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/* trace_test.c
* Mon Feb 2 07:57:47 1998
*
* Test driver for Viterbi tracebacks.
*
* CVS $Id: trace_test.c,v 1.8 2003/10/04 18:26:49 eddy Exp $
*/
#include "config.h"
#include <stdio.h>
#include <string.h>
#include <time.h>
#include <math.h>
#include "structs.h"
#include "funcs.h"
#include "globals.h"
#include "squid.h"
static char banner[] = "\
trace_test : testing of Plan7 Viterbi traceback code";
static char usage[] = "\
Usage: trace_test [-options]\n\
Available options are:\n\
-h : help; display this usage info\n\
-v : be verbose\n\
";
static char experts[] = "\
--hmm <f> : use HMM in file <f>\n\
--seq <f> : use seq(s) in file <f>\n\
--small : run P7SmallViterbi()\n\
\n";
static struct opt_s OPTIONS[] = {
{ "-h", TRUE, sqdARG_NONE },
{ "-v", TRUE, sqdARG_NONE },
{ "--hmm", FALSE, sqdARG_STRING },
{ "--seq", FALSE, sqdARG_STRING },
{ "--small", FALSE, sqdARG_NONE },
};
#define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s))
int
main(int argc, char **argv)
{
char *hmmfile; /* file to read HMM(s) from */
HMMFILE *hmmfp; /* opened hmmfile for reading */
char *seqfile; /* file to read target sequence(s) from */
SQFILE *sqfp; /* opened seqfile for reading */
char *seq; /* target sequence */
SQINFO sqinfo; /* optional info for seq */
unsigned char *dsq; /* digitized target sequence */
struct plan7_s *hmm; /* HMM to search with */
struct dpmatrix_s *mx; /* reusable, growable DP matrix */
struct p7trace_s *tr; /* traceback */
int nseq;
float sc;
int be_verbose;
int do_small; /* TRUE to invoke P7SmallViterbi */
char *optname; /* name of option found by Getopt() */
char *optarg; /* argument found by Getopt() */
int optind; /* index in argv[] */
/***********************************************
* Parse command line
***********************************************/
be_verbose = FALSE;
hmmfile = "trace_test.hmm";
seqfile = "trace_test.seq";
do_small = FALSE;
while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage,
&optind, &optname, &optarg)) {
if (strcmp(optname, "-v") == 0) be_verbose = TRUE;
else if (strcmp(optname, "--hmm") == 0) hmmfile = optarg;
else if (strcmp(optname, "--seq") == 0) seqfile = optarg;
else if (strcmp(optname, "--small") == 0) do_small = TRUE;
else if (strcmp(optname, "-h") == 0) {
HMMERBanner(stdout, banner);
puts(usage);
puts(experts);
exit(0);
}
}
if (argc - optind != 0)
Die("Incorrect number of arguments.\n%s\n", usage);
/***********************************************
* Open test sequence file
***********************************************/
if ((sqfp = SeqfileOpen(seqfile, SQFILE_UNKNOWN, "BLASTDB")) == NULL)
Die("Failed to open sequence database file %s\n%s\n", seqfile, usage);
/***********************************************
* Open HMM file
* Read a single HMM from it. (Config HMM, if necessary).
***********************************************/
if ((hmmfp = HMMFileOpen(hmmfile, NULL)) == NULL)
Die("Failed to open HMM file %s\n%s", hmmfile, usage);
if (!HMMFileRead(hmmfp, &hmm))
Die("Failed to read any HMMs from %s\n", hmmfile);
if (hmm == NULL)
Die("HMM file %s corrupt or in incorrect format? Parse failed", hmmfile);
P7Logoddsify(hmm, TRUE);
/***********************************************
* Search HMM against each sequence
***********************************************/
nseq = 0;
mx = CreatePlan7Matrix(1, hmm->M, 25, 0);
while (ReadSeq(sqfp, sqfp->format, &seq, &sqinfo))
{
nseq++;
dsq = DigitizeSequence(seq, sqinfo.len);
if (do_small) sc = P7SmallViterbi(dsq, sqinfo.len, hmm, mx, &tr);
else sc = P7Viterbi(dsq, sqinfo.len, hmm, mx, &tr);
if (be_verbose)
{
printf("test sequence %d: score %.1f : %s %s\n",
nseq, sc, sqinfo.name,
sqinfo.flags & SQINFO_DESC ? sqinfo.desc : "");
P7PrintTrace(stdout, tr, hmm, dsq);
}
if (! TraceVerify(tr, hmm->M, sqinfo.len))
Die("Trace verify failed on seq #%d, %s\n", nseq, sqinfo.name);
FreeSequence(seq, &sqinfo);
P7FreeTrace(tr);
free(dsq);
}
FreePlan7Matrix(mx);
FreePlan7(hmm);
HMMFileClose(hmmfp);
SeqfileClose(sqfp);
return EXIT_SUCCESS;
}
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