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/*****************************************************************
* @LICENSE@
*****************************************************************/
/* seqstat_main.c
* Wed Aug 10 15:47:14 1994
*
* Look at a sequence file, determine some simple statistics.
* CVS $Id: seqstat_main.c,v 1.13 2004/06/16 14:43:01 eddy Exp $
*/
#include "squidconf.h"
#include <stdio.h>
#include <string.h>
#include <limits.h>
#include <ctype.h>
#include "squid.h"
#include "msa.h"
static char banner[] = "seqstat - show some simple statistics on a sequence file";
static char usage[] = "\
Usage: seqstat [-options] <seqfile>\n\
Available options:\n\
-a : report per-sequence info, not just a summary\n\
-h : help; display usage and version\n\
";
static char experts[] = "\
--gccomp : with -a, include GC composition in report (DNA/RNA only)\n\
--informat <s> : specify sequence file format <s>\n\
--quiet : suppress verbose header (used in regression testing)\n\
";
static struct opt_s OPTIONS[] = {
{ "-a", TRUE, sqdARG_NONE },
{ "-h", TRUE, sqdARG_NONE },
{ "--gccomp", FALSE, sqdARG_NONE },
{ "--informat", FALSE, sqdARG_STRING },
{ "--quiet", FALSE, sqdARG_NONE },
};
#define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s))
static float gc_composition(char *seq);
int
main(int argc, char **argv)
{
char *seqfile; /* name of sequence file */
SQFILE *dbfp; /* open sequence file */
int fmt; /* format of seqfile */
char *seq; /* sequence */
SQINFO sqinfo; /* extra info about sequence */
int nseqs;
long long small; /* smallest length */
long long large; /* largest length */
long long total; /* total length */
int type; /* kAmino, kDNA, kRNA, or kOtherSeq */
int allreport; /* TRUE to do a short table for each sequence */
int be_quiet; /* TRUE to suppress header */
int do_gccomp; /* TRUE to include GC composition in per-seq report */
float gc; /* fractional gc composition, 0..1 */
char *optname;
char *optarg;
int optind;
/***********************************************
* Parse command line
***********************************************/
fmt = SQFILE_UNKNOWN; /* default: autodetect format */
allreport = FALSE; /* default: file summary only */
be_quiet = FALSE; /* show header info by default */
type = kOtherSeq; /* just to silence gcc uninit warning */
do_gccomp = FALSE;
while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage,
&optind, &optname, &optarg))
{
if (strcmp(optname, "-a") == 0) allreport = TRUE;
else if (strcmp(optname, "--quiet") == 0) be_quiet = TRUE;
else if (strcmp(optname, "--gccomp") == 0) do_gccomp = TRUE;
else if (strcmp(optname, "--informat") == 0) {
fmt = String2SeqfileFormat(optarg);
if (fmt == SQFILE_UNKNOWN)
Die("unrecognized sequence file format \"%s\"", optarg);
}
else if (strcmp(optname, "-h") == 0) {
SqdBanner(stdout, banner);
puts(usage);
puts(experts);
exit(EXIT_SUCCESS);
}
}
if (argc - optind != 1) Die("%s\n", usage);
seqfile = argv[argc-1];
if (! be_quiet) SqdBanner(stdout, banner);
/* Try to work around inability to autodetect from a pipe or .gz:
* assume FASTA format
*/
if (fmt == SQFILE_UNKNOWN &&
(Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0))
fmt = SQFILE_FASTA;
/***********************************************
* Read the file.
***********************************************/
if ((dbfp = SeqfileOpen(seqfile, fmt, NULL)) == NULL)
Die("Failed to open sequence file %s for reading", seqfile);
if (allreport) {
printf(" %-15s %-5s %s%s\n", " NAME", "LEN",
do_gccomp? " f_GC " : "",
"DESCRIPTION");
printf(" --------------- ----- %s-----------\n",
do_gccomp ? "----- " : "");
}
nseqs = 0;
small = -1;
large = -1;
total = 0L;
while (ReadSeq(dbfp, dbfp->format, &seq, &sqinfo))
{
if (nseqs == 0) type = Seqtype(seq);
if (do_gccomp) gc = gc_composition(seq);
if (allreport) {
if (do_gccomp) {
printf("* %-15s %5d %.3f %-50.50s\n", sqinfo.name, sqinfo.len,
gc,
sqinfo.flags & SQINFO_DESC ? sqinfo.desc : "");
} else {
printf("* %-15s %5d %-50.50s\n", sqinfo.name, sqinfo.len,
sqinfo.flags & SQINFO_DESC ? sqinfo.desc : "");
}
}
if (small == -1 || sqinfo.len < small) small = (long long) sqinfo.len;
if (large == -1 || sqinfo.len > large) large = (long long) sqinfo.len;
total += (long long) sqinfo.len;
nseqs++;
FreeSequence(seq, &sqinfo);
}
if (allreport) puts("");
printf("Format: %s\n", SeqfileFormat2String(dbfp->format));
printf("Type (of 1st seq): ");
switch (type)
{
case kDNA: puts("DNA"); break;
case kRNA: puts("RNA"); break;
case kAmino: puts("Protein"); break;
case kOtherSeq: puts("Unknown"); break;
default: Die("oops.");
}
printf("Number of sequences: %d\n", nseqs);
printf("Total # residues: %lld\n", total);
printf("Smallest: %lld\n", small);
printf("Largest: %lld\n", large);
printf("Average length: %.1f\n", (float) total / (float) nseqs);
SeqfileClose(dbfp);
return 0;
}
/* Function: gc_composition()
* Date: SRE, Mon Apr 23 10:01:48 2001 [St. Louis]
*
* Purpose: Calculate the fractional GC composition of
* an input RNA or DNA sequence. Deals appropriately
* with IUPAC degeneracy. Case-insensitive.
* Ignores gap symbols. Other unexpected characters
* make it die with an error (protein, for instance).
*
* Args: seq - the DNA or RNA sequence
*
* Returns: fractional GC composition, 0-1
*/
static float
gc_composition(char *seq)
{
int c;
float total;
float gc;
gc = total = 0.;
for (; *seq != '\0'; seq++)
{
c = toupper((int) *seq);
if (isgap(c)) continue;
total += 1.0;
switch (c) {
case 'C':
case 'G':
case 'S': gc += 1.0; break;
case 'A':
case 'T':
case 'U':
case 'W': gc += 0.0; break;
case 'N':
case 'R':
case 'Y':
case 'M':
case 'K': gc += 0.5; break;
case 'H':
case 'D': gc += 0.3333; break;
case 'B':
case 'V': gc += 0.6667; break;
default:
Die("unrecognized nucleic acid character %c in sequence", c);
}
}
return (gc/total);
}
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