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/*****************************************************************
* @LICENSE@
*****************************************************************/
/* sindex_main.c, SRE, Fri Feb 16 08:38:39 2001 [St. Louis]
*
* sindex -- create SSI index of sequence file(s) for sfetch
*
* CVS $Id: sindex_main.c,v 1.8 2003/04/14 16:00:16 eddy Exp $
*/
#include "squidconf.h"
#include <stdio.h>
#include <string.h>
#include "squid.h"
#include "msa.h"
#include "ssi.h"
static char banner[] = "sindex - create SSI index of sequence file(s) for sfetch";
static char usage[] = "\
Usage: sindex [-options] <seqfile>...\n\
Available options:\n\
-h : help; print version and usage info.\n\
-o <f> : output the SSI index to file named <f>\n\
";
static char experts[] = "\
--64 : force index mode to 64-bit, even on small files\n\
--external : force index compilation to use external (on-disk) sorting\n\
--informat <s> : specify input sequence file format <s>\n\
--pfamseq : index a FASTA file with >(name) (accession) (desc)\n\
";
struct opt_s OPTIONS[] = {
{ "-h", TRUE, sqdARG_NONE },
{ "-o", TRUE, sqdARG_STRING },
{ "--64", FALSE, sqdARG_NONE },
{ "--external", FALSE, sqdARG_NONE },
{ "--informat", FALSE, sqdARG_STRING },
{ "--pfamseq", FALSE, sqdARG_NONE },
};
#define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s))
int
main(int argc, char **argv)
{
char *file; /* name of a sequence file */
SQFILE *sfp; /* open sequence file */
int format; /* forced sequence file format, if any */
int mode; /* SSI_OFFSET_I32 or SSI_OFFSET_I64 */
int idx; /* counter over files */
int status; /* return status from an SSI call */
SSIINDEX *ssi; /* the index we're creating */
char *ssifile; /* file name for the SSI index */
int fh; /* handle on current file */
char *seq; /* a sequence read from the file */
SQINFO sqinfo; /* info on the sequence */
int do_pfamseq; /* TRUE to index name and accession in a FASTA*/
int do_external; /* TRUE to force external sorting */
char *optname;
char *optarg;
int optind;
/***********************************************
* Parse the command line
***********************************************/
/* initializations and defaults */
format = SQFILE_UNKNOWN; /* autodetecting format is the default */
mode = SSI_OFFSET_I32; /* default = 32 bit mode */
ssifile = NULL; /* default: set SSI file name as <file>.ssi */
do_pfamseq = FALSE; /* default: don't hack FASTA parsing, duh */
do_external = FALSE; /* default: use in-memory sorting if possible */
while (Getopt(argc, argv, OPTIONS, NOPTIONS, usage,
&optind, &optname, &optarg))
{
if (strcmp(optname, "-o") == 0) ssifile = sre_strdup(optarg, -1);
else if (strcmp(optname, "--64") == 0) mode = SSI_OFFSET_I64;
else if (strcmp(optname, "--external") == 0) do_external = TRUE;
else if (strcmp(optname, "--pfamseq") == 0) do_pfamseq = TRUE;
else if (strcmp(optname, "--informat") == 0) {
format = String2SeqfileFormat(optarg);
if (format == SQFILE_UNKNOWN)
Die("unrecognized input 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("Incorrect number of command line arguments.\n%s\n", usage);
/*****************************************************************
* Get set up...
*****************************************************************/
/* Determine whether we'll index in 32-bit or 64-bit mode.
* 32-bit is default, but 64-bit trumps; if any file needs 64-bit,
* we index them all that way.
*/
for (idx = optind; idx < argc; idx++)
{
file = argv[idx];
if ((status = SSIRecommendMode(file)) == -1)
Die("Couldn't stat %s - file doesn't exist, or is too big", file);
if (status == SSI_OFFSET_I64) mode = SSI_OFFSET_I64;
}
if (ssifile == NULL) {
ssifile = sre_strdup(file, -1);
sre_strcat(&ssifile, -1, ".ssi", -1);
}
if ((ssi = SSICreateIndex(mode)) == NULL)
Die("Couldn't allocate/initialize the new SSI index\n");
if (do_external)
SSIForceExternalSort(ssi);
/*****************************************************************
* Go through the files one at a time and compile index.
*****************************************************************/
for (idx = optind; idx < argc; idx++)
{
file = argv[idx];
printf("Working on file %s... \t", file);
fflush(stdout);
if ((sfp = SeqfileOpenForIndexing(file, format, NULL, mode)) == NULL)
Die("Failed to open sequence file %s for reading", file);
if ((status = SSIAddFileToIndex(ssi, file, sfp->format, &fh)) != 0)
Die("SSI error: %s\n", SSIErrorString(status));
while (ReadSeq(sfp, sfp->format, &seq, &sqinfo)) {
if ((status = SSIAddPrimaryKeyToIndex(ssi, sqinfo.name, fh,
&(sfp->r_off), &(sfp->d_off),
sqinfo.len)) != 0)
Die("SSI error: %s\n", SSIErrorString(status));
#if DEBUGLEVEL >= 2
if (mode == SSI_OFFSET_I32)
SQD_DPRINTF2(("Added primary key %s: r_off=%lu, d_off=%lu len=%d\n",
sqinfo.name, sfp->r_off.off.i32,
sfp->d_off.off.i32, sqinfo.len));
else
SQD_DPRINTF2(("Added primary key %s: r_off=%llu, d_off=%llu len=%d\n",
sqinfo.name, sfp->r_off.off.i64, sfp->d_off.off.i64,
sqinfo.len));
#endif
if (sqinfo.flags & SQINFO_ID) {
if ((status = SSIAddSecondaryKeyToIndex(ssi, sqinfo.id, sqinfo.name)) != 0)
Die("SSI error: %s\n", SSIErrorString(status));
}
if (sqinfo.flags & SQINFO_ACC) {
if ((status = SSIAddSecondaryKeyToIndex(ssi, sqinfo.acc, sqinfo.name)) != 0)
Die("SSI error: %s\n", SSIErrorString(status));
}
if (do_pfamseq && sfp->format == SQFILE_FASTA && sqinfo.desc != NULL) {
char *acc, *s;
s = sqinfo.desc;
acc = sre_strtok(&s, " \t", NULL);
if (acc != NULL) {
if ((status = SSIAddSecondaryKeyToIndex(ssi, acc, sqinfo.name)) != 0)
Die("SSI error: %s\n", SSIErrorString(status));
}
}
FreeSequence(seq, &sqinfo);
}
if (sfp->bpl > 0 && sfp->rpl > 0) {
if ((status = SSISetFileForSubseq(ssi, fh, sfp->bpl, sfp->rpl)) != 0)
Die("SSI error: %s\n", SSIErrorString(status));
printf("FAST_SUBSEQ set...\t");
} else
printf(" \t");
SeqfileClose(sfp);
printf("[done]\n");
}
printf("Sorting and writing index to SSI file %s...\t", ssifile);
fflush(stdout);
if ((status = SSIWriteIndex(ssifile, ssi)) != 0)
Die("SSIWriteIndex() failed: %s", SSIErrorString(status));
printf("[done]\n");
printf("%s:\n", ssifile);
printf("Mode: %s\n",
mode == SSI_OFFSET_I32 ? "32-bit" : "64-bit");
printf("Files: %d\n", ssi->nfiles);
printf("Primary keys: %d\n", ssi->nprimary);
printf("Secondary keys: %d\n", ssi->nsecondary);
SSIFreeIndex(ssi);
free(ssifile);
return 0;
}
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