Natalie

Introduction

Usage

Usage:
  ./natalie [--help|-h|-help] [-beta num] [-c num] [-d] [-e num] [-g1 str]
     [-g2 str] [-gm str] [-if1 int] [-if2 int] [-ifm int] [-k int] [-l int]
     [-maxSwitches int] [-n int] [-nd int] [-no int] [-ns int] [-o str]
     [-of str] [-op int] [-phi num] [-s int] [-sf int] [-t int] [-tau num]
     [-v|--verbosity int] [-version] [-w]
Where:
  --help|-h|-help
     Print a short help message
  -beta num
     Parameter used in the objective function (default: 1)
  -c num
     Specifies the correlation threshold 
     (only used in conjunction with -ifm 2, default: 0.9)
  -d
     Force binary edge weights
  -e num
     Specifies e value cutoff 
     (only used in conjunction with -ifm 1 and -ifm 2, default: 10)
  -g1 str
     File name of input graph G_1
  -g2 str
     File name of input graph G_2
  -gm str
     File name in which matching edges of G_m are defined;
     if omitted, the complete graph is used
  -if1 int
     Specifies the input file format for G_1:
     0 - GML format
     1 - GraphML format
     2 - STRING format (default)
     3 - LGF format
     4 - CSV format
     5 - LEDA format
  -if2 int
     Specifies the input file format for G_2:
     0 - GML format
     1 - GraphML format
     2 - STRING format (default)
     3 - LGF format
     4 - CSV format
     5 - LEDA format
  -ifm int
     Specifies the input file format for G_m:
     0 - Candidate list
     1 - BLAST (default)
     2 - Co-expression
     3 - LGF
  -k int
     Number of nondecreasing iterations after which
     to update mu (default: 20)
  -l int
     Number of increasing iterations after which
     to update mu (default: 10)
  -maxSwitches int
     Maximum number of switches
     (only used in conjunction with -s 3, default: 3)
  -n int
     Number of iterations to compute (default -1: no limit)
  -nd int
     Number of dual descent steps before switching method
     in the combined solver (default: 100)
  -no int
     Number of outputs to generate (default 1)
  -ns int
     Number of subgradient steps before switching method
     in the combined solver (default: -1; switch when subgradient
     method has converged)
  -o str
     Output file name
  -of str
     Specifies the output file format:
     0 - DOT format
     1 - GML format
     2 - LGF format
     3 - SIF format (default)
     4 - JSON format
     5 - NEATO format
     6 - CSV (matched) format
     7 - CSV (unmatched in G_1) format
     8 - CSV (unmatched in G_2) format
     9 - CSV (alignment) format
  -op int
     Specifies parts of the matching graph to output:
     0 - Nodes and matching edges present in the solution
     1 - Nodes, matching edges and original edges present
         in the solution (default)
     2 - Nodes and matching edges present in the solution
         as well as all original edges
  -phi num
     Parameter phi of dual descent procedure
  -s int
     Specifies the solver to use:
     0 - Subgradient optimization
     1 - Dual descent method
     2 - Enhanced dual descent method
     3 - Combined method (default)
  -sf int
     Specifies the score function to be used:
     0 - Average weights (default)
     1 - Coexpression-based
  -t int
     Time limit in seconds (default -1: no limit)
  -tau num
     Parameter tau of dual descent procedure
  -v|--verbosity int
     Specifies the verbosity level:
     0 - No output
     1 - Only necessary output
     2 - More verbose output (default)
     3 - Debug output
  -version
     Show version number
  -w
     Web server mode

Sample data

References

Download