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README file for pySCA
03.2015
Copyright (C) 2015 Olivier Rivoire, Rama Ranganathan, Kimberly Reynolds
This program is free software distributed under the BSD 3-clause
license, please see the file LICENSE for details. #############################################################
The current version of the Statistical Coupling Analysis (SCA) analysis is implemented in python. This directory contains the necessary code for running the SCA calculations, as well examples/tutorials for the dihydrofolate reductase (DHFR) enzyme family, the S1A serine proteases, the small G-protein family and the Beta-lactamase enzyme family. The tutorials are distributed as iPython notebooks; for details please see: http://ipython.org/notebook.html
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For installation instructions, and an introduction to using the toolbox, please see:
https://github.com/reynoldsk/pySCA
or open the html files included with the pySCA distribution in a browser:
html_docs/index.html
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Contents
Inputs/ : Directory containing input files (including those needed for the tutorials)
Outputs/ : Directory for output files (empty at install)
html_docs/ : Directory containing html documentation
annotate_MSA.py : Python script that annotates alignments with phylogenetic/taxonomic information
scaProcessMSA.py : Python script that conducts some initial processing of the sequence alignment
scaCore.py : Python script that runs the core SCA calculations
scaSectorID.py : Python script that defines sectors given the results of the calculations in scaCore
scaTools.py : The SCA toolbox - contains all functions needed for the SCA calculations
SCA_DHFR.ipynb : Python notebook example for DHFR
SCA_G.ipynb : Python notebook example for the small G proteins
SCA_betalactamase.ipynb: Python notebook example for the beta-lactamases
SCA_S1A.ipynb : Python notebook example for the S1A serine protease #############################################################