Beispiel #1
0
int main(int argc, char **argv)
{
    AjPSeqall seqall;
    AjPSeq seq = NULL;
    AjPFile primerFile;		  /* read the primer pairs from a file */
    AjPFile outf;
    AjPList primerList;

    ajint mmp = 0;

    embInit("primersearch", argc, argv);

    seqall     = ajAcdGetSeqall("seqall");
    outf       = ajAcdGetOutfile("outfile");
    primerFile = ajAcdGetInfile("infile");
    mmp        = ajAcdGetInt("mismatchpercent");

    /* build list of forward/reverse primer pairs as read from primerfile */
    primerList = ajListNew();

    /* read in primers from primerfile, classify and compile them */
    primersearch_read_primers(&primerList,primerFile, mmp);

    /* check there are primers to be searched */
    if(!ajListGetLength(primerList))
    {
	ajErr("No suitable primers found - exiting");
	embExitBad();
	return 0;

    }

    /* query sequences one by one */
    while(ajSeqallNext(seqall,&seq))
	primersearch_primer_search(primerList, seq);

    /* output the results */
    primersearch_print_hits(primerList, outf);

    /* delete all nodes of list, then the list itself */
    ajListMap(primerList, primersearch_free_primer, NULL);
    ajListFree(&primerList);
    ajListFree(&primerList);

    ajFileClose(&outf);

    ajSeqallDel(&seqall);
    ajSeqDel(&seq);

    ajFileClose(&primerFile);

    embExit();

    return 0;
}
Beispiel #2
0
static ajint supermatcher_findstartpoints(AjPTable seq1MatchTable,
					  const AjPSeq b,
					  const AjPSeq a, ajint *start1,
					  ajint *start2, ajint *end1,
					  ajint *end2)
{
    ajint max = -10;
    ajint offset = 0;
    AjPList matchlist = NULL;
    AjPList ordered = NULL;
    ajint amax;
    ajint bmax;
    ajint bega;
    ajint begb;

    amax = ajSeqGetLen(a)-1;
    bmax = ajSeqGetLen(b)-1;
    bega = ajSeqGetOffset(a);
    begb = ajSeqGetOffset(b);


    ajDebug("supermatcher_findstartpoints len %d %d off %d %d\n",
	     amax, bmax, bega, begb);
    matchlist = embWordBuildMatchTable(seq1MatchTable, b, ajTrue);

    if(!matchlist)
	return 0;
    else if(!matchlist->Count)
    {
        embWordMatchListDelete(&matchlist);
	return 0;
    }


    /* order and add if the gap is gapmax or less */

    /* create list header bit*/
    ordered = ajListNew();

    supermatcher_orderandconcat(matchlist, ordered);

    /* this sets global structure conmax to point to a matchlist element */
    ajListMap(ordered,supermatcher_findmax, &max);

    ajDebug("findstart conmax off:%d count:%d total:%d\n",
	    conmax->offset, conmax->count, conmax->total,
	    ajListGetLength(conmax->list));
    offset = conmax->offset;

    /* the offset is all we needed! we can delete everything */

    ajListMap(ordered,supermatcher_removelists, NULL);
    ajListFree(&ordered);
    embWordMatchListDelete(&matchlist);	/* free the match structures */


    if(offset > 0)
    {
	*start1 = offset;
	*start2 = 0;
    }
    else
    {
	*start2 = 0-offset;
	*start1 = 0;
    }
    *end1 = *start1;
    *end2 = *start2;

    ajDebug("++ end1 %d -> %d end2 %d -> %d\n", *end1, amax, *end2, bmax);
    while(*end1<amax && *end2<bmax)
    {
	(*end1)++;
	(*end2)++;
    }

    ajDebug("++ end1 %d end2 %d\n", *end1, *end2);
    
    
    ajDebug("supermatcher_findstartpoints has %d..%d [%d] %d..%d [%d]\n",
	    *start1, *end1, ajSeqGetLen(a), *start2, *end2, ajSeqGetLen(b));

    return 1;
}
Beispiel #3
0
static void supermatcher_orderandconcat(AjPList list,AjPList ordered)
{
    ajListMap(list,supermatcher_matchListOrder, ordered);

    return;
}
int main(int argc, char **argv)
{

    AjPList idlist;
    AjPList* fieldList = NULL;

