genecoder 1.0.0

code analysis for genes

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)"

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 install git+https://github.com/kerug/genecoder.git
$ pyside_postinstall.py -install

Usage examples

Calculate RC distance:

$ genecoder distance --coder bch_n3_1 --coder bch_n3_2 -gf4 ATGC --seq label1:ATGCATGCATGC --output [result]
$ genecoder --all --gf4all --input [FASTA]

Survival analysis:

$ genecoder stat --graph --coder bch_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.

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

Changes

1.0.0

first version