/* h2_multiline()
*
* Used to print the command log to HMMER2 ASCII save files.
* H3 records command numbers in brackets, as in "COM [1] hmmbuild ..."
* H2 just records commands, as in "COM hmmbuild ...".
* Compare p7_hmmfile.c::multiline().
*
* Given a record (like the comlog) that contains
* multiple lines, print it as multiple lines with
* a given prefix. e.g.:
*
* given: "COM ", "foo\nbar\nbaz"
* print: COM foo
* COM bar
* COM baz
*
* If <s> is NULL, no-op. Otherwise <s> must be a <NUL>-terminated
* string. It does not matter if it ends in <\n> or not. <pfx>
* must be a valid <NUL>-terminated string; it may be empty.
*
* Args: fp: FILE to print to
* pfx: prefix for each line
* s: line to break up and print; tolerates a NULL
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any write error.
*/
static int
h2_multiline(FILE *fp, const char *pfx, char *s)
{
char *sptr = s;
char *end = NULL;
int n = 0;
do {
end = strchr(sptr, '\n');
if (end != NULL) /* if there's no \n left, end == NULL */
{
n = end - sptr; /* n chars exclusive of \n */
if (fprintf(fp, "%s ", pfx) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed");
if (fwrite(sptr, sizeof(char), n, fp) != n) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed"); /* using fwrite lets us write fixed # of chars */
if (fprintf(fp, "\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed"); /* while writing \n w/ printf allows newline conversion */
sptr += n + 1; /* +1 to get past \n */
}
else
{
if (fprintf(fp, "%s %s\n", pfx, sptr) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed"); /* last line */
}
} while (end != NULL && *sptr != '\0'); /* *sptr == 0 if <s> terminates with a \n */
return eslOK;
}
/* Function: p7_bg_Write()
* Synopsis: Write a <P7_BG> object to a stream in its save file format.
*
* Purpose: Write the residue frequencies of <P7_BG> object <bg> to
* stream <fp> in save file format. Only the residue
* frequencies are written (there are other parts of a
* <P7_BG> object, having to do with the bias filter and
* biased composition score correction.)
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any write error, such as filling the disk.
*/
int
p7_bg_Write(FILE *fp, P7_BG *bg)
{
int x;
if (fprintf(fp, "%s\n", esl_abc_DecodeType(bg->abc->type)) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "bg model write failed");
for (x = 0; x < bg->abc->K; x++)
{ if (fprintf(fp, "%c %.5f\n", bg->abc->sym[x], bg->f[x]) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "bg model write failed"); }
return eslOK;
}
/* Function: esl_mixgev_Plot()
*
* Purpose: Plot some function <func> (for instance, <esl_mixgev_pdf()>)
* for mixture GEV parameters <mg>, for a range of
* quantiles x from <xmin> to <xmax> in steps of <xstep>;
* output to an open stream <fp> in xmgrace XY input format.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any system write error.
*/
int
esl_mixgev_Plot(FILE *fp, ESL_MIXGEV *mg,
double (*func)(double x, ESL_MIXGEV *mg),
double xmin, double xmax, double xstep)
{
double x;
for (x = xmin; x <= xmax; x += xstep)
if (fprintf(fp, "%f\t%g\n", x, (*func)(x, mg)) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "mixgev plot write failed");
if (fprintf(fp, "&\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "mixgev plot write failed");
return eslOK;
}
/* Function: esl_gev_Plot()
*
* Purpose: Plot some GEV function <func> (for instance,
* <esl_gev_pdf()>) for parameters <mu> and <lambda>, for
* a range of quantiles x from <xmin> to <xmax> in steps of <xstep>;
* output to an open stream <fp> in xmgrace XY input format.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any system write error, such as filled disk.
*/
int
esl_gev_Plot(FILE *fp, double mu, double lambda, double alpha,
double (*func)(double x, double mu, double lambda, double alpha),
double xmin, double xmax, double xstep)
{
double x;
for (x = xmin; x <= xmax; x += xstep)
if (fprintf(fp, "%f\t%g\n", x, (*func)(x, mu, lambda, alpha)) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "gev plot write failed");
if (fprintf(fp, "&\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "gev plot write failed");
return eslOK;
}
/* Function: esl_hxp_Plot()
*
* Purpose: Plot some function <func> (for instance, <esl_hxp_pdf()>)
* for hyperexponential parameters <h>, for a range of
* quantiles x from <xmin> to <xmax> in steps of <xstep>;
* output to an open stream <fp> in xmgrace XY input format.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any system write error.
*/
int
esl_hxp_Plot(FILE *fp, ESL_HYPEREXP *h,
double (*func)(double x, ESL_HYPEREXP *h),
double xmin, double xmax, double xstep)
{
double x;
for (x = xmin; x <= xmax; x += xstep)
if (fprintf(fp, "%f\t%g\n", x, (*func)(x, h)) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "hyperexp plot write failed");
if (fprintf(fp, "&\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "hyperexp plot write failed");
return eslOK;
}
/* Function: esl_wei_Plot()
*
* Purpose: Plot some Weibull function <func> (for instance, <esl_wei_pdf()>)
* for Weibull parameters <mu>, <lambda>, and <tau>, for a range of
* quantiles x from <xmin> to <xmax> in steps of <xstep>;
* output to an open stream <fp> in xmgrace XY input format.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any system write error, such as filled disk.
*/
int
esl_wei_Plot(FILE *fp, double mu, double lambda, double tau,
double (*func)(double x, double mu, double lambda, double tau),
double xmin, double xmax, double xstep)
{
double x;
for (x = xmin; x <= xmax; x += xstep)
if (x > mu || tau >= 1.) /* don't try to plot at mu where pdf blows up */
if (fprintf(fp, "%f\t%g\n", x, (*func)(x, mu, lambda, tau)) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "weibull plot write failed");
if (fprintf(fp, "&\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "weibull plot write failed");
return eslOK;
}
/* Function: esl_stopwatch_Display()
*
* Purpose: Output a usage summary line from a stopped
* stopwatch, showing elapsed, cpu, and system time
* between the last calls to
* <esl_stopwatch_Start()> and <esl_stopwatch_Stop()>.
*
* The string <prefix> will be prepended to the output
* line. Use <""> to prepend nothing. If <prefix> is NULL,
* a default <"CPU Time: "> prefix is used.
*
* For <prefix> = <"CPU Time: "> an example output line is:\\
* <CPU Time: 142.55u 7.17s 00:02:29.72 Elapsed: 00:02:35>
*
* Args: fp - output stream
* w - stopped stopwatch
* prefix - output line prefix ("" for nothing)
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any system write error, such as filled disk.
