/* Open the source sequence database for negative subseqs;
* upon return, cfg->dbfp is open (digital, SSI indexed);
* cfg->db_maxL and cfg->db_nseq are set.
*/
static int
process_dbfile(struct cfg_s *cfg, char *dbfile, int dbfmt)
{
ESL_SQ *sq = esl_sq_CreateDigital(cfg->abc);
int status;
/* Open the sequence file in digital mode */
status = esl_sqfile_OpenDigital(cfg->abc, dbfile, dbfmt, NULL, &(cfg->dbfp));
if (status == eslENOTFOUND) esl_fatal("No such file %s", dbfile);
else if (status == eslEFORMAT) esl_fatal("Format of seqfile %s unrecognized.", dbfile);
else if (status == eslEINVAL) esl_fatal("Can't autodetect stdin or .gz.");
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
/* Read info on each sequence */
cfg->db_nseq = 0;
cfg->db_maxL = 0;
while ((status = esl_sqio_ReadInfo(cfg->dbfp, sq)) == eslOK) {
cfg->db_maxL = ESL_MAX(sq->L, cfg->db_maxL);
cfg->db_nseq++;
esl_sq_Reuse(sq);
}
if (status != eslEOF) esl_fatal("Something went wrong with reading the seq db");
/* Open SSI index */
if (esl_sqfile_OpenSSI(cfg->dbfp, NULL) != eslOK) esl_fatal("Failed to open SSI index file");
if (cfg->dbfp->data.ascii.ssi->nprimary != cfg->db_nseq) esl_fatal("oops, nprimary != nseq");
esl_sq_Destroy(sq);
return eslOK;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *seqfile = NULL; /* sequence file name */
char *maskfile = NULL; /* mask coordinate file name */
int infmt = eslSQFILE_UNKNOWN; /* format code for seqfile */
int outfmt = eslSQFILE_FASTA; /* format code for output seqs */
ESL_SQFILE *sqfp = NULL; /* open sequence file */
ESL_FILEPARSER *maskefp = NULL; /* open mask coord file */
FILE *ofp = NULL; /* output stream for masked seqs */
char *source = NULL; /* name of current seq to mask */
char *p1, *p2; /* pointers used in parsing */
int64_t start, end; /* start, end coord for masking */
int64_t i, j, pos; /* coords in a sequence */
int64_t overmask; /* # of extra residues to mask */
ESL_SQ *sq = esl_sq_Create(); /* current sequence */
int do_fetching;
int do_lowercase;
int maskchar;
int status; /* easel return code */
/****************************************************************************
* Parse command line
****************************************************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
do_fetching = esl_opt_GetBoolean(go, "-R");
do_lowercase = esl_opt_GetBoolean(go, "-l");
overmask = (esl_opt_IsOn(go, "-x") ? esl_opt_GetInteger(go, "-x") : 0);
maskchar = (esl_opt_IsOn(go, "-m") ? esl_opt_GetChar(go, "-m") : 'X');
seqfile = esl_opt_GetArg(go, 1);
maskfile = esl_opt_GetArg(go, 2);
/* Open the <seqfile>: text mode, not digital */
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) cmdline_failure(argv[0], "%s is not a valid input sequence file format for --informat");
}
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) cmdline_failure(argv[0], "Sequence file %s not found.\n", seqfile);
else if (status == eslEFORMAT) cmdline_failure(argv[0], "Format of file %s unrecognized.\n", seqfile);
else if (status == eslEINVAL) cmdline_failure(argv[0], "Can't autodetect stdin or .gz.\n");
else if (status != eslOK) cmdline_failure(argv[0], "Open failed, code %d.\n", status);
if(do_fetching)
{
status = esl_sqfile_OpenSSI(sqfp, NULL);
if (status == eslEFORMAT) cmdline_failure(argv[0], "SSI index is in incorrect format\n");
else if (status == eslERANGE) cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
else if (status != eslOK) cmdline_failure(argv[0], "Failed to open SSI index\n");
}
/* Open the <maskfile> */
if (esl_fileparser_Open(maskfile, NULL, &maskefp) != eslOK)
cmdline_failure(argv[0], "Failed to open mask coordinate file %s\n", maskfile);
esl_fileparser_SetCommentChar(maskefp, '#');
/* Open the output file, if any */
if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/****************************************************************************
* Main loop over lines in <maskfile>
****************************************************************************/
/* Read one data line at a time from the <maskfile>;
* parse into data fields <seqname> <start> <end>
*/
while (esl_fileparser_NextLine(maskefp) == eslOK)
{
/* First field is sequence name */
if (esl_fileparser_GetTokenOnLine(maskefp, &source, NULL) != eslOK)
esl_fatal("Failed to read source seq name on line %d of file %s\n", maskefp->linenumber, maskfile);
/* Get the sequence */
if (do_fetching)
