自学教程：C++ sqlMustGetResult函数代码示例

void hgGetNrOmimGene(char *database, char *outFileName)/* hgGetNrOmimGene - Generate omimGene entries related to NR_xxxx RefSeq. */{struct sqlConnection *conn2, *conn3; char query2[256], query3[256];struct sqlResult *sr2, *sr3;char **row2, **row3;FILE *outf;char *chrom, *txStart, *txEnd;char *omimId;outf = fopen(outFileName, "w");conn2= hAllocConn(database);conn3= hAllocConn(database);	/* first get all RefSeq entries that begin with "NR_" and have related OMIM entries */sprintf(query2,"select g.chrom, g.txStart, g.txEnd, omimId from refGene g, refLink l, omimGene o where l.mrnaAcc=g.name and g.name like 'NR_%c' and omimId <>0 limit 1000", '%');sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);while (row2 != NULL)    {    chrom 	= row2[0];    txStart 	= row2[1];    txEnd	= row2[2];    omimId	= row2[3];    /* then check if this omimId is already in the omimGene table */    sprintf(query3,"select name from %s.omimGene where name='%s'",    	    database, omimId);    sr3 = sqlMustGetResult(conn3, query3);    row3 = sqlNextRow(sr3);    /* if not, create a new omimGene entry */    if (row3 == NULL)	{	fprintf(outf,"%s/t%s/t%s/t%s/n", chrom, txStart, txEnd, omimId);	}    sqlFreeResult(&sr3);    row2 = sqlNextRow(sr2);    }sqlFreeResult(&sr2);hFreeConn(&conn2);hFreeConn(&conn3);fclose(outf);}

int searchProteinsInSwissProtByGene(char *queryGeneID)/* search Swiss-Prot database to see if it contains the protein   Input: queryGeneID   return: number of proteins found in Swiss-Prot*/{int  proteinCnt;struct sqlConnection *conn;char query[256];struct sqlResult *sr;char **row;conn = sqlConnect(UNIPROT_DB_NAME);sqlSafef(query, sizeof(query),            "select count(*) from gene, displayId, accToTaxon,taxon "            "where gene.val='%s' and gene.acc=displayId.acc and accToTaxon.taxon=taxon.id "            "and accToTaxon.acc=gene.acc order by taxon.id",            queryGeneID);sr  = sqlMustGetResult(conn, query);row = sqlNextRow(sr);if (row == NULL)    {    errAbort("Error occured during mySQL query: %s/n", query);    }proteinCnt = atoi(row[0]);sqlFreeResult(&sr);sqlDisconnect(&conn);return(proteinCnt);}

int main(int argc, char *argv[]){char *database;char *outFn;struct sqlConnection *conn2;char query2[256];struct sqlResult *sr2;char **row2;int iCnt;char *chp1, *chp2;if (argc != 3) usage();database = argv[1];conn2= hAllocConn(database);outFn = argv[2];outf = mustOpen(outFn, "w");sprintf(query2,"select gene_rgd_id, uniprot_id from genes_rat where uniprot_id <> /"/"");sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);while (row2 != NULL)    {    boolean oneGeneDone;        rgdId = row2[0];    iCnt = 0;    chp1 = row2[1];    oneGeneDone = FALSE;    while (!oneGeneDone)     	{	iCnt++;	chp2 = strstr(chp1,",");	if (chp2 != NULL)	    {	    *chp2 = '/0';	    fprintf(outf, "RGD:%s/t%s/n", rgdId, chp1);            chp2++;	    chp1 = chp2;	    }	else	    {	    fprintf(outf, "RGD:%s/t%s/n", rgdId, chp1);	    oneGeneDone = TRUE;	    }	}    row2 = sqlNextRow(sr2);    }sqlFreeResult(&sr2);fclose(outf);hFreeConn(&conn2);return(0);}