*/
int
esl_stopwatch_Display(FILE *fp, ESL_STOPWATCH *w, char *prefix)
{
char buf[128]; /* (safely holds up to 10^14 years; I'll be dead by then) */
if (prefix == NULL) { if (fputs("CPU Time: ", fp) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "stopwatch display write failed"); }
else { if (fputs(prefix, fp) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "stopwatch display write failed"); }
format_time_string(buf, w->user+w->sys, TRUE);
#ifdef HAVE_TIMES
if (fprintf(fp, "%.2fu %.2fs %s ", w->user, w->sys, buf) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "stopwatch display write failed");
#else
if (fprintf(fp, "%.2fu %s ", w->user, buf) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "stopwatch display write failed");
#endif
format_time_string(buf, w->elapsed, TRUE);
if (fprintf(fp, "Elapsed: %s\n", buf) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "stopwatch display write failed");
return eslOK;
}
static int
output_header(FM_METADATA *meta, FILE *ofp, const ESL_GETOPTS *go, char *fmfile, char *qfile)
{
char *alph;
char *appname = NULL;
int status;
if (meta->alph_type == fm_DNA) alph = "dna";
else if (meta->alph_type == fm_AMINO) alph = "amino";
if ((status = esl_FileTail(go->argv[0], FALSE, &appname)) != eslOK) return status;
if (fprintf(ofp, "# %s :: %s\n", appname, banner) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# %s\n", EASEL_COPYRIGHT) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# %s\n", EASEL_LICENSE) < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# input binary-formatted HMMER database: %s\n", fmfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# input file of query sequences: %s\n", qfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--out")) {
char *outfile = esl_opt_GetString(go, "--out");
if (fprintf(ofp, "# output file containing list of hits: %s\n", (esl_strcmp(outfile, "-") == 0 ? "stdout" : outfile)) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
if (esl_opt_IsUsed(go, "--count_only") && fprintf(ofp, "# output only counts, not hit locations\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# alphabet : %s\n", alph) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# bin_length : %d\n", meta->freq_cnt_b) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# suffix array sample rate: %d\n", meta->freq_SA) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (appname) free(appname);
return eslOK;
ERROR:
if (appname) free(appname);
return status;
}
static int
output_header(const ESL_GETOPTS *go, FILE *ofp, char *alifile, char *postmsafile)
{
p7_banner(ofp, go->argv[0], banner);
if (fprintf(ofp, "# input alignment file: %s\n", alifile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--alirange") || esl_opt_IsUsed(go, "--modelrange") ) {
if (fprintf(ofp, "# output alignment file: %s\n", postmsafile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
if (esl_opt_IsUsed(go, "--alirange") && fprintf(ofp, "# alignment range: %s\n", esl_opt_GetString(go, "--alirange")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--modelrange") && fprintf(ofp, "# model range: %s\n", esl_opt_GetString(go, "--modelrange"))< 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--apendmask") && fprintf(ofp, "# add to existing mask: [on]\n" )< 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--model2ali") && fprintf(ofp, "# ali ranges for model range: %s\n", esl_opt_GetString(go, "--model2ali")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--ali2model") && fprintf(ofp, "# model ranges for ali range: %s\n", esl_opt_GetString(go, "--ali2model")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", esl_opt_GetString(go, "-o")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--amino") && fprintf(ofp, "# input alignment is asserted as: protein\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--dna") && fprintf(ofp, "# input alignment is asserted as: DNA\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--rna") && fprintf(ofp, "# input alignment is asserted as: RNA\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--fast") && fprintf(ofp, "# model architecture construction: fast/heuristic\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--hand") && fprintf(ofp, "# model architecture construction: hand-specified by RF annotation\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--symfrac") && fprintf(ofp, "# sym fraction for model structure: %.3f\n", esl_opt_GetReal(go, "--symfrac")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--fragthresh") && fprintf(ofp, "# seq called frag if L <= x*alen: %.3f\n", esl_opt_GetReal(go, "--fragthresh")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--wpb") && fprintf(ofp, "# relative weighting scheme: Henikoff PB\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--wgsc") && fprintf(ofp, "# relative weighting scheme: G/S/C\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--wblosum") && fprintf(ofp, "# relative weighting scheme: BLOSUM filter\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--wnone") && fprintf(ofp, "# relative weighting scheme: none\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--wid") && fprintf(ofp, "# frac id cutoff for BLOSUM wgts: %f\n", esl_opt_GetReal(go, "--wid")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--seed")) {
if (esl_opt_GetInteger(go, "--seed") == 0 && fprintf(ofp,"# random number seed: one-time arbitrary\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
else if ( fprintf(ofp,"# random number seed set to: %d\n", esl_opt_GetInteger(go, "--seed")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
return eslOK;
}
static int
output_header(FILE *ofp, const ESL_GETOPTS *go)
{
p7_banner(ofp, go->argv[0], banner);
if (esl_opt_IsUsed(go, "--eval2score")) {
if ( fprintf(ofp, "# show score required to reach E-value: %.2g\n", esl_opt_GetReal(go, "-E")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
if (esl_opt_IsUsed(go, "--score2eval")) {
if ( fprintf(ofp, "# show E-value corresponding to score: %.2g\n", esl_opt_GetReal(go, "-S")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
if (esl_opt_IsUsed(go, "--eval2score") || esl_opt_IsUsed(go, "--score2eval")) {
if (esl_opt_IsUsed(go, "--baseZ") ) {
if ( fprintf(ofp, "# using base count (search both strands): %d Mb\n", esl_opt_GetInteger(go, "--baseZ")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
} else if (esl_opt_IsUsed(go, "--baseZ1") ) {
if ( fprintf(ofp, "# using base count (search single strand): %d Mb\n", esl_opt_GetInteger(go, "--baseZ1")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
} else {
if ( fprintf(ofp, "# using database sequence count: %d\n", esl_opt_GetInteger(go, "-Z")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
}
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
return eslOK;
}
/* serial_master()
* The serial version of hmmsearch.
* For each query HMM in <hmmdb> search the database for hits.
*
* A master can only return if it's successful. All errors are handled
* immediately and fatally with p7_Fail().
