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ClassiCOL version 1.0.0

Code and User's Guide

The steps and explanations below will be adapted shortly.

Installation

  1. Download the code in this repository.
  2. Navigate to the download location using the command prompt.
  3. Install the required packages using pip install -r requirements.txt.

Usage

Use the following command to start the algorithm with the demo data:

$ python Classicol.py -d path_to_the_script -l Demo -s MASCOT

You can use the arguments as follows:

  • -l Demo (in case you want to test the algorithm) or the folder location containing your personal Mascot *.csv or MaxQuant *.txt output files
  • -s MASCOT or MaxQuant (specify the search engine used)
  • -t (optional) you can restrict the taxonomy by specifying it, e.g., Pecora or multiple taxonomy Pecora|Primates
  • -m specify the fixed modification used during protein extraction, e.g., C,45.987721 or multiple with C,45.98|M,...
  • -f (optional) location of the folder containing a custom database in fasta format

WARNING_1: First time the algorithm is used it will have to calculate all the protein distances and can take some time. This only needs to be calculated once, as it is saved after calculations making subsequent runs faster.

WARNING_2: The algorithm can use a substantial amount of the available CPU and memory. When not enough is free, there is a chance the algorithm will go into error.