    AjBool systemsort;
    AjBool cleanup;

    ajint blastv = 0;
    char dbtype  = '\0';

    ajuint maxindex;
    ajuint maxidlen = 0;
    ajuint maxlen;

    AjPStr version = NULL;
    AjPStr seqtype = NULL;

    AjPFile elistfile  = NULL;
    AjPFile* alistfile = NULL;

    AjPStr dbname   = NULL;
    AjPStr release  = NULL;
    AjPStr datestr  = NULL;
    AjPStr sortopt  = NULL;
    void **entryIds = NULL;

    AjBool usesrc = AJTRUE;

    AjPStr directory;
    AjPStr indexdir;
    AjPStr filename;
    AjPStr exclude;
    AjPStr curfilename = NULL;

    AjPStr idformat = NULL;

    EmbPEntry entry;

    PBlastDb db = NULL;

    ajuint idCount = 0;
    ajuint idDone;
    AjPList listTestFiles = NULL;
    void ** testFiles = NULL;
    ajuint nfiles;
    ajuint ifile;
    ajuint jfile;

    ajuint filesize;
    short recsize;
    ajuint maxfilelen = 20;
    char date[4] =
    {
	0,0,0,0
    };

    AjPStr tmpfname = NULL;
    AjPStr* fields  = NULL;

    AjPFile entFile = NULL;

    AjPStr* divfiles   = NULL;
    ajint* maxFieldLen = NULL;

    ajuint ifield  = 0;
    ajuint nfields = 0;

    AjPFile logfile = NULL;
    ajuint* countField = NULL;
    ajuint* fieldTot = NULL;
    ajuint idCountFile = 0;
    ajuint i = 0;

    embInit("dbiblast", argc, argv);

    idformat = ajStrNewC("NCBI");

    fields     = ajAcdGetList("fields");
    directory  = ajAcdGetDirectoryName("directory");
    indexdir   = ajAcdGetOutdirName("indexoutdir");
    filename   = ajAcdGetString("filenames");
    exclude    = ajAcdGetString("exclude");
    dbname     = ajAcdGetString("dbname");
    release    = ajAcdGetString("release");
    datestr    = ajAcdGetString("date");
    systemsort = ajAcdGetBoolean("systemsort");
    cleanup    = ajAcdGetBoolean("cleanup");
    sortopt    = ajAcdGetString("sortoptions");
    maxindex   = ajAcdGetInt("maxindex");
    version    = ajAcdGetListSingle("blastversion");
    seqtype    = ajAcdGetListSingle("seqtype");
    usesrc     = ajAcdGetBoolean("sourcefile");
    logfile    = ajAcdGetOutfile("outfile");

    while(fields[nfields])		/* array ends with a NULL */
	nfields++;

    if(nfields)
    {
	AJCNEW(maxFieldLen, nfields);
	AJCNEW0(countField, nfields);
	AJCNEW0(fieldTot, nfields);
	for(ifield=0; ifield < nfields; ifield++)
	    maxFieldLen[ifield] = (ajint) maxindex * -1;

	if(systemsort)
	    AJCNEW(alistfile, nfields);
	else
	{
	    AJCNEW(fieldList, nfields);
	    for(ifield=0; ifield < nfields; ifield++)
		fieldList[ifield] = ajListNew();
	}
    }
    
    if(ajStrMatchC(datestr, "00/00/00"))
	ajFmtPrintS(&datestr, "%D", ajTimeRefTodayFmt("dbindex"));

    ajStrRemoveWhite(&dbname);		/* used for temp filenames */
    embDbiDateSet(datestr, date);
    idlist = ajListNew();
    
    if(ajUtilGetBigendian())
	readReverse = ajFalse;
    else
	readReverse = ajTrue;
    