*/
static int
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
FILE *ofp = stdout; /* output file for results (default stdout) */
FILE *tblfp = NULL; /* output stream for tabular per-seq (--tblout) */
FILE *dfamtblfp = NULL; /* output stream for tabular Dfam format (--dfamtblout) */
FILE *aliscoresfp = NULL; /* output stream for alignment scores (--aliscoresout) */
// P7_HMM *hmm = NULL; /* one HMM query */
// P7_SCOREDATA *scoredata = NULL;
int seqfmt = eslSQFILE_UNKNOWN; /* format of seqfile */
ESL_SQFILE *sqfp = NULL; /* open seqfile */
P7_HMMFILE *hfp = NULL; /* open HMM database file */
ESL_ALPHABET *abc = NULL; /* sequence alphabet */
P7_OPROFILE *om = NULL; /* target profile */
ESL_STOPWATCH *w = NULL; /* timing */
ESL_SQ *qsq = NULL; /* query sequence */
int nquery = 0;
int textw;
int status = eslOK;
int hstatus = eslOK;
int sstatus = eslOK;
int i;
int ncpus = 0;
int infocnt = 0;
WORKER_INFO *info = NULL;
#ifdef HMMER_THREADS
P7_OM_BLOCK *block = NULL;
ESL_THREADS *threadObj= NULL;
ESL_WORK_QUEUE *queue = NULL;
#endif
char errbuf[eslERRBUFSIZE];
double window_beta = -1.0 ;
int window_length = -1;
if (esl_opt_IsUsed(go, "--w_beta")) { if ( ( window_beta = esl_opt_GetReal(go, "--w_beta") ) < 0 || window_beta > 1 ) esl_fatal("Invalid window-length beta value\n"); }
if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")) < 4 ) esl_fatal("Invalid window length value\n"); }
w = esl_stopwatch_Create();
if (esl_opt_GetBoolean(go, "--notextw")) textw = 0;
else textw = esl_opt_GetInteger(go, "--textw");
/* If caller declared an input format, decode it */
if (esl_opt_IsOn(go, "--qformat")) {
seqfmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--qformat"));
if (seqfmt == eslSQFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--qformat"));
}
/* validate options if running as a daemon */
// if (esl_opt_IsOn(go, "--daemon")) {
/* running as a daemon, the input format must be type daemon */
// if (seqfmt != eslSQFILE_UNKNOWN && seqfmt != eslSQFILE_DAEMON)
// esl_fatal("Input format %s not supported. Must be daemon\n", esl_opt_GetString(go, "--qformat"));
// seqfmt = eslSQFILE_DAEMON;
// if (strcmp(cfg->seqfile, "-") != 0) esl_fatal("Query sequence file must be '-'\n");
// }
/* Open the target profile database to get the sequence alphabet */
status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem, trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, cfg->hmmfile, errbuf);
if (! hfp->is_pressed) p7_Fail("Failed to open binary auxfiles for %s: use hmmpress first\n", hfp->fname);
hstatus = p7_oprofile_ReadMSV(hfp, &abc, &om);
if (hstatus == eslEFORMAT) p7_Fail("bad format, binary auxfiles, %s:\n%s", cfg->hmmfile, hfp->errbuf);
else if (hstatus == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile);
else if (hstatus != eslOK) p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile);
p7_oprofile_Destroy(om);
p7_hmmfile_Close(hfp);
/* Open the query sequence database */
status = esl_sqfile_OpenDigital(abc, cfg->seqfile, seqfmt, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n", cfg->seqfile);
else if (status == eslEFORMAT) p7_Fail("Sequence file %s is empty or misformatted\n", cfg->seqfile);
else if (status == eslEINVAL) p7_Fail("Can't autodetect format of a stdin or .gz seqfile");
else if (status != eslOK) p7_Fail("Unexpected error %d opening sequence file %s\n", status, cfg->seqfile);
if (sqfp->format > 100) // breaking the law! That range is reserved for msa, for aligned formats
p7_Fail("%s contains a multiple sequence alignment; expect unaligned sequences, like FASTA\n", cfg->seqfile);
qsq = esl_sq_CreateDigital(abc);
/* Open the results output files */
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
if (esl_opt_IsOn(go, "--dfamtblout")) { if ((dfamtblfp = fopen(esl_opt_GetString(go, "--dfamtblout"),"w")) == NULL) esl_fatal("Failed to open tabular dfam output file %s for writing\n", esl_opt_GetString(go, "--dfamtblout")); }
if (esl_opt_IsOn(go, "--aliscoresout")) { if ((aliscoresfp = fopen(esl_opt_GetString(go, "--aliscoresout"),"w")) == NULL) esl_fatal("Failed to open alignment scores output file %s for writing\n", esl_opt_GetString(go, "--aliscoresout")); }
output_header(ofp, go, cfg->hmmfile, cfg->seqfile);
#ifdef HMMER_THREADS
/* initialize thread data */
if (esl_opt_IsOn(go, "--cpu")) ncpus = esl_opt_GetInteger(go, "--cpu");
else esl_threads_CPUCount(&ncpus);
if (ncpus > 0)
{
threadObj = esl_threads_Create(&pipeline_thread);
queue = esl_workqueue_Create(ncpus * 2);
}
#endif
infocnt = (ncpus == 0) ? 1 : ncpus;
ESL_ALLOC(info, sizeof(*info) * infocnt);
for (i = 0; i < infocnt; ++i)
{
info[i].bg = p7_bg_Create(abc);
#ifdef HMMER_THREADS
info[i].queue = queue;
#endif
}
#ifdef HMMER_THREADS
for (i = 0; i < ncpus * 2; ++i)
{
block = p7_oprofile_CreateBlock(BLOCK_SIZE);
if (block == NULL) esl_fatal("Failed to allocate sequence block");
status = esl_workqueue_Init(queue, block);
if (status != eslOK) esl_fatal("Failed to add block to work queue");
}
#endif
/* Outside loop: over each query sequence in <seqfile>. */
while ((sstatus = esl_sqio_Read(sqfp, qsq)) == eslOK)
{
if (sstatus == eslEMEM) p7_Fail("Memory allocation error reading sequence file\n", status);
if (sstatus == eslEINCONCEIVABLE) p7_Fail("Unexpected error %d reading sequence file\n", status);
// if (qsq->L > NHMMER_MAX_RESIDUE_COUNT) p7_Fail("Input sequence %s in file %s exceeds maximum length of %d bases.\n", qsq->name, cfg->seqfile, NHMMER_MAX_RESIDUE_COUNT);
nquery++;
esl_stopwatch_Start(w);
/* Open the target profile database */
status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, NULL);
if (status != eslOK) p7_Fail("Unexpected error %d in opening hmm file %s.\n", status, cfg->hmmfile);
#ifdef HMMER_THREADS
/* if we are threaded, create a lock to prevent multiple readers */
if (ncpus > 0)
{
status = p7_hmmfile_CreateLock(hfp);
if (status != eslOK) p7_Fail("Unexpected error %d creating lock\n", status);
}
#endif
if (fprintf(ofp, "Query: %s [L=%ld]\n", qsq->name, (long) qsq->n) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (qsq->acc[0] != 0 && fprintf(ofp, "Accession: %s\n", qsq->acc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (qsq->desc[0] != 0 && fprintf(ofp, "Description: %s\n", qsq->desc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
for (i = 0; i < infocnt; ++i)
{
/* Create processing pipeline and hit list */
info[i].th = p7_tophits_Create();
info[i].pli = p7_pipeline_Create(go, 100, 100, TRUE, p7_SCAN_MODELS); /* M_hint = 100, L_hint = 100 are just dummies for now */
info[i].pli->hfp = hfp; /* for two-stage input, pipeline needs <hfp> */
p7_pli_NewSeq(info[i].pli, qsq);
info[i].qsq = qsq;
if ( esl_opt_IsUsed(go, "--toponly") )
info[i].pli->strand = p7_STRAND_TOPONLY;
else if ( esl_opt_IsUsed(go, "--bottomonly") )
info[i].pli->strand = p7_STRAND_BOTTOMONLY;
else
info[i].pli->strand = p7_STRAND_BOTH;
#ifdef HMMER_THREADS
if (ncpus > 0) esl_threads_AddThread(threadObj, &info[i]);
#endif
}
#ifdef HMMER_THREADS
if (ncpus > 0) hstatus = thread_loop(threadObj, queue, hfp);
else hstatus = serial_loop(info, hfp);
#else
hstatus = serial_loop(info, hfp);
#endif
switch(hstatus)
{
case eslEFORMAT: p7_Fail("bad file format in HMM file %s", cfg->hmmfile); break;
case eslEINCOMPAT: p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile); break;
case eslEOF:
case eslOK: /* do nothing */
break;
default: p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile);
}
/* merge the results of the search results */
for (i = 1; i < infocnt; ++i)
{
p7_tophits_Merge(info[0].th, info[i].th);
p7_pipeline_Merge(info[0].pli, info[i].pli);