{ /* If the <seqfile> is SSI indexed, try to reposition it and read <source> seq by random access */
status = esl_sqio_Fetch(sqfp, source, sq);
if (status == eslENOTFOUND) esl_fatal("seq %s not found in SSI index for file %s\n", source, sqfp->filename);
else if (status == eslEINVAL) esl_fatal("No SSI index or can't reposition in file %s\n", sqfp->filename);
else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslOK) esl_fatal("Unexpected failure in fetching %s from file %s\n", source, sqfp->filename);
}
else
{ /* else, assume we're reading sequentially; <sqfile> and <maskfile> have seqs in same order */
status = esl_sqio_Read(sqfp, sq);
if (status == eslEOF) esl_fatal("File %s ended prematurely; didn't find %s\n", sqfp->filename, source);
else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslOK) esl_fatal("Unexpected error reading sequence file %s\n", sqfp->filename);
if ((strcmp(sq->name, source) != 0) && (strcmp(sq->acc, source) != 0))
esl_fatal("Sequences in <sqfile> and <maskfile> aren't in same order; try -R");
}
/* If we're masking by lowercase, first make sure everything's uppercase */
if (do_lowercase)
for (pos = 0; pos < sq->n; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = toupper(sq->seq[pos]);
/* Next two fields are <start>, <end> for the masking */
/* possible future extension: wrap loop around this, enable multiple masked regions */
if (esl_fileparser_GetTokenOnLine(maskefp, &p1, NULL) != eslOK)
esl_fatal("Failed to read start coord on line %d of file %s\n", maskefp->linenumber, maskfile);
start = strtoll(p1, &p2, 0) - 1;
if (esl_fileparser_GetTokenOnLine(maskefp, &p2, NULL) != eslOK)
esl_fatal("Failed to read end coord on line %d of file %s\n", maskefp->linenumber, maskfile);
end = strtoll(p2, &p1, 0) - 1;
/* Do the masking */
if (esl_opt_GetBoolean(go, "-r")) /* Reverse masking */
{ /* leave start..end unmasked; mask prefix 0..start-1, end+1..L-1 */
i = 0;
j = ESL_MIN(sq->n-1, start - 1 + overmask);
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
i = ESL_MAX(0, end + 1 - overmask);
j = sq->n-1;
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
}
else
{ /* normal: mask start..end */
i = ESL_MAX(0, start - overmask);
j = ESL_MIN(sq->n-1, end + overmask);
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
}
esl_sqio_Write(ofp, sq, outfmt, FALSE);
esl_sq_Reuse(sq);
}
esl_sq_Destroy(sq);
esl_fileparser_Close(maskefp);
esl_sqfile_Close(sqfp);
esl_getopts_Destroy(go);
if (ofp != stdout) fclose(ofp);
return 0;
}
/* serial_master()
* The serial version of hmmsearch.
* For each query HMM in <hmmfile> search the database for hits.
*
* A master can only return if it's successful. All errors are handled
* immediately and fatally with p7_Fail(). We also use the
* ESL_EXCEPTION and ERROR: mechanisms, but only because we know we're
* using a fatal exception handler.
*/
static int
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
FILE *ofp = stdout; /* results output file (-o) */
P7_HMMFILE *hfp = NULL; /* open input HMM file */
ESL_SQFILE *dbfp = NULL; /* open input sequence file */
P7_HMM *hmm = NULL; /* one HMM query */
ESL_ALPHABET *abc = NULL; /* digital alphabet */
int dbfmt = eslSQFILE_UNKNOWN; /* format code for sequence database file */
ESL_STOPWATCH *w;
int textw = 0;
int nquery = 0;
int status = eslOK;
int hstatus = eslOK;
int sstatus = eslOK;
int i;
int ncpus = 0;
int infocnt = 0;
WORKER_INFO *info = NULL;
char errbuf[eslERRBUFSIZE];
w = esl_stopwatch_Create();
if (esl_opt_GetBoolean(go, "--notextw")) textw = 0;
else textw = esl_opt_GetInteger(go, "--textw");
if (esl_opt_IsOn(go, "--tformat")) {
dbfmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--tformat"));
if (dbfmt == eslSQFILE_UNKNOWN) p7_Fail("%s is not a recognized sequence database file format\n", esl_opt_GetString(go, "--tformat"));
}
/* Open the target sequence database */
status = esl_sqfile_Open(cfg->dbfile, dbfmt, p7_SEQDBENV, &dbfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n", cfg->dbfile);
else if (status == eslEFORMAT) p7_Fail("Sequence file %s is empty or misformatted\n", cfg->dbfile);
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->dbfile);
if (esl_opt_IsUsed(go, "--restrictdb_stkey") || esl_opt_IsUsed(go, "--restrictdb_n")) {
if (esl_opt_IsUsed(go, "--ssifile"))
esl_sqfile_OpenSSI(dbfp, esl_opt_GetString(go, "--ssifile"));
else
esl_sqfile_OpenSSI(dbfp, NULL);
}