    ajStrToInt(version, &blastv);
    dbtype = ajStrGetCharFirst(seqtype);
    
    ajDebug("reading '%S/%S'\n", directory, filename);
    ajDebug("writing '%S/'\n", indexdir);
    
    listTestFiles = embDbiFileListExc(directory, filename, exclude);
    ajListSort(listTestFiles, ajStrVcmp);
    nfiles = ajListToarray(listTestFiles, &testFiles);
    if(!nfiles)
        ajDie("No input files in '%S' matched filename '%S'",
              directory, filename);
    
    embDbiLogHeader(logfile, dbname, release, datestr,
		     indexdir, maxindex);

    embDbiLogFields(logfile, fields, nfields);
    embDbiLogSource(logfile, directory, filename, exclude,
		    (AjPStr*) testFiles, nfiles);
    embDbiLogCmdline(logfile);

    AJCNEW0(divfiles, nfiles);
    
    /*
    ** process each input file, one at a time
    */
    
    jfile = 0;
    for(ifile=0; ifile < nfiles; ifile++)
    {
	curfilename = (AjPStr) testFiles[ifile];
	if(!dbiblast_blastopenlib(curfilename,
				  usesrc, blastv, dbtype, &db))
	    continue;	 /* could be the wrong file type with "*.*" */

	ajDebug("processing filename '%S' ...\n", curfilename);
	ajDebug("processing file '%S' ...\n", db->TFile->Name);


	ajStrAssignS(&divfiles[jfile], db->TFile->Name);
	ajFilenameTrimPath(&divfiles[jfile]);
	if(ajStrGetLen(divfiles[jfile]) >= maxfilelen)
	    maxfilelen = ajStrGetLen(divfiles[jfile]) + 1;

	if(systemsort)	 /* elistfile for entries, alist for fields */
	    elistfile = embDbiSortOpen(alistfile, jfile,
				       dbname, fields, nfields);

	idCountFile = 0;
	for(i=0;i<nfields;i++)
	    countField[i] = 0;
	while((entry=dbiblast_nextblastentry(db, jfile,
					     idformat, systemsort,
					     fields,
					     maxFieldLen,
					     &maxidlen, countField,
					     elistfile, alistfile)))
	{
	    idCountFile++;
	    if(!systemsort)	    /* save the entry data in lists */
	    {
		embDbiMemEntry(idlist, fieldList, nfields, entry, jfile);
	    }
	}
	idCount += idCountFile;
	if(systemsort)
	{
	    embDbiSortClose(&elistfile, alistfile, nfields);
	    /* lost the entry, so can't free it :-) */
	}

	embDbiLogFile(logfile, curfilename, idCountFile, fields,
		      countField, nfields);
	dbiblast_dbfree(&db);
	jfile++;
    }
    nfiles = jfile;
    
    /*
    ** write the division.lkp file
    */
    
    embDbiWriteDivision(indexdir, dbname, release, date,
			maxfilelen, nfiles, divfiles, NULL);
    
    /*
    ** Write the entryname.idx index
    */
    
    ajStrAssignC(&tmpfname, "entrynam.idx");
    entFile = ajFileNewOutNamePathS(tmpfname, indexdir);
    
    recsize = maxidlen+10;
    filesize = 300 + (idCount*(ajint)recsize);
    embDbiHeader(entFile, filesize, idCount, recsize, dbname, release, date);
    
    if(systemsort)
        idDone = embDbiSortWriteEntry(entFile, maxidlen,
				      dbname, nfiles, cleanup, sortopt);
    else			  /* save entries in entryIds array */
    {
        idDone = embDbiMemWriteEntry(entFile, maxidlen,
				     idlist, &entryIds);
	if(idDone != idCount)
	    ajFatal("Duplicates not allowed for in-memory processing");
    }
    
    embDbiHeaderSize(entFile, 300+(idDone*(ajint)recsize), idDone);
    ajFileClose(&entFile);
    