p7_pipeline_Destroy(info[i].pli);
p7_tophits_Destroy(info[i].th);
}
/* modify e-value to account for number of models */
for (i = 0; i < info->th->N ; i++)
{
info->th->unsrt[i].lnP += log((float)info->pli->nmodels);
info->th->unsrt[i].dcl[0].lnP = info->th->unsrt[i].lnP;
info->th->unsrt[i].sortkey = -1.0 * info->th->unsrt[i].lnP;
}
/* it's possible to have duplicates based on how viterbi ranges can overlap */
p7_tophits_SortByModelnameAndAlipos(info->th);
p7_tophits_RemoveDuplicates(info->th, info->pli->use_bit_cutoffs);
/* Print results */
p7_tophits_SortBySortkey(info->th);
p7_tophits_Threshold(info->th, info->pli);
//tally up total number of hits and target coverage
info->pli->n_output = info->pli->pos_output = 0;
for (i = 0; i < info->th->N; i++) {
if ( (info->th->hit[i]->flags & p7_IS_REPORTED) || info->th->hit[i]->flags & p7_IS_INCLUDED) {
info->pli->n_output++;
info->pli->pos_output += abs(info->th->hit[i]->dcl[0].jali - info->th->hit[i]->dcl[0].iali) + 1;
}
}
p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (tblfp) p7_tophits_TabularTargets(tblfp, qsq->name, qsq->acc, info->th, info->pli, (nquery == 1));
if (dfamtblfp) p7_tophits_TabularXfam(dfamtblfp, qsq->name, NULL, info->th, info->pli);
if (aliscoresfp) p7_tophits_AliScores(aliscoresfp, qsq->name, info->th );
esl_stopwatch_Stop(w);
info->pli->nseqs = 1;
p7_pli_Statistics(ofp, info->pli, w);
if (fprintf(ofp, "//\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
fflush(ofp);
p7_hmmfile_Close(hfp);
p7_pipeline_Destroy(info->pli);
p7_tophits_Destroy(info->th);
esl_sq_Reuse(qsq);
}
if (sstatus == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (sstatus != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
sstatus, sqfp->filename);
/* Terminate outputs - any last words?
*/
if (tblfp) p7_tophits_TabularTail(tblfp, "hmmscan", p7_SCAN_MODELS, cfg->seqfile, cfg->hmmfile, go);
if (ofp) { if (fprintf(ofp, "[ok]\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }
/* Cleanup - prepare for successful exit
*/
for (i = 0; i < infocnt; ++i)
p7_bg_Destroy(info[i].bg);
#ifdef HMMER_THREADS
if (ncpus > 0)
{
esl_workqueue_Reset(queue);
while (esl_workqueue_Remove(queue, (void **) &block) == eslOK)
p7_oprofile_DestroyBlock(block);
esl_workqueue_Destroy(queue);
esl_threads_Destroy(threadObj);
}
#endif
free(info);
esl_sq_Destroy(qsq);
esl_stopwatch_Destroy(w);
esl_alphabet_Destroy(abc);
esl_sqfile_Close(sqfp);
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
if (dfamtblfp) fclose(dfamtblfp);
if (aliscoresfp) fclose(aliscoresfp);
return eslOK;
ERROR:
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
if (dfamtblfp) fclose(dfamtblfp);
if (aliscoresfp) fclose(aliscoresfp);
return status;
}
static int
output_header(FILE *ofp, ESL_GETOPTS *go, char *hmmfile, char *seqfile)
{
p7_banner(ofp, go->argv[0], banner);
if (fprintf(ofp, "# query sequence file: %s\n", seqfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# target HMM database: %s\n", hmmfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", esl_opt_GetString(go, "-o")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", esl_opt_GetString(go, "--tblout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--dfamtblout") && fprintf(ofp, "# hits output in Dfam format: %s\n", esl_opt_GetString(go, "--dfamtblout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--aliscoresout") && fprintf(ofp, "# alignment scores output: %s\n", esl_opt_GetString(go, "--aliscoresout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimited\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--textw") && fprintf(ofp, "# max ASCII text line length: %d\n", esl_opt_GetInteger(go, "--textw")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-E") && fprintf(ofp, "# profile reporting threshold: E-value <= %g\n", esl_opt_GetReal(go, "-E")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-T") && fprintf(ofp, "# profile reporting threshold: score >= %g\n", esl_opt_GetReal(go, "-T")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--incE") && fprintf(ofp, "# profile inclusion threshold: E-value <= %g\n", esl_opt_GetReal(go, "--incE")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--incT") && fprintf(ofp, "# profile inclusion threshold: score >= %g\n", esl_opt_GetReal(go, "--incT")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--cut_ga") && fprintf(ofp, "# model-specific thresholding: GA cutoffs\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--cut_nc") && fprintf(ofp, "# model-specific thresholding: NC cutoffs\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--cut_tc") && fprintf(ofp, "# model-specific thresholding: TC cutoffs\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--max") && fprintf(ofp, "# Max sensitivity mode: on [all heuristic filters off]\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--F1") && fprintf(ofp, "# MSV filter P threshold: <= %g\n", esl_opt_GetReal(go, "--F1")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--F2") && fprintf(ofp, "# Vit filter P threshold: <= %g\n", esl_opt_GetReal(go, "--F2")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--F3") && fprintf(ofp, "# Fwd filter P threshold: <= %g\n", esl_opt_GetReal(go, "--F3")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--nobias") && fprintf(ofp, "# biased composition HMM filter: off\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--B1") && fprintf(ofp, "# biased comp MSV window len: %d\n", esl_opt_GetInteger(go, "--B1")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--B2") && fprintf(ofp, "# biased comp Viterbi window len: %d\n", esl_opt_GetInteger(go, "--B2")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--B3") && fprintf(ofp, "# biased comp Forward window len: %d\n", esl_opt_GetInteger(go, "--B3")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--nonull2") && fprintf(ofp, "# null2 bias corrections: off\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--toponly") && fprintf(ofp, "# search only top strand: on\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--bottomonly") && fprintf(ofp, "# search only bottom strand: on\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-Z") && fprintf(ofp, "# sequence search space set to: %.0f\n", esl_opt_GetReal(go, "-Z")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--seed")) {
if (esl_opt_GetInteger(go, "--seed")==0 && fprintf(ofp, "# random number seed: one-time arbitrary\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
else if ( fprintf(ofp, "# random number seed set to: %d\n", esl_opt_GetInteger(go, "--seed")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
if (esl_opt_IsUsed(go, "--qformat") && fprintf(ofp, "# input seqfile format asserted: %s\n", esl_opt_GetString(go, "--qformat")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--w_beta") && fprintf(ofp, "# window length beta value: %g\n", esl_opt_GetReal(go, "--w_beta")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--w_length") && fprintf(ofp, "# window length : %d\n", esl_opt_GetInteger(go, "--w_length")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
// if (esl_opt_IsUsed(go, "--daemon") && fprintf(ofp, "run as a daemon process\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
#ifdef HMMER_THREADS
if (esl_opt_IsUsed(go, "--cpu") && fprintf(ofp, "# number of worker threads: %d\n", esl_opt_GetInteger(go, "--cpu")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
#endif
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
return eslOK;
}
/* Function: p7_tophits_Domains()
* Synopsis: Standard output format for top domain hits and alignments.