/* Open the query profile HMM file */
status = p7_hmmfile_OpenE(cfg->hmmfile, NULL, &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 in 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);
/* Open the results output files */
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w+")) == NULL) p7_Fail("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
infocnt = 1;
ESL_ALLOC(info, sizeof(*info) * infocnt);
/* <abc> is not known 'til first HMM is read. */
hstatus = p7_hmmfile_Read(hfp, &abc, &hmm);
if (hstatus == eslOK)
{
/* One-time initializations after alphabet <abc> becomes known */
// output_header(ofp, go, cfg->hmmfile, cfg->dbfile);
// dbfp->abc = abc; //ReadBlock requires knowledge of the alphabet to decide how best to read blocks
// for (i = 0; i < infocnt; ++i)
// {
// info[i].bg = p7_bg_Create(abc);
// }
}
/* Outer loop: over each query HMM in <hmmfile>. */
// while (hstatus == eslOK)
// {
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL; /* optimized query profile */
nquery++;
esl_stopwatch_Start(w);
/* seqfile may need to be rewound (multiquery mode) */
if (nquery > 1)
{
if (! esl_sqfile_IsRewindable(dbfp))
esl_fatal("Target sequence file %s isn't rewindable; can't search it with multiple queries", cfg->dbfile);
if (! esl_opt_IsUsed(go, "--restrictdb_stkey") )
esl_sqfile_Position(dbfp, 0); //only re-set current position to 0 if we're not planning to set it in a moment
}
if ( cfg->firstseq_key != NULL ) { //it's tempting to want to do this once and capture the offset position for future passes, but ncbi files make this non-trivial, so this keeps it general
sstatus = esl_sqfile_PositionByKey(dbfp, cfg->firstseq_key);
if (sstatus != eslOK)
p7_Fail("Failure setting restrictdb_stkey to %d\n", cfg->firstseq_key);
}
// if (fprintf(ofp, "Query: %s [M=%d]\n", hmm->name, hmm->M) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
// if (hmm->acc) { if (fprintf(ofp, "Accession: %s\n", hmm->acc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }
// if (hmm->desc) { if (fprintf(ofp, "Description: %s\n", hmm->desc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }
/* Convert to an optimized model */
gm = p7_profile_Create (hmm->M, abc);
om = p7_oprofile_Create(hmm->M, abc);
// p7_ProfileConfig(hmm, info->bg, gm, 100, p7_LOCAL); /* 100 is a dummy length for now; and MSVFilter requires local mode */
p7_oprofile_Convert(gm, om); /* <om> is now p7_LOCAL, multihit */
for (i = 0; i < infocnt; ++i)
{
/* Create processing pipeline and hit list */
info[i].th = p7_tophits_Create();
info[i].om = p7_oprofile_Clone(om);
info[i].pli = p7_pipeline_Create(go, om->M, 100, FALSE, p7_SEARCH_SEQS); /* L_hint = 100 is just a dummy for now */
P7_PIPELINE *pli = info[i].pli;
pli->nmodels++;
pli->nnodes += info[i].om->M;
// if (pli->Z_setby == p7_ZSETBY_NTARGETS && pli->mode == p7_SCAN_MODELS) pli->Z = pli->nmodels;
// if (pli->do_biasfilter) p7_bg_SetFilter(info[i].bg, info[i].om->M, info[i].om->compo);
// if (pli->mode == p7_SEARCH_SEQS)
// status = p7_pli_NewModelThresholds(pli, info[i].om);
pli->W = info[i].om->max_length;
}
sstatus = serial_loop(info, dbfp, cfg->n_targetseq, ofp);
switch(sstatus)
{
case eslEFORMAT:
esl_fatal("Parse failed (sequence file %s):\n%s\n",
dbfp->filename, esl_sqfile_GetErrorBuf(dbfp));
break;
case eslEOF:
/* do nothing */
break;
default:
esl_fatal("Unexpected error %d reading sequence file %s", sstatus, dbfp->filename);
}
/* 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);
p7_oprofile_Destroy(info[i].om);
}
/* Print the results. */
p7_tophits_SortBySortkey(info->th);
p7_tophits_Threshold(info->th, info->pli);
// 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");
esl_stopwatch_Stop(w);
// p7_pli_Statistics(ofp, info->pli, w);
// if (fprintf(ofp, "//\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
p7_pipeline_Destroy(info->pli);
p7_tophits_Destroy(info->th);
p7_oprofile_Destroy(info->om);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_hmm_Destroy(hmm);
// hstatus = p7_hmmfile_Read(hfp, &abc, &hmm);
// } /* end outer loop over query HMMs */
switch(hstatus) {
case eslEOD: p7_Fail("read failed, HMM file %s may be truncated?", cfg->hmmfile); break;
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. EOF is what we want. */ break;
default: p7_Fail("Unexpected error (%d) in reading HMMs from %s", hstatus, cfg->hmmfile);
}
/* Terminate outputs... any last words?
