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code analysis for genes

Project description


  • Qt4

Qt4 (Mac OS X)

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

$ ruby -e "$(curl -fsSL"

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 genecoder
$ -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.

Mac OS X users can be installed via Homebrew:

$ brew install pyenv-virtualenv

How to construct an environment:

$ git clone
$ 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


$ python test

Sometimes, the following commands are needed:

$ -install
$ pyenv rehash

Qt creator’s user-interface (*.ui) can be converted to python code as follows:

$ pyside-uic -o 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]




add auto ext recognition


add –compress option


change results-header of distance mode


fix csv2fasta mode


fix csv2fasta mode


update support coders


fix list mode


first version

Project details

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genecoder-1.1.1.tar.gz (1.6 MB view hashes)

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