/* Function: PAMPrior()
*
* Purpose: Produces an ad hoc "Dirichlet mixture" prior for
* match emissions, using a PAM matrix.
*
* Side effect notice: PAMPrior() replaces the match
* emission section of an existing Dirichlet prior,
* which is /expected/ to be a simple one-component
* kind of prior. The insert emissions /must/ be a
* one-component prior (because of details in how
* PriorifyEmissionVector() is done). However,
* the transitions /could/ be a mixture Dirichlet prior
* without causing problems. In other words, the
* -p and -P options of hmmb can coexist, but there
* may be conflicts. PAMPrior() checks for these,
* so there's no serious problem, except that the
* error message from PAMPrior() might be confusing to
* a user.
*/
void
PAMPrior(char *pamfile, struct p7prior_s *pri, float wt)
{
FILE *fp;
char *blastpamfile; /* BLAST looks in aa/ subdirectory of BLASTMAT */
int **pam;
float scale;
int xi, xj;
int idx1, idx2;
if (Alphabet_type != hmmAMINO)
Die("PAM prior is only valid for protein sequences");
if (pri->strategy != PRI_DCHLET)
Die("PAM prior may only be applied over an existing Dirichlet prior");
if (pri->inum != 1)
Die("PAM prior requires that the insert emissions be a single Dirichlet");
if (MAXDCHLET < 20)
Die("Whoa, code is misconfigured; MAXDCHLET must be >= 20 for PAM prior");
blastpamfile = FileConcat("aa", pamfile);
if ((fp = fopen(pamfile, "r")) == NULL &&
(fp = EnvFileOpen(pamfile, "BLASTMAT", NULL)) == NULL &&
(fp = EnvFileOpen(blastpamfile, "BLASTMAT", NULL)) == NULL)
Die("Failed to open PAM scoring matrix file %s", pamfile);
if (! ParsePAMFile(fp, &pam, &scale))
Die("Failed to parse PAM scoring matrix file %s", pamfile);
fclose(fp);
free(blastpamfile);
pri->strategy = PRI_PAM;
pri->mnum = 20;
/* Convert PAM entries back to conditional prob's P(xj | xi),
* which we'll use as "pseudocounts" weighted by wt.
*/
for (xi = 0; xi < Alphabet_size; xi++)
for (xj = 0; xj < Alphabet_size; xj++)
{
idx1 = Alphabet[xi] - 'A';
idx2 = Alphabet[xj] - 'A';
pri->m[xi][xj] = aafq[xj] * exp((float) pam[idx1][idx2] * scale);
}
/* Normalize so that rows add up to wt.
* i.e. Sum(xj) mat[xi][xj] = wt for every row xi
*/
for (xi = 0; xi < Alphabet_size; xi++)
{
pri->mq[xi] = 1. / Alphabet_size;
FNorm(pri->m[xi], Alphabet_size);
FScale(pri->m[xi], Alphabet_size, wt);
}
Free2DArray((void **)pam,27);
}
/* Function: MSAFileOpen()
* Date: SRE, Tue May 18 13:22:01 1999 [St. Louis]
*
* Purpose: Open an alignment database file and prepare
* for reading one alignment, or sequentially
* in the (rare) case of multiple MSA databases
* (e.g. Stockholm format).
*
* Args: filename - name of file to open
* if "-", read stdin
* if it ends in ".gz", read from pipe to gunzip -dc
* format - format of file (e.g. MSAFILE_STOCKHOLM)
* env - environment variable for path (e.g. BLASTDB)
*
* Returns: opened MSAFILE * on success.
* NULL on failure:
* usually, because the file doesn't exist;
* for gzip'ed files, may also mean that gzip isn't in the path.
*/
MSAFILE *
MSAFileOpen(char *filename, int format, char *env)
{
MSAFILE *afp;
afp = MallocOrDie(sizeof(MSAFILE));
if (strcmp(filename, "-") == 0)
{
afp->f = stdin;
afp->do_stdin = TRUE;
afp->do_gzip = FALSE;
afp->fname = sre_strdup("[STDIN]", -1);
afp->ssi = NULL; /* can't index stdin because we can't seek*/
}
#ifndef SRE_STRICT_ANSI
/* popen(), pclose() aren't portable to non-POSIX systems; disable */
else if (Strparse("^.*\\.gz$", filename, 0))
{
char cmd[256];
/* Note that popen() will return "successfully"
* if file doesn't exist, because gzip works fine
* and prints an error! So we have to check for
* existence of file ourself.
*/
if (! FileExists(filename))
Die("%s: file does not exist", filename);
if (strlen(filename) + strlen("gzip -dc ") >= 256)
Die("filename > 255 char in MSAFileOpen()");
sprintf(cmd, "gzip -dc %s", filename);
if ((afp->f = popen(cmd, "r")) == NULL)
return NULL;
afp->do_stdin = FALSE;
afp->do_gzip = TRUE;
afp->fname = sre_strdup(filename, -1);
/* we can't index a .gz file, because we can't seek in a pipe afaik */
afp->ssi = NULL;
}
#endif /*SRE_STRICT_ANSI*/
else
{
char *ssifile;
char *dir;
/* When we open a file, it may be either in the current
* directory, or in the directory indicated by the env
* argument - and we have to construct the SSI filename accordingly.
