IGCexpansion

Gene Conversion Project

Code for IGC inference as described in Ji-Griffing-Thorne 2016 MBE paper is available here. This is the first approach with the smallest possible multi-gene family (only two paralogs).

Data: Yeast (stored in MafftAlignment folder)

Dependent:

jsonctmctree package (powerful likelihood calculation engine by Alex Griffing)

Biopython (you could install it by pip install --user Biopython)

Coding Language: Python 2.7

Instruction of how to run this code:

0, To install python packages, you need to use pip (package management).

1, Install jsonctmctree package:

pip install --user git+https://github.com/argriffing/jsonctmctree.git

2, Install IGCexpansion package:

git clone https://github.com/xji3/JGT_MBE_2016.git

cd JGT_MBE_2016/IGCexpansion

pip install --user . (preferred)

or

python setup.py install (hard to uninstall)

3, Similarly install any other python packages

pip install --user networkx

pip install --user Biopython

4, use Run.py to perform analyses with following example commands:

python Run.py --model MG94 --paralog1 YBL087C --paralog2 YER117W --no-force --no-clock

To uninstall:

pip uninstall IGCexpansion

Some known issues:

1. If you encounter "ValueError: LAPACK function dlange could not be found" when running the code. First, update your scipy packages, it's very likely to be out-dated. You can do this by pip install --user --upgrade numpy scipy If the problem persists, you may solve it by either updating your LAPCK package to atlas or installing an older version of jsonctmctree by the following code:

   pip uninstall jsonctmctree

   pip install --user git+https://github.com/argriffing/jsonctmctree.git@cb1ba60ee2b57d6703cd9a3987000c2fd4dd68a5

2. If you encounter "NotImplementedError: Wrong number or type of arguments for overloaded function 'coo_matvec'". Please update your scipy and numpy packages to the newest versions.

3. If you are using windows operating system, and encountered "numpy.distutils.system_info.NotFoundError: no lapack/blas resources found" when building/upgrading scipy package. Please try Enthought Canopy or Anaconda as suggested Here. They come with built in packages like numpy and scipy.

4. If you encountered "Fatal error in launcher: Unable to create process using ..." when using pip in cmd (windows os). Please try python -m pip install xxx as suggested here.

Contact me at: xji3 at ncsu.edu