.2 cannot be installed via pip.

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

• 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