    /*
    ** Write the fields index files
    */
    
    for(ifield=0; ifield < nfields; ifield++)
    {

        if(maxindex)
	    maxlen = maxindex;
	else
	{
	    if(maxFieldLen[ifield] >= 0)
		maxlen = maxFieldLen[ifield];
	    else
		maxlen = - maxFieldLen[ifield];
	}

        if(systemsort)
	    fieldTot[ifield] = embDbiSortWriteFields(dbname, release,
						     date, indexdir,
						     fields[ifield], maxlen,
						     nfiles, idCount,
						     cleanup, sortopt);
	else
	    fieldTot[ifield] = embDbiMemWriteFields(dbname, release,
						    date, indexdir,
						    fields[ifield], maxlen,
						    fieldList[ifield],
						    entryIds);
    }
    
    embDbiLogFinal(logfile,maxindex, maxFieldLen, fields, fieldTot,
		   nfields, nfiles, idDone, idCount);

    if(systemsort)
	embDbiRmEntryFile(dbname, cleanup);
    
    ajListMap(idlist, embDbiEntryDelMap, NULL);
    ajListFree(&idlist);
    AJFREE(entryIds);

    ajStrDelarray(&fields);

    for(i=0;i<nfields;i++)
    {
	if(systemsort)
	{
	    ajFileClose(&alistfile[i]);
	}
	else
	{
	    ajListMap(fieldList[i], embDbiFieldDelMap, NULL);
	    ajListFree(&fieldList[i]);
	}
    }
    AJFREE(alistfile);
    AJFREE(fieldList);
    ajStrDel(&version);
    ajStrDel(&seqtype);
    ajFileClose(&elistfile);
    for(i=0;i<nfiles;i++)
    {
	ajStrDel(&divfiles[i]);
    }
    AJFREE(countField);
    AJFREE(fieldTot);

    ajStrDel(&dbname);
    ajStrDel(&release);
    ajStrDel(&datestr);
    ajStrDel(&sortopt);
    ajStrDel(&directory);
    ajStrDel(&indexdir);
    ajStrDel(&filename);
    ajStrDel(&exclude);
    ajStrDel(&idformat);
    ajStrDel(&tmpfname);

    AJFREE(maxFieldLen);

    ajFileClose(&logfile);

    ajListstrFreeData(&listTestFiles);

    ajStrDel(&t);
    ajStrDel(&id);
    ajStrDel(&acc);
    ajStrDel(&hline);
    ajStrDel(&tmpdes);
    ajStrDel(&tmpfd);
    ajStrDel(&tmpgi);
    ajStrDel(&tmpdb);
    ajStrDel(&tmpac);
    ajStrDel(&tmpsv);
    ajRegFree(&wrdexp);

    embDbiEntryDel(&dbiblastEntry);

    if(fdl)
    {
        for(i=0; i < nfields; i++)
            ajListFree(&fdl[i]);
        AJFREE(fdl);
    }

    for(i=0;i<nfiles;i++)
    {
        ajStrDel(&divfiles[i]);
    }
    AJFREE(divfiles);
    AJFREE(testFiles);

    embExit();

    return 0;
}
Beispiel #5
0
int main(int argc, char **argv)
{
    AjPList idlist;
    AjPList* fieldList = NULL;

    AjBool systemsort;
    AjBool cleanup;

    ajuint maxindex;
    ajuint maxidlen = 0;
    ajuint maxlen;

    AjPFile elistfile  = NULL;
    AjPFile* alistfile = NULL;

    AjPStr dbname   = NULL;
    AjPStr release  = NULL;
    AjPStr datestr  = NULL;
    AjPStr sortopt  = NULL;
    void **entryIds = NULL;

    AjPStr directory;
    AjPStr indexdir;
    AjPStr filename;
    AjPStr exclude;
    AjPStr curfilename = NULL;

    AjPFile libr=NULL;
    AjPStr idformat = NULL;