*/
/* Cleanup - prepare for exit
*/
// for (i = 0; i < infocnt; ++i)
// p7_bg_Destroy(info[i].bg);
free(info);
p7_hmmfile_Close(hfp);
esl_sqfile_Close(dbfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
if (ofp != stdout) fclose(ofp);
printf("44HHHH \n");
return eslOK;
ERROR:
return eslFAIL;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *seqfile = NULL; /* sequence file name */
int infmt = eslSQFILE_UNKNOWN; /* format code for seqfile */
ESL_SQFILE *sqfp = NULL; /* open sequence file */
FILE *ofp = NULL; /* output stream for sequences */
int status; /* easel return code */
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) < 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
/* Open the sequence file */
seqfile = esl_opt_GetArg(go, 1);
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat", esl_opt_GetString(go, "--informat"));
}
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) cmdline_failure(argv[0], "Sequence file %s not found.\n", seqfile);
else if (status == eslEFORMAT) cmdline_failure(argv[0], "Format of file %s unrecognized.\n", seqfile);
else if (status == eslEINVAL) cmdline_failure(argv[0], "Can't autodetect stdin or .gz.\n");
else if (status != eslOK) cmdline_failure(argv[0], "Open failed, code %d.\n", status);
/* Open the output file, if any */
if (esl_opt_GetBoolean(go, "-O"))
{
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetArg(go, 2));
}
else if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/* Indexing mode */
if (esl_opt_GetBoolean(go, "--index"))
{
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
if (sqfp->data.ascii.do_gzip) cmdline_failure(argv[0], "Can't index a .gz compressed file");
if (sqfp->data.ascii.do_stdin) cmdline_failure(argv[0], "Can't index a standard input pipe");
create_ssi_index(go, sqfp);
}
/* List retrieval mode */
else if (esl_opt_GetBoolean(go, "-f"))
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
/* Open the SSI index for retrieval */
if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->format))
{
status = esl_sqfile_OpenSSI(sqfp, NULL);
if (status == eslEFORMAT) cmdline_failure(argv[0], "SSI index is in incorrect format\n");
else if (status == eslERANGE) cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
else if (status != eslOK) cmdline_failure(argv[0], "Failed to open SSI index\n");
}
if (esl_opt_GetBoolean(go, "-C")) multifetch_subseq(go, ofp, esl_opt_GetArg(go, 2), sqfp);
else multifetch (go, ofp, esl_opt_GetArg(go, 2), sqfp);
}
/* Single sequence retrieval mode */
else
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
char *key = esl_opt_GetArg(go, 2);
char *cstring = esl_opt_GetString(go, "-c");
char *newname = esl_opt_GetString(go, "-n");
/* Open the SSI index for retrieval */
if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->format))
{
status = esl_sqfile_OpenSSI(sqfp, NULL);
if (status == eslEFORMAT) cmdline_failure(argv[0], "SSI index is in incorrect format\n");
else if (status == eslERANGE) cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
else if (status != eslOK) cmdline_failure(argv[0], "Failed to open SSI index\n");
}
/* -c: subsequence retrieval; else full sequence retrieval */
if (cstring != NULL)
{
uint32_t start, end;
status = esl_regexp_ParseCoordString(cstring, &start, &end);
if (status == eslESYNTAX) esl_fatal("-c takes arg of subseq coords <from>..<to>; %s not recognized", cstring);
if (status == eslFAIL) esl_fatal("Failed to find <from> or <to> coord in %s", cstring);
onefetch_subseq(go, ofp, sqfp, newname, key, start, end);
if (ofp != stdout) printf("\n\nRetrieved subsequence %s/%d-%d.\n", key, start, end);
}
else
{
onefetch(go, ofp, esl_opt_GetArg(go, 2), sqfp);
if (ofp != stdout) printf("\n\nRetrieved sequence %s.\n", esl_opt_GetArg(go, 2));
}
}
esl_sqfile_Close(sqfp);
esl_getopts_Destroy(go);
return 0;
}
