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/*****************************************************************
* @LICENSE@
*****************************************************************/
/* main for compalign
*
* Compalign -- a program to compare two sequence alignments
* SRE, Tue Nov 3 07:38:03 1992
* RCS $Id: compalign_main.c,v 1.6 2003/04/14 16:00:16 eddy Exp $
*
* incorporated into SQUID, Thu Jan 26 16:52:41 1995
*
* Usage: compalign <trusted-alignment> <test-alignment>
*
* Calculate the fractional "identity" between the trusted alignment
* and the test alignment. The two files must contain exactly the same
* sequences, in exactly the same order.
*
* The identity of the multiple sequence alignments is defined as
* the averaged identity over all N(N-1)/2 pairwise alignments.
*
* The fractional identity of two sets of pairwise alignments
* is in turn defined as follows (for aligned known sequences k1 and k2,
* and aligned test sequences t1 and t2):
*
* matched columns / total columns,
*
* where total columns = the total number of columns in
* which there is a valid (nongap) symbol in k1 or k2;
*
* matched columns = the number of columns in which one of the
* following is true:
*
* k1 and k2 both have valid symbols at a given column; t1 and t2
* have the same symbols aligned in a column of the t1/t2
* alignment;
*
* k1 has a symbol aligned to a gap in k2; that symbol in t1
* is also aligned to a gap;
*
* k2 has a symbol aligned to a gap in k1; that symbol in t2
* is also aligned to a gap.
*
* Because scores for all possible pairs are calculated, the
* algorithm is of order (N^2)L for N sequences of length L;
* large sequence sets will take a while.
*
* Sean Eddy, Tue Nov 3 07:46:59 1992
*
*/
#include "squidconf.h"
#include <stdio.h>
#include <string.h>
#include "squid.h"
#include "msa.h"
static char banner[] = "compalign - compare two multiple alignments";
static char usage[] = "\
Usage: compalign [-options] <trusted.ali> <test.ali>\n\
Available options:\n\
-c : only compare under marked #=CS consensus structure\n\
-h : print short help and usage info\n\
";
static char experts[] = "\
--informat <s> : specify that both alignments are in format <s> (MSF, for instance)\n\
--quiet : suppress verbose header (used in regression testing)\n\
";
struct opt_s OPTIONS[] = {
{ "-c", TRUE, sqdARG_NONE },
{ "-h", TRUE, sqdARG_NONE },
{ "--informat", FALSE, sqdARG_STRING },
{ "--quiet", FALSE, sqdARG_NONE },
};
#define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s))
int
main(int argc, char **argv)
{
char *kfile; /* name of file of trusted (known) alignment */
char *tfile; /* name of file of test alignment */
MSAFILE *kfp; /* open ptr into trusted (known) alignfile */
MSAFILE *tfp; /* open ptr into test alignment file */
int format; /* expected format of alignment files */
MSA *kmsa; /* a trusted (known) alignment */
MSA *tmsa; /* a test alignment */
char **kraw; /* dealigned trusted seqs */
char **traw; /* dealigned test sequences */
int idx; /* counter for sequences */
int apos; /* position in alignment */
float score; /* RESULT: score for the comparison */
int cs_only; /* TRUE to compare under #=CS annotation only */
int *ref = NULL; /* init only to silence gcc warning */
int be_quiet; /* TRUE to suppress verbose header */
char *optname;
char *optarg;
int optind;
/***********************************************
* Parse command line
***********************************************/
format = MSAFILE_UNKNOWN;
cs_only = FALSE;
be_quiet = FALSE;
while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage,
&optind, &optname, &optarg))
{
if (strcmp(optname, "-c") == 0) cs_only = TRUE;
else if (strcmp(optname, "--quiet") == 0) be_quiet = TRUE;
else if (strcmp(optname, "--informat") == 0) {
format = String2SeqfileFormat(optarg);
if (format == MSAFILE_UNKNOWN)
Die("unrecognized sequence file format \"%s\"", optarg);
if (! IsAlignmentFormat(format))
Die("%s is an unaligned format, can't read as an alignment", optarg);
}
else if (strcmp(optname, "-h") == 0) {
SqdBanner(stdout, banner);
puts(usage);
puts(experts);
exit(EXIT_SUCCESS);
}
}
if (argc - optind != 2)
Die("Incorrect number of command line arguments.\n%s\n", usage);
kfile = argv[optind++];
tfile = argv[optind];
if (! be_quiet) SqdBanner(stdout, banner);
/***********************************************
* Read in the alignments
* Capable of handling full Stockholm: >1 alignment/file
***********************************************/
if ((kfp = MSAFileOpen(kfile, format, NULL)) == NULL)
Die("Trusted alignment file %s could not be opened for reading", kfile);
if ((tfp = MSAFileOpen(tfile, format, NULL)) == NULL)
Die("Test alignment file %s could not be opened for reading", tfile);
while ((kmsa = MSAFileRead(kfp)) != NULL)
{
if ((tmsa = MSAFileRead(tfp)) == NULL)
Die("Failed to get a test alignment to match with the trusted alignment");
/* test that they're the same! */
if (kmsa->nseq != tmsa->nseq)
Die("files %s and %s do not contain same number of seqs!\n", kfile, tfile);
for (idx = 0; idx < kmsa->nseq; idx++)
{
s2upper(kmsa->aseq[idx]);
s2upper(tmsa->aseq[idx]);
}
/* another sanity check */
for (idx = 0; idx < kmsa->nseq; idx++)
if (strcmp(kmsa->sqname[idx], tmsa->sqname[idx]) != 0)
Die("seqs in %s and %s don't seem to be in the same order\n (%s != %s)",
kfile, tfile, kmsa->sqname[idx], tmsa->sqname[idx]);
/* and *another* sanity check */
DealignAseqs(kmsa->aseq, kmsa->nseq, &kraw);
DealignAseqs(tmsa->aseq, tmsa->nseq, &traw);
for (idx = 0; idx < kmsa->nseq; idx++)
if (strcmp(kraw[idx], traw[idx]) != 0)
Die("raw seqs in %s and %s are not the same (died at %s, number %d)\n",
kfile, tfile, kmsa->sqname[idx], idx);
Free2DArray((void **) kraw, kmsa->nseq);
Free2DArray((void **) traw, tmsa->nseq);
if (cs_only)
{
if (kmsa->ss_cons == NULL)
Die("Trusted alignment %s has no consensus structure annotation\n -- can't use -c!\n",
kfile);
ref = (int *) MallocOrDie (sizeof(int) * kmsa->alen);
for (apos = 0; apos < kmsa->alen; apos++)
ref[apos] = (isgap(kmsa->ss_cons[apos])) ? FALSE : TRUE;
}
/***********************************************
* Compare the alignments, print results
***********************************************/
if (cs_only)
score = CompareRefMultAlignments(ref, kmsa->aseq, tmsa->aseq, kmsa->nseq);
else
score = CompareMultAlignments(kmsa->aseq, tmsa->aseq, kmsa->nseq);
printf("Trusted alignment: %s\n", kmsa->name != NULL ? kmsa->name : kfile);
printf("Test alignment: %s\n", tmsa->name != NULL ? tmsa->name : tfile);
printf("Total sequences: %d\n", kmsa->nseq);
printf("Alignment identity: %.4f\n", score);
puts("//");
if (cs_only) free(ref);
MSAFree(kmsa);
MSAFree(tmsa);
}
MSAFileClose(kfp);
MSAFileClose(tfp);
return 0;
}
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