    EmbPEntry entry;

    ajuint idtype  = 0;

    ajuint idCount = 0;
    ajuint idDone;
    AjPList listInputFiles = NULL;
    void ** inputFiles = NULL;
    ajuint nfiles;
    ajuint ifile;

    ajuint filesize;
    short recsize;
    ajuint maxfilelen = 20;
    char date[4] =
    {
	0,0,0,0
    };

    AjPStr tmpfname = NULL;
    AjPStr* fields  = NULL;

    AjPFile entFile  = NULL;

    AjPStr* divfiles   = NULL;
    AjPRegexp regIdExp      = NULL;
    ajint* maxFieldLen = NULL;

    ajuint ifield  = 0;
    ajuint nfields = 0;

    AjPFile logfile = NULL;
    ajuint* countField = NULL;
    ajuint* fieldTot = NULL;
    ajuint idCountFile = 0;
    ajuint i;

    embInit("dbifasta", argc, argv);

    idformat   = ajAcdGetListSingle("idformat");
    fields     = ajAcdGetList("fields");
    directory  = ajAcdGetDirectoryName("directory");
    indexdir   = ajAcdGetOutdirName("indexoutdir");
    filename   = ajAcdGetString("filenames");
    exclude    = ajAcdGetString("exclude");
    dbname     = ajAcdGetString("dbname");
    release    = ajAcdGetString("release");
    datestr    = ajAcdGetString("date");
    systemsort = ajAcdGetBoolean("systemsort");
    cleanup    = ajAcdGetBoolean("cleanup");
    sortopt    = ajAcdGetString("sortoptions");
    maxindex   = ajAcdGetInt("maxindex");
    logfile    = ajAcdGetOutfile("outfile");

    while(fields[nfields])		/* array ends with a NULL */
	nfields++;

    if(nfields)
    {
	AJCNEW(maxFieldLen, nfields);
	AJCNEW0(countField, nfields);
	AJCNEW0(fieldTot, nfields);
	for(ifield=0; ifield < nfields; ifield++)
	    maxFieldLen[ifield] = (ajint)maxindex * -1;

	if(systemsort)
	    AJCNEW(alistfile, nfields);
	else
	{
	    AJCNEW(fieldList, nfields);
	    for(ifield=0; ifield < nfields; ifield++)
		fieldList[ifield] = ajListNew();
	}
    }

    if(ajStrMatchC(datestr, "00/00/00"))
	ajFmtPrintS(&datestr, "%D", ajTimeRefTodayFmt("dbindex"));

    ajStrRemoveWhite(&dbname);		/* used for temp filenames */
    embDbiDateSet(datestr, date);
    idlist = ajListNew();

    regIdExp = dbifasta_getExpr(idformat, &idtype);

    ajDebug("reading '%S/%S'\n", directory, filename);
    ajDebug("writing '%S/'\n", indexdir);

    listInputFiles = embDbiFileListExc(directory, filename, exclude);
    ajListSort(listInputFiles, &ajStrVcmp);
    nfiles = (ajuint) ajListToarray(listInputFiles, &inputFiles);
    if(!nfiles)
        ajDie("No input files in '%S' matched filename '%S'",
              directory, filename);

    embDbiLogHeader(logfile, dbname, release, datestr,
		     indexdir, maxindex);

    embDbiLogFields(logfile, fields, nfields);
    embDbiLogSource(logfile, directory, filename, exclude,
		    (AjPStr*) inputFiles, nfiles);
    embDbiLogCmdline(logfile);

    AJCNEW0(divfiles, nfiles);

