MQ2 0.1.2

MQ² aims at extracting and find QTLs from MapQTL output

Author:

Pierre-Yves Chibon <[e-mail]>, <[e-mail]>

A simple python module to process output from MapQTL analysis.

Assuming one QTL per linkage group and using the LOD threshold set by the user. This application extracts all the QTLs detected by MapQTL, using the JoinMap map file, it finds the closest marker and finally put the number of QTLs found for each marker on the map.

This approach quickly allows you to find potential QTL hotspot in your dataset. This is particularly usefull for large QTL analysis on a large number of traits.

Get this project:

Sources: https://github.com/PBR/MQ2

Release: http://pypi.python.org/packages/source/M/MQ2/MQ2-0.1.0.tar.gz

Run it on the web at: http://www.plantbreeding.wur.nl/mq2

Dependencies:

• python (2.5 minimum)

Install the project:

There are two ways to install this project:

From the sources

• clone the source

git clone https://github.com/PBR/MQ2.git

• Enter the folder and run the setup.py script

cd MQ2
sudo python setup.py install

From pypi

• Download and install the project from pypi

easy_install MQ2

Run the project:

To run the project, simply run the MQ2 script provided.

See MQ2 --help or MQ2 -h for the different argument available.

Testing:

This project contains unit-tests allowing you to check if the code behaves as it should.

To run them, two ways, either:

nosetests

from the MQ2 folder, or:

python test.py

within the test folder

License:

This project is licensed GPLv3+.