2.4 Network analysis

dyno_4_networks.py will read the J-matrix -j and using cluster leading eigenvector algorithm will identify communities of residues. All residues with 0 J-scores will be filtered out for this analysis.

input options:

  -j FJMAT, --fjmat FJMAT J-matrix file
  -g FGML, --fgml FGML  GML file with network data
  -e FEVC, --fevc FEVC  Output file with eigenvector centrality scores of the community graphs
  -o FSTATS, --fstats FSTATS Output file with data by residue
  -v NVEC, --nvec NVEC  Pick the column for network analysis, default is 4. 
                        2: Coevolution Score; 
                        3: Scaled coevolution score; 
                        4: J-score for vector 1; 
                        5 onwards is J-score for vector 2 and so on... 

sample usage:

dyno_4_networks.py -j jmatrix.txt -q 0.8 -o label -v 4