bcormut.cpp File Reference

A program to analyze protein sequences for correlated mutations. More...

#include "seq_analysis.h"
#include "rwmolecule.h"
#include "rwimg.h"
#include "utilities.h"
#include "options.h"
#include "timer.h"

Functions
int	main (int argc, char **argv)

Variables
int	verbose
const char *	use []

Detailed Description

A program to analyze protein sequences for correlated mutations.

Author

Bernard Heymann

Date

Created: 19990123

Modified: 20200916

Function Documentation

main()

int main	(	int	argc,
		char **	argv
	)

Variable Documentation

use

const char* use[]

Initial value:

= {
" ",
"Usage: bcormut [options] input.pir output.pir",
"---------------------------------------------",
"Analyzes for correlated mutations in aligned protein sequences.",
"The -cutoff option must be used to do the correlated mutation analysis.",
"All sequence numbers and position numbers start at 1.",
"Sequence numbering is according to the input, including gaps.",
" ",
"Actions:",
"-cutoff 0.3              Correlated mutations: cutoff to report.",
"-limit                   Limit output to reference sequence.",
" ",
"Parameters:",
"-verbose 7               Verbosity of output.",
"-datatype b              Set the output image data type.",
"-reference HUMAN         Reference sequence identifier (substring).",
" ",
"Input:",
"-properties file.star    Property file (default = internal values).",
" ",
"Output:",
"-matrix file.mat         Correlation coefficient matrix.",
"-image file.map          Correlation coefficient matrix as an image.",
" ",
"Examples:",
"bcormut -verbose 7 -cutoff 0.4 -image coeff.map -datatype byte seq.pir",
" ",
NULL
}

verbose

int verbose

extern