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kmerGodel

The aim of the project is to create a dictionary of all k-mers within an input file, count their multiplicities, calculate their godel numbers and use them as features to create data matrices.

Inputs

The input of the project should be a single .fasta file.

Run command from terminal

cd localmachine/path/to/kmerGodel
python run.py kmin kmax /localmachine/path/to/input_file.fasta

Clarifications

  1. localmachine/path/to/kmerGodel : the full path of the local repository
  2. kmin and kmax are integers
  3. localmachine/path/to/input_file.fasta: the full path of the input .fasta file within your local machine

Singularity definition file folder

Inside the folder there is a .def file that creates a singularity image file for the project. There is also a README file with instructions on how to create and run it.