*
* Purpose: For each reportable target sequence, output a tabular summary
* of reportable domains found in it, followed by alignments of
* each domain.
*
* Similar to <p7_tophits_Targets()>; see additional notes there.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> if a write to <ofp> fails; for example, if
* the disk fills up.
*/
int
p7_tophits_Domains(FILE *ofp, P7_TOPHITS *th, P7_PIPELINE *pli, int textw)
{
int h, d;
int nd;
int namew, descw;
char *showname;
int status;
if (pli->long_targets)
{
if (fprintf(ofp, "Annotation for each hit %s:\n",
pli->show_alignments ? " (and alignments)" : "") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, "Domain annotation for each %s%s:\n",
pli->mode == p7_SEARCH_SEQS ? "sequence" : "model",
pli->show_alignments ? " (and alignments)" : "") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
for (h = 0; h < th->N; h++)
if (th->hit[h]->flags & p7_IS_REPORTED)
{
if (pli->show_accessions && th->hit[h]->acc != NULL && th->hit[h]->acc[0] != '\0')
{
showname = th->hit[h]->acc;
namew = strlen(th->hit[h]->acc);
}
else
{
showname = th->hit[h]->name;
namew = strlen(th->hit[h]->name);
}
if (textw > 0)
{
descw = ESL_MAX(32, textw - namew - 5);
if (fprintf(ofp, ">> %s %-.*s\n", showname, descw, (th->hit[h]->desc == NULL ? "" : th->hit[h]->desc)) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, ">> %s %s\n", showname, (th->hit[h]->desc == NULL ? "" : th->hit[h]->desc)) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
if (th->hit[h]->nreported == 0)
{
if (fprintf(ofp," [No individual domains that satisfy reporting thresholds (although complete target did)]\n\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
continue;
}
if (pli->long_targets) {
/* The dna hit table is 119 char wide:
score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to hqfrom hq to sq len acc
------ ----- --------- ------- ------- --------- --------- --------- --------- --------- --------- --------- ----
! 82.7 104.4 4.9e-22 782 998 .. 241981174 241980968 .. 241981174 241980966 .. 241981174 241980968 234234233 0.78
*/
if (fprintf(ofp, " %6s %5s %9s %9s %9s %2s %9s %9s %2s %9s %9s %9s %2s %4s\n", "score", "bias", " Evalue", "hmmfrom", "hmm to", " ", " alifrom ", " ali to ", " ", " envfrom ", " env to ", " sq len ", " ", "acc") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
if (fprintf(ofp, " %6s %5s %9s %9s %9s %2s %9s %9s %2s %9s %9s %9s %2s %4s\n", "------", "-----", "---------", "-------", "-------", " ", "---------", "---------", " ", "---------", "---------", "---------", " ", "----") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
} else {
/* The domain table is 101 char wide:
# score bias Evalue hmmfrom hmmto alifrom ali to envfrom env to acc
--- ------ ----- --------- ------- ------- ------- ------- ------- ------- ----
1 ? 123.4 23.1 6.8e-9 3 1230 .. 1 492 [] 2 490 .] 0.90
123 ! 1234.5 123.4 123456789 1234567 1234567 .. 1234567 1234567 [] 1234567 1234568 .] 0.12
*/
if (fprintf(ofp, " %3s %6s %5s %9s %9s %7s %7s %2s %7s %7s %2s %7s %7s %2s %4s\n", "#", "score", "bias", "c-Evalue", "i-Evalue", "hmmfrom", "hmm to", " ", "alifrom", "ali to", " ", "envfrom", "env to", " ", "acc") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
if (fprintf(ofp, " %3s %6s %5s %9s %9s %7s %7s %2s %7s %7s %2s %7s %7s %2s %4s\n", "---", "------", "-----", "---------", "---------", "-------", "-------", " ", "-------", "-------", " ", "-------", "-------", " ", "----") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
nd = 0;
for (d = 0; d < th->hit[h]->ndom; d++)
if (th->hit[h]->dcl[d].is_reported)
{
nd++;
if (pli->long_targets)
{
if (fprintf(ofp, " %c %6.1f %5.1f %9.2g %9d %9d %c%c %9" PRId64 " %9" PRId64 " %c%c %9d %9d %c%c %9" PRId64 " %4.2f\n",
//nd,
th->hit[h]->dcl[d].is_included ? '!' : '?',
th->hit[h]->dcl[d].bitscore,
th->hit[h]->dcl[d].dombias * eslCONST_LOG2R, /* convert NATS to BITS at last moment */
exp(th->hit[h]->dcl[d].lnP),
th->hit[h]->dcl[d].ad->hmmfrom,
th->hit[h]->dcl[d].ad->hmmto,
(th->hit[h]->dcl[d].ad->hmmfrom == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ad->hmmto == th->hit[h]->dcl[d].ad->M) ? ']' : '.',
th->hit[h]->dcl[d].ad->sqfrom,
th->hit[h]->dcl[d].ad->sqto,
(th->hit[h]->dcl[d].ad->sqfrom == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ad->sqto == th->hit[h]->dcl[d].ad->L) ? ']' : '.',
th->hit[h]->dcl[d].iae,
th->hit[h]->dcl[d].ibe,
(th->hit[h]->dcl[d].iae == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ibe == th->hit[h]->dcl[d].ad->L) ? ']' : '.',
th->hit[h]->dcl[d].ad->L,
(th->hit[h]->dcl[d].oasc / (1.0 + fabs((float) (th->hit[h]->dcl[d].ibe - th->hit[h]->dcl[d].iae))))) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, " %3d %c %6.1f %5.1f %9.2g %9.2g %7d %7d %c%c %7" PRId64 " %7" PRId64 " %c%c %7d %7d %c%c %4.2f\n",
nd,
th->hit[h]->dcl[d].is_included ? '!' : '?',
th->hit[h]->dcl[d].bitscore,
th->hit[h]->dcl[d].dombias * eslCONST_LOG2R, /* convert NATS to BITS at last moment */
exp(th->hit[h]->dcl[d].lnP) * pli->domZ,
exp(th->hit[h]->dcl[d].lnP) * pli->Z,
th->hit[h]->dcl[d].ad->hmmfrom,
th->hit[h]->dcl[d].ad->hmmto,
(th->hit[h]->dcl[d].ad->hmmfrom == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ad->hmmto == th->hit[h]->dcl[d].ad->M) ? ']' : '.',
th->hit[h]->dcl[d].ad->sqfrom,
th->hit[h]->dcl[d].ad->sqto,
(th->hit[h]->dcl[d].ad->sqfrom == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ad->sqto == th->hit[h]->dcl[d].ad->L) ? ']' : '.',
th->hit[h]->dcl[d].iae,
th->hit[h]->dcl[d].ibe,
(th->hit[h]->dcl[d].iae == 1) ? '[' : '.',
(th->hit[h]->dcl[d].ibe == th->hit[h]->dcl[d].ad->L) ? ']' : '.',
(th->hit[h]->dcl[d].oasc / (1.0 + fabs((float) (th->hit[h]->dcl[d].ibe - th->hit[h]->dcl[d].iae))))) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
}
if (pli->show_alignments)
{
if (pli->long_targets)
{
if (fprintf(ofp, "\n Alignment:\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, "\n Alignments for each domain:\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
nd = 0;
}
for (d = 0; d < th->hit[h]->ndom; d++)
if (th->hit[h]->dcl[d].is_reported)
{
nd++;
if (!pli->long_targets)
{
if (fprintf(ofp, " == domain %d", nd ) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
if (fprintf(ofp, " score: %.1f bits", th->hit[h]->dcl[d].bitscore) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
if (!pli->long_targets)
{
if (fprintf(ofp, "; conditional E-value: %.2g\n", exp(th->hit[h]->dcl[d].lnP) * pli->domZ) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
