code analysis for genes
Project description
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]
Changes
1.0.0
first version
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