    /*
    ** process each input file, one at a time
    */

    for(ifile=0; ifile < nfiles; ifile++)
    {
	ajStrAssignS(&curfilename,(AjPStr) inputFiles[ifile]);
	embDbiFlatOpenlib(curfilename, &libr);
	ajFilenameTrimPath(&curfilename);
	if(ajStrGetLen(curfilename) >= maxfilelen)
	    maxfilelen = ajStrGetLen(curfilename) + 1;

	ajDebug("processing filename '%S' ...\n", curfilename);
	ajDebug("processing file '%F' ...\n", libr);
	ajStrAssignS(&divfiles[ifile], curfilename);

	if(systemsort)	 /* elistfile for entries, alist for fields */
	    elistfile = embDbiSortOpen(alistfile, ifile,
				       dbname, fields, nfields);

	idCountFile = 0;
	for(i=0;i<nfields;i++)
	    countField[i] = 0;
	while((entry=dbifasta_NextFlatEntry(libr, ifile,
					    regIdExp, idtype,
					    systemsort, fields, 
					    maxFieldLen, &maxidlen,
					    countField, elistfile,
					    alistfile)))
	{
	    idCountFile++;
	    if(!systemsort)	    /* save the entry data in lists */
		embDbiMemEntry(idlist, fieldList, nfields,
			       entry, ifile);
		entry = NULL;
	}
	idCount += idCountFile;
	if(systemsort)
	{
	    embDbiSortClose(&elistfile, alistfile, nfields);
	    AJFREE(entry);
	}
	else
	{
	    embDbiEntryDel(&dbifastaGEntry);
	}
	embDbiLogFile(logfile, curfilename, idCountFile, fields,
		      countField, nfields);
    }

    /*  write the division.lkp file */
    embDbiWriteDivision(indexdir, dbname, release, date,
			maxfilelen, nfiles, divfiles, NULL);

    /* Write the entryname.idx index */
    ajStrAssignC(&tmpfname, "entrynam.idx");
    entFile = ajFileNewOutNamePathS(tmpfname, indexdir);

    recsize = maxidlen+10;
    filesize = 300 + (idCount*(ajint)recsize);
    embDbiHeader(entFile, filesize, idCount, recsize, dbname, release, date);

    if(systemsort)
        idDone = embDbiSortWriteEntry(entFile, maxidlen,
				      dbname, nfiles, cleanup, sortopt);
    else			  /* save entries in entryIds array */
    {
        idDone = embDbiMemWriteEntry(entFile, maxidlen,
				     idlist, &entryIds);
	if(idDone != idCount)
	    ajFatal("Duplicates not allowed for in-memory processing");
    }

    embDbiHeaderSize(entFile, 300+(idDone*(ajint)recsize), idDone);
    ajFileClose(&entFile);

    /* Write the fields index files */
    for(ifield=0; ifield < nfields; ifield++)
    {
        if(maxindex)
	    maxlen = maxindex;
	else
	{
	    if(maxFieldLen[ifield] >= 0)
		maxlen = maxFieldLen[ifield];
	    else
		maxlen = - maxFieldLen[ifield];
	}

        if(systemsort)
	    fieldTot[ifield] = embDbiSortWriteFields(dbname, release,
						     date, indexdir,
						     fields[ifield], maxlen,
						     nfiles, idCount,
						     cleanup, sortopt);
	else
	    fieldTot[ifield] = embDbiMemWriteFields(dbname, release,
						    date, indexdir,
						    fields[ifield], maxlen,
						    fieldList[ifield],
						    entryIds);
    }

    embDbiLogFinal(logfile,maxindex, maxFieldLen, fields, fieldTot,
		   nfields, nfiles, idDone, idCount);

    if(systemsort)
	embDbiRmEntryFile(dbname, cleanup);

    ajStrDel(&idformat);
    ajStrDelarray(&fields);
    ajStrDel(&filename);
    ajStrDel(&exclude);
    ajStrDel(&dbname);
    ajStrDel(&release);
    ajStrDel(&datestr);
    ajStrDel(&sortopt);
    ajStrDel(&directory);
    ajStrDel(&indexdir);
    ajStrDel(&tmpfname);
    ajFileClose(&libr);
    ajFileClose(&logfile);

    for(i=0;i<nfields;i++)
    {
	if(systemsort)
	{
	    ajFileClose(&alistfile[i]);
	}
	else
	{
	    ajListMap(fieldList[i], &embDbiFieldDelMap, NULL);
	    ajListFree(&fieldList[i]);
	}
    }