*/
if ((afp->f = fopen(filename, "r")) != NULL)
{
ssifile = MallocOrDie(sizeof(char) * (strlen(filename) + 5));
sprintf(ssifile, "%s.ssi", filename);
}
else if ((afp->f = EnvFileOpen(filename, env, &dir)) != NULL)
{
char *full;
full = FileConcat(dir, filename);
ssifile = MallocOrDie(sizeof(char) * (strlen(full) + strlen(filename) + 5));
sprintf(ssifile, "%s.ssi", full);
free(dir);
}
else return NULL;
afp->do_stdin = FALSE;
afp->do_gzip = FALSE;
afp->fname = sre_strdup(filename, -1);
afp->ssi = NULL;
/* Open the SSI index file. If it doesn't exist, or
* it's corrupt, or some error happens, afp->ssi stays NULL.
*/
SSIOpen(ssifile, &(afp->ssi));
free(ssifile);
}
/* Invoke autodetection if we haven't already been told what
* to expect.
*/
if (format == MSAFILE_UNKNOWN)
{
if (afp->do_stdin == TRUE || afp->do_gzip)
Die("Can't autodetect alignment file format from a stdin or gzip pipe");
format = MSAFileFormat(afp);
if (format == MSAFILE_UNKNOWN)
Die("Can't determine format of multiple alignment file %s", afp->fname);
}
afp->format = format;
afp->linenumber = 0;
afp->buf = NULL;
afp->buflen = 0;
return afp;
}
/* Function: CP9_HMMFileOpen()
*
* Purpose: Open an HMM file for reading. The file may be either
* an index for a library of HMMs, or an HMM.
*
* Args: hmmfile - name of file
* env - NULL, or environment variable for HMM database.
*
* Return: Valid HMMFILE *, or NULL on failure.
*/
CP9HMMFILE *
CP9_HMMFileOpen(char *hmmfile, char *env)
{
CP9HMMFILE *hmmfp;
unsigned int magic;
char buf[512];
char *ssifile;
char *dir; /* dir name in which HMM file was found */
int status;
hmmfp = (CP9HMMFILE *) MallocOrDie (sizeof(CP9HMMFILE));
hmmfp->f = NULL;
hmmfp->parser = NULL;
hmmfp->is_binary = FALSE;
hmmfp->byteswap = FALSE;
hmmfp->is_seekable= TRUE; /* always; right now, an HMM must always be in a file. */
/* Open the file. Look in current directory.
* If that doesn't work, check environment var for
* a second possible directory (usually the location
* of a system-wide HMM library).
* Using dir name if necessary, construct correct SSI file name.
*/
hmmfp->f = NULL;
hmmfp->ssi = NULL;
if ((hmmfp->f = fopen(hmmfile, "r")) != NULL)
{
ssifile = MallocOrDie(sizeof(char) * (strlen(hmmfile) + 5));
sprintf(ssifile, "%s.ssi", hmmfile);
if ((hmmfp->mode = SSIRecommendMode(hmmfile)) == -1)
Die("SSIRecommendMode() failed");
}
else if ((hmmfp->f = EnvFileOpen(hmmfile, env, &dir)) != NULL)
{
char *full;
full = FileConcat(dir, hmmfile);
ssifile = MallocOrDie(sizeof(char) * (strlen(full) + strlen(hmmfile) + 5));
sprintf(ssifile, "%s.ssi", full);
if ((hmmfp->mode = SSIRecommendMode(full)) == -1)
Die("SSIRecommendMode() failed");
free(full);
free(dir);
}
else return NULL;
/* Open the SSI index file. If it doesn't exist, or it's corrupt, or
* some error happens, hmmfp->ssi stays NULL.
*/
SQD_DPRINTF1(("Opening ssifile %s...\n", ssifile));
SSIOpen(ssifile, &(hmmfp->ssi));
free(ssifile);
/* Initialize the disk offset stuff.
*/
status = SSIGetFilePosition(hmmfp->f, hmmfp->mode, &(hmmfp->offset));
if (status != 0) Die("SSIGetFilePosition() failed");
/* Check for binary or byteswapped binary format
* by peeking at first 4 bytes.
*/
if (! fread((char *) &magic, sizeof(unsigned int), 1, hmmfp->f)) {
CP9_HMMFileClose(hmmfp);
return NULL;
}
rewind(hmmfp->f);
if (magic == vCP9magic) {
hmmfp->parser = CP9_read_bin_hmm;
hmmfp->is_binary = TRUE;
return hmmfp;
}
else if (magic == vCP9swap) {
SQD_DPRINTF1(("Opened an Infernal CP9 HMM binary file [byteswapped]\n"));
hmmfp->parser = CP9_read_bin_hmm;
hmmfp->is_binary = TRUE;
hmmfp->byteswap = TRUE;
return hmmfp;
}
/* else we fall thru; it may be an ASCII file. */
/* If magic looks binary but we don't recognize it, choke and die.
*/
if (magic & 0x80000000) {
Warn("\
%s appears to be a binary but not a CM plan 9 format that we recognize\n\
It may be from HMMER,\n\
or may be a different kind of binary altogether.\n", hmmfile);
CP9_HMMFileClose(hmmfp);
return NULL;
}