else
{
if (fprintf(ofp, "\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
if ((status = p7_alidisplay_Print(ofp, th->hit[h]->dcl[d].ad, 40, textw, pli->show_accessions)) != eslOK) return status;
if (fprintf(ofp, "\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
}
else
{
if (fprintf(ofp, "\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
}
if (th->nreported == 0)
{
if (fprintf(ofp, "\n [No targets detected that satisfy reporting thresholds]\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "domain hit list: write failed");
}
return eslOK;
}
/* printprob()
* Print a probability (with a leading space), formatted
* for an H2 ASCII save file.
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any write failure.
*/
static int
printprob(FILE *fp, int fieldwidth, float p, float null)
{
if (p == 0.0) { if (fprintf(fp, " %*s", fieldwidth, "*") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed"); }
else if (null == 1.0 && p == 1.0) { if (fprintf(fp, " %*d", fieldwidth, 0) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed"); }
else { if (fprintf(fp, " %*d", fieldwidth, (int) floor(0.5 + 1442.695 * log(p/null))) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "h2 profile write failed"); }
return eslOK;
}
/* Function: p7_tophits_Targets()
* Synopsis: Format and write a top target hits list to an output stream.
*
* Purpose: Output a list of the reportable top target hits in <th>
* in human-readable ASCII text format to stream <ofp>, using
* final pipeline accounting stored in <pli>.
*
* The tophits list <th> should already be sorted (see
* <p7_tophits_Sort()> and thresholded (see
* <p7_tophits_Threshold>).
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on write failure.
*/
int
p7_tophits_Targets(FILE *ofp, P7_TOPHITS *th, P7_PIPELINE *pli, int textw)
{
char newness;
int h;
int d;
int namew;
int posw;
int descw;
char *showname;
int have_printed_incthresh = FALSE;
/* when --acc is on, we'll show accession if available, and fall back to name */
if (pli->show_accessions) namew = ESL_MAX(8, p7_tophits_GetMaxShownLength(th));
else namew = ESL_MAX(8, p7_tophits_GetMaxNameLength(th));
if (pli->long_targets)
{
posw = ESL_MAX(6, p7_tophits_GetMaxPositionLength(th));
if (textw > 0) descw = ESL_MAX(32, textw - namew - 2*posw - 32); /* 32 chars excluding desc and two posw's is from the format: 2 + 9+2 +6+2 +5+2 +<name>+1 +<startpos>+1 +<endpos>+1 +1 */
else descw = 0; /* unlimited desc length is handled separately */
if (fprintf(ofp, "Scores for complete hit%s:\n", pli->mode == p7_SEARCH_SEQS ? "s" : "") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
if (fprintf(ofp, " %9s %6s %5s %-*s %*s %*s %s\n",
"E-value", " score", " bias", namew, (pli->mode == p7_SEARCH_SEQS ? "Sequence":"Model"), posw, "start", posw, "end", "Description") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
if (fprintf(ofp, " %9s %6s %5s %-*s %*s %*s %s\n",
"-------", "------", "-----", namew, "--------", posw, "-----", posw, "-----", "-----------") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
}
else
{
if (textw > 0) descw = ESL_MAX(32, textw - namew - 61); /* 61 chars excluding desc is from the format: 2 + 22+2 +22+2 +8+2 +<name>+1 */
else descw = 0; /* unlimited desc length is handled separately */
/* The minimum width of the target table is 111 char: 47 from fields, 8 from min name, 32 from min desc, 13 spaces */
if (fprintf(ofp, "Scores for complete sequence%s (score includes all domains):\n", pli->mode == p7_SEARCH_SEQS ? "s" : "") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
if (fprintf(ofp, " %22s %22s %8s\n", " --- full sequence ---", " --- best 1 domain ---", "-#dom-") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
if (fprintf(ofp, " %9s %6s %5s %9s %6s %5s %5s %2s %-*s %s\n",
"E-value", " score", " bias", "E-value", " score", " bias", " exp", "N", namew, (pli->mode == p7_SEARCH_SEQS ? "Sequence":"Model"), "Description") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
if (fprintf(ofp, " %9s %6s %5s %9s %6s %5s %5s %2s %-*s %s\n",
"-------", "------", "-----", "-------", "------", "-----", " ----", "--", namew, "--------", "-----------") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
}
for (h = 0; h < th->N; h++)
if (th->hit[h]->flags & p7_IS_REPORTED)
{
d = th->hit[h]->best_domain;
if (! (th->hit[h]->flags & p7_IS_INCLUDED) && ! have_printed_incthresh)
{
if (fprintf(ofp, " ------ inclusion threshold ------\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
have_printed_incthresh = TRUE;
}
if (pli->show_accessions)
{ /* the --acc option: report accessions rather than names if possible */
if (th->hit[h]->acc != NULL && th->hit[h]->acc[0] != '\0') showname = th->hit[h]->acc;
else showname = th->hit[h]->name;
}
else
showname = th->hit[h]->name;
if (th->hit[h]->flags & p7_IS_NEW) newness = '+';
else if (th->hit[h]->flags & p7_IS_DROPPED) newness = '-';
else newness = ' ';
if (pli->long_targets)
{
if (fprintf(ofp, "%c %9.2g %6.1f %5.1f %-*s %*d %*d ",
newness,
exp(th->hit[h]->lnP), // * pli->Z,
th->hit[h]->score,
eslCONST_LOG2R * th->hit[h]->dcl[d].dombias, // an nhmmer hit is really a domain, so this is the hit's bias correction
namew, showname,
posw, th->hit[h]->dcl[d].ia,
posw, th->hit[h]->dcl[d].ib) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
}
else
{
if (fprintf(ofp, "%c %9.2g %6.1f %5.1f %9.2g %6.1f %5.1f %5.1f %2d %-*s ",
newness,
exp(th->hit[h]->lnP) * pli->Z,
th->hit[h]->score,
th->hit[h]->pre_score - th->hit[h]->score, /* bias correction */
exp(th->hit[h]->dcl[d].lnP) * pli->Z,
th->hit[h]->dcl[d].bitscore,
eslCONST_LOG2R * th->hit[h]->dcl[d].dombias, /* convert NATS to BITS at last moment */
th->hit[h]->nexpected,
th->hit[h]->nreported,
namew, showname) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
}
if (textw > 0)
{
if (fprintf(ofp, " %-.*s\n", descw, th->hit[h]->desc == NULL ? "" : th->hit[h]->desc) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
}
else
{
if (fprintf(ofp, " %s\n", th->hit[h]->desc == NULL ? "" : th->hit[h]->desc) < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
}
/* do NOT use *s with unlimited (INT_MAX) line length. Some systems
* have an fprintf() bug here (we found one on an Opteron/SUSE Linux
* system (#h66)
*/
}
if (th->nreported == 0)
{
if (fprintf(ofp, "\n [No hits detected that satisfy reporting thresholds]\n") < 0)
ESL_EXCEPTION_SYS(eslEWRITE, "per-sequence hit list: write failed");