void webMain(struct sqlConnection *conn)/* Set up fancy web page with hotlinks bar and * sections. */{struct section *sectionList = NULL;char query[256];struct sqlResult *sr;char **row;sectionList = loadSectionList(conn);puts("<FORM ACTION=/"/cgi-bin/gsidSubj/" NAME=/"mainForm/" METHOD=/"GET/">/n");/* display GSID logo image here */printf("<img src=/"/images/gsid_header.jpg/" alt=/"/" name=/"gsid_header/" width=/"800/" height=/"86/" border=/"1/" usemap=/"#gsid_headerMap/">");hPrintf("<br><br>");hotLinks();printf("<font size=/"5/"><BR><B>Subject View   </B></font>");if (sameWord(curSubjId, ""))    {    printf("<BR><H3>Please enter a subject ID./n");    printf("<input type=/"text/" name=/"hgs_subj/" value=/"%s/">/n", curSubjId);    cgiMakeButton("submit", "Go!");    printf("</H3>");    printf("For example: GSID4123");fflush(stdout);    }else    {    sqlSafef(query, sizeof(query), "select subjId from %s.gsidSubjInfo where subjId = '%s'",    	  database, curSubjId);    sr = sqlMustGetResult(conn, query);    row = sqlNextRow(sr);    sqlFreeResult(&sr);    if (row != NULL)    	{    	printf(	"&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;search for another subject:&nbsp;");    	printf("<input type=/"text/" name=/"hgs_subj/" value=/"/">/n");	cgiMakeButton("submit", "Go!");    	printSections(sectionList, conn, curSubjId);    	}    else    	{    	printf("<H3><span style='color:red;'>%s</span> is not a valid subject ID.</H3>", curSubjId);    	printf("<H3>Please enter a valid subject ID./n");    	printf("<input type=/"text/" name=/"hgs_subj/" value=/"%s/">/n", "");    	cgiMakeButton("submit", "Go!");    	printf("<BR><BR>For example: GSID4123");	printf("</H3>");	fflush(stdout);	}    }puts("</FORM>/n");}

void doH1n1Gene(struct trackDb *tdb, char *item)/* Show details page for H1N1 Genes and Regions annotations track. */{struct sqlConnection *conn  = hAllocConn(database);struct sqlResult *sr;char query[256];char **row;char *chrom, *chromStart, *chromEnd;char *gene=NULL;genericHeader(tdb, item);gene = item;printf("<B>Gene: </B> %s/n<BR>", gene);sqlSafef(query, sizeof query, "select chrom, chromStart, chromEnd from h1n1Gene where name='%s';", gene);sr = sqlMustGetResult(conn, query);row = sqlNextRow(sr);if (row != NULL)   {   chrom      = row[0];   chromStart = row[1];   chromEnd   = row[2];   printPosOnChrom(chrom, atoi(chromStart), atoi(chromEnd), NULL, FALSE, item);   }sqlFreeResult(&sr);hFreeConn(&conn);htmlHorizontalLine();printf("<H3>Protein Structure Analysis and Prediction</H3>");printf("<B>3D Structure Prediction of consensus sequence (with variations of all selected sequences highlighted):");printf("<BR>PDB file:</B> ");char pdbUrl[PATH_LEN];safef(pdbUrl, sizeof(pdbUrl), "%s/%s/decoys/%s.try1-opt3.pdb.gz", getH1n1StructUrl(), item, item);// Modeller stuffchar modelPdbUrl[PATH_LEN];if (getH1n1Model(gene, modelPdbUrl))    {    char *selectFile = cartOptionalString(cart, gisaidAaSeqList);    struct tempName imageFile, chimeraScript, chimerax;    mkH1n1StructData(gene, selectFile, NULL, &imageFile, &chimeraScript);    mkChimerax(gene, modelPdbUrl, chimeraScript.forCgi, &chimerax);    printf("<A HREF=/"%s/" TARGET=_blank>%s</A>, view with <A HREF=/"%s/">Chimera</A><BR>/n",     	   modelPdbUrl, gene, chimerax.forHtml);    printf("<TABLE>/n");    printf("<TR>/n");    printf("<TD ALIGN=/"center/"><img src=/"%s/"></TD>", imageFile.forHtml);    printf("</TR>/n");    printf("</TABLE>/n");    }htmlHorizontalLine();printTrackHtml(tdb);sqlFreeResult(&sr);hFreeConn(&conn);}

int main(int argc, char *argv[]){char *database;struct sqlConnection *conn2;char query2[256];struct sqlResult *sr2;char **row2;char *tableName;int expCnt;char *probeId;char *expScores;char *chp, *chp9;char *outFn;FILE *outf;if (argc != 4) usage();database  = argv[1];tableName = argv[2];outFn     = argv[3];outf = mustOpen(outFn, "w");conn2= hAllocConn(database);sqlSafef(query2, sizeof query2, "select name, expCount, expScores from %s", tableName);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);expCnt = 0;while (row2 != NULL)    {    probeId = row2[0];    expScores = row2[2];    chp    = expScores;    chp9   = strstr(chp, ",");    expCnt = 0;    while ((chp9 != NULL