    AJFREE(alistfile);
    AJFREE(fieldList);
    AJFREE(maxFieldLen);
    AJFREE(countField);
    AJFREE(fieldTot);

    for(i=0;i<nfiles;i++)
    {
	ajStrDel(&divfiles[i]);
    }

    AJFREE(divfiles);
    AJFREE(inputFiles);

    embDbiEntryDel(&dbifastaGEntry);

    ajStrDel(&dbifastaGRline);
    ajStrDel(&dbifastaGTmpId);

    if(dbifastaGFdl)
    {
	for(i=0; i < nfields; i++)
	    ajListFree(&dbifastaGFdl[i]);
	AJFREE(dbifastaGFdl);
    }

    ajListMap(idlist, &embDbiEntryDelMap, NULL);
    ajListFree(&idlist);
    ajListstrFreeData(&listInputFiles);
    AJFREE(entryIds);
    ajRegFree(&dbifastaGIdexp);
    ajRegFree(&dbifastaGWrdexp);
    ajRegFree(&regIdExp);

    ajStrDel(&dbifastaGTmpAc);
    ajStrDel(&dbifastaGTmpSv);
    ajStrDel(&dbifastaGTmpGi);
    ajStrDel(&dbifastaGTmpDb);
    ajStrDel(&dbifastaGTmpDes);
    ajStrDel(&dbifastaGTmpFd);
    ajStrDel(&curfilename);

    embExit();

    return 0;
}
int main(int argc, char **argv)
{

    AjPSeqall seqall;
    AjPFile primfile;
    AjPStr rdline = NULL;

    Primer primdata;
    AjPStrTok handle = NULL;

    AjPList primList = NULL;

    embInit("stssearch", argc, argv);

    primfile = ajAcdGetInfile("infile");
    out      = ajAcdGetOutfile("outfile");
    seqall   = ajAcdGetSeqall("seqall");

    while(ajReadlineTrim(primfile, &rdline))
    {
	if(ajStrGetCharFirst(rdline) == '#')
	    continue;
	if(ajStrSuffixC(rdline, ".."))
	    continue;

	AJNEW(primdata);
	primdata->Name   = NULL;
	primdata->Oligoa = NULL;
	primdata->Oligob = NULL;

	handle = ajStrTokenNewC(rdline, " \t");
	ajStrTokenNextParse(&handle, &primdata->Name);

	if(!(nprimers % 1000))
	    ajDebug("Name [%d]: '%S'\n", nprimers, primdata->Name);

	ajStrTokenNextParse(&handle, &primdata->Oligoa);
	ajStrFmtUpper(&primdata->Oligoa);
	primdata->Prima = ajRegComp(primdata->Oligoa);

	ajStrTokenNextParse(&handle, &primdata->Oligob);
	ajStrFmtUpper(&primdata->Oligob);
	primdata->Primb = ajRegComp(primdata->Oligob);
	ajStrTokenDel(&handle);

	if(!nprimers)
	    primList = ajListNew();

	ajListPushAppend(primList, primdata);
	nprimers++;
    }

    if(!nprimers)
	ajFatal("No primers read\n");

    ajDebug("%d primers read\n", nprimers);

    while(ajSeqallNext(seqall, &seq))
    {
	ajSeqFmtUpper(seq);
	ajStrAssignS(&seqstr, ajSeqGetSeqS(seq));
	ajStrAssignS(&revstr, ajSeqGetSeqS(seq));
	ajSeqstrReverse(&revstr);
	ajDebug("Testing: %s\n", ajSeqGetNameC(seq));
	ntests = 0;
	ajListMap(primList, stssearch_primTest, NULL);
    }

    ajFileClose(&out);

    ajSeqallDel(&seqall);
    ajSeqDel(&seq);
    ajFileClose(&out);
    ajStrDel(&revstr);
    ajStrDel(&seqstr);
    ajFileClose(&primfile);
    ajListMap(primList, stssearch_primDel, NULL);
    ajListFree(&primList);
    ajStrDel(&rdline);


    embExit();

    return 0;
}