}
return eslOK;
}
/* Function: output_header()
* Synopsis: Print details of FM-index construction
*/
static int
output_header(FILE *ofp, const ESL_GETOPTS *go, char *seqfile, char *fmfile)
{
p7_banner(ofp, go->argv[0], banner);
if (fprintf(ofp, "# input sequence file: %s\n", seqfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# output binary-formatted HMMER database: %s\n", fmfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# alphabet : %s\n", esl_opt_GetString(go, "--alph")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# bin_length : %d\n", esl_opt_GetInteger(go, "--bin_length")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# suffix array sample rate: %d\n", esl_opt_GetInteger(go, "--sa_freq")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
return eslOK;
}
/* Function: p7_oprofile_Write()
* Synopsis: Write an optimized profile in two files.
*
* Purpose: Write the MSV filter part of <om> to open binary stream
* <ffp>, and the rest of the model to <pfp>. These two
* streams will typically be <.h3f> and <.h3p> files
* being created by hmmpress.
*
* Args: ffp - open binary stream for saving MSV filter part
* pfp - open binary stream for saving rest of profile
* om - optimized profile to save
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any write failure, such as filling
* the disk.
*/
int
p7_oprofile_Write(FILE *ffp, FILE *pfp, P7_OPROFILE *om)
{
int Q4 = P7_NVF(om->M);
int Q8 = P7_NVW(om->M);
int Q16 = P7_NVB(om->M);
int Q16x = P7_NVB(om->M) + p7O_EXTRA_SB;
int n = strlen(om->name);
int x;
/* <ffp> is the part of the oprofile that MSVFilter() needs */
if (fwrite((char *) &(v3f_fmagic), sizeof(uint32_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->M), sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->abc->type), sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &n, sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->name, sizeof(char), n+1, ffp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->max_length),sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->tbm_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->tec_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->tjb_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->scale_b), sizeof(float), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->base_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->bias_b), sizeof(uint8_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < om->abc->Kp; x++)
if (fwrite( (char *) om->sbv[x], sizeof(__m128i), Q16x, ffp) != Q16x) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < om->abc->Kp; x++)
if (fwrite( (char *) om->rbv[x], sizeof(__m128i), Q16, ffp) != Q16) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->evparam, sizeof(float), p7_NEVPARAM, ffp) != p7_NEVPARAM) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->offs, sizeof(off_t), p7_NOFFSETS, ffp) != p7_NOFFSETS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->compo, sizeof(float), p7_MAXABET, ffp) != p7_MAXABET) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(v3f_fmagic), sizeof(uint32_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); /* sentinel */
/* <pfp> gets the rest of the oprofile */
if (fwrite((char *) &(v3f_pmagic), sizeof(uint32_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->M), sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->abc->type), sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->name, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (om->acc == NULL) {
n = 0;
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
} else {
n = strlen(om->acc);
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->acc, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
}
if (om->desc == NULL) {
n = 0;
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
} else {
n = strlen(om->desc);
if (fwrite((char *) &n, sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->desc, sizeof(char), n+1, pfp) != n+1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
}
if (fwrite((char *) om->rf, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->mm, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->cs, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->consensus, sizeof(char), om->M+2, pfp) != om->M+2) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
/* ViterbiFilter part */
if (fwrite((char *) om->twv, sizeof(__m128i), 8*Q8, pfp) != 8*Q8) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < om->abc->Kp; x++)
if (fwrite( (char *) om->rwv[x], sizeof(__m128i), Q8, pfp) != Q8) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < p7O_NXSTATES; x++)
if (fwrite( (char *) om->xw[x], sizeof(int16_t), p7O_NXTRANS, pfp) != p7O_NXTRANS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->scale_w), sizeof(float), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->base_w), sizeof(int16_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->ddbound_w), sizeof(int16_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->ncj_roundoff), sizeof(float), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
/* Forward/Backward part */
if (fwrite((char *) om->tfv, sizeof(__m128), 8*Q4, pfp) != 8*Q4) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < om->abc->Kp; x++)
if (fwrite( (char *) om->rfv[x], sizeof(__m128), Q4, pfp) != Q4) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
for (x = 0; x < p7O_NXSTATES; x++)
if (fwrite( (char *) om->xf[x], sizeof(float), p7O_NXTRANS, pfp) != p7O_NXTRANS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->cutoff, sizeof(float), p7_NCUTOFFS, pfp) != p7_NCUTOFFS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->nj), sizeof(float), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->mode), sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->L) , sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(v3f_pmagic), sizeof(uint32_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); /* sentinel */
return eslOK;
}
static int
output_header(FILE *ofp, const ESL_GETOPTS *go, char *hmmfile, char *seqfile)
{
p7_banner(ofp, go->argv[0], banner);
