dinaghiassian/diamond

DIseAse MODule identification algorithim

DIAMOnD

DIAMOnD.py runs the DIAMOnD algorithm as described in

A DIseAse MOdule Detection (DIAMOnD) Algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the Human Interactome. PlOS Comp Bio (in press), 2015.

by Susan Dina Ghiassian, Joerg Menche & Albert-Laszlo Barabasi

The DIAMOnD website can be found at:

Instruction to use the source code:

1. Download the code.
2. Make sure you are in the main directory where the code is.
3. Run the following.
   

   python3 DIAMOnD.py  network_file seed_file  n  alpha(optional)  outfile_name(optional)

-------------------

Directory Example

contains two input files:

1. seed_genes.txt (list of genes associated with a phenotype of interest)
2. PPI.txt (Protein-protein interaction network. note that gene IDs should be consistent in the two input files)
   The following command will generate the first 100 DIAMOnD nodes and save them in a file)
   

   python3  DIAMOnD.py  Example/PPI.txt  Example/seed_genes.txt  100

diamond's Issues

Running from ipython/command line

Hi,

the code runs fine with the presented syntax:
run DIAMOnD.py x y 10

when entered in ipython/spyder. When called from CMD using os.system, the code runs, but I have no access to the output of DIAMOnD.py, e.g. added_nodes to a network.
I would like to call the algorithm from within another script, but struggle to provide the right arguments (just running above line works, when entered with another line of code, it stops). Any help would be appreciated!

Compatibility Python 3.8 + KeyError : 'nix'

Hi, I'm using the code for an. important research. I've tried firstly to update it for the 3.8 version of python (I don't know if I did it correctly), then i constantly get the same error which is KeyError : 'nix'. Strangely i get this mistakes while working with my seeds samples and PPI files, while the examples one you provided work just fine.
DIAMOnD3.py.zip
I'm attaching the file I created