if (fprintf(ofp, "# query HMM file: %s\n", hmmfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# target sequence database: %s\n", seqfile) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-o") && fprintf(ofp, "# output directed to file: %s\n", esl_opt_GetString(go, "-o")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-A") && fprintf(ofp, "# MSA of all hits saved to file: %s\n", esl_opt_GetString(go, "-A")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--tblout") && fprintf(ofp, "# per-seq hits tabular output: %s\n", esl_opt_GetString(go, "--tblout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--domtblout") && fprintf(ofp, "# per-dom hits tabular output: %s\n", esl_opt_GetString(go, "--domtblout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--pfamtblout") && fprintf(ofp, "# pfam-style tabular hit output: %s\n", esl_opt_GetString(go, "--pfamtblout")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--acc") && fprintf(ofp, "# prefer accessions over names: yes\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--noali") && fprintf(ofp, "# show alignments in output: no\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--notextw") && fprintf(ofp, "# max ASCII text line length: unlimited\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--textw") && fprintf(ofp, "# max ASCII text line length: %d\n", esl_opt_GetInteger(go, "--textw")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-E") && fprintf(ofp, "# sequence reporting threshold: E-value <= %g\n", esl_opt_GetReal(go, "-E")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-T") && fprintf(ofp, "# sequence reporting threshold: score >= %g\n", esl_opt_GetReal(go, "-T")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--domE") && fprintf(ofp, "# domain reporting threshold: E-value <= %g\n", esl_opt_GetReal(go, "--domE")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--domT") && fprintf(ofp, "# domain reporting threshold: score >= %g\n", esl_opt_GetReal(go, "--domT")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--incE") && fprintf(ofp, "# sequence inclusion threshold: E-value <= %g\n", esl_opt_GetReal(go, "--incE")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--incT") && fprintf(ofp, "# sequence inclusion threshold: score >= %g\n", esl_opt_GetReal(go, "--incT")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--incdomE") && fprintf(ofp, "# domain inclusion threshold: E-value <= %g\n", esl_opt_GetReal(go, "--incdomE")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--incdomT") && fprintf(ofp, "# domain inclusion threshold: score >= %g\n", esl_opt_GetReal(go, "--incdomT")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--cut_ga") && fprintf(ofp, "# model-specific thresholding: GA cutoffs\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--cut_nc") && fprintf(ofp, "# model-specific thresholding: NC cutoffs\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--cut_tc") && fprintf(ofp, "# model-specific thresholding: TC cutoffs\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--max") && fprintf(ofp, "# Max sensitivity mode: on [all heuristic filters off]\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--F1") && fprintf(ofp, "# MSV filter P threshold: <= %g\n", esl_opt_GetReal(go, "--F1")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--F2") && fprintf(ofp, "# Vit filter P threshold: <= %g\n", esl_opt_GetReal(go, "--F2")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--F3") && fprintf(ofp, "# Fwd filter P threshold: <= %g\n", esl_opt_GetReal(go, "--F3")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--nobias") && fprintf(ofp, "# biased composition HMM filter: off\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--restrictdb_stkey") && fprintf(ofp, "# Restrict db to start at seq key: %s\n", esl_opt_GetString(go, "--restrictdb_stkey")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--restrictdb_n") && fprintf(ofp, "# Restrict db to # target seqs: %d\n", esl_opt_GetInteger(go, "--restrictdb_n")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--ssifile") && fprintf(ofp, "# Override ssi file to: %s\n", esl_opt_GetString(go, "--ssifile")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--nonull2") && fprintf(ofp, "# null2 bias corrections: off\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "-Z") && fprintf(ofp, "# sequence search space set to: %.0f\n", esl_opt_GetReal(go, "-Z")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--domZ") && fprintf(ofp, "# domain search space set to: %.0f\n", esl_opt_GetReal(go, "--domZ")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (esl_opt_IsUsed(go, "--seed")) {
if (esl_opt_GetInteger(go, "--seed") == 0 && fprintf(ofp, "# random number seed: one-time arbitrary\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
else if ( fprintf(ofp, "# random number seed set to: %d\n", esl_opt_GetInteger(go, "--seed")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
}
if (esl_opt_IsUsed(go, "--tformat") && fprintf(ofp, "# targ <seqfile> format asserted: %s\n", esl_opt_GetString(go, "--tformat")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (fprintf(ofp, "# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
return eslOK;
}
/* Function: p7_oprofile_Write()
* Synopsis: Write an optimized profile in two files.
*
* Purpose: Write the MSV filter part of <om> to open binary stream
* <ffp>, and the rest of the model to <pfp>. These two
* streams will typically be <.h3f> and <.h3p> files
* being created by hmmpress.
*
* Args: ffp - open binary stream for saving MSV filter part
* pfp - open binary stream for saving rest of profile
* om - optimized profile to save
*
* Returns: <eslOK> on success.
*
* Throws: <eslEWRITE> on any write failure; for example,
* if disk is full.
*/
int
p7_oprofile_Write(FILE *ffp, FILE *pfp, P7_OPROFILE *om)
{
/* <ffp> is the part of the oprofile that MSVFilter() needs */
if (fwrite((char *) &(v3f_fmagic), sizeof(uint32_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->M), sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->abc->type), sizeof(int), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) om->offs, sizeof(off_t), p7_NOFFSETS, ffp) != p7_NOFFSETS) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(v3f_fmagic), sizeof(uint32_t), 1, ffp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); /* sentinel */
/* <pfp> gets the rest of the oprofile */
if (fwrite((char *) &(v3f_pmagic), sizeof(uint32_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->M), sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(om->abc->type), sizeof(int), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed");
if (fwrite((char *) &(v3f_pmagic), sizeof(uint32_t), 1, pfp) != 1) ESL_EXCEPTION_SYS(eslEWRITE, "oprofile write failed"); /* sentinel */
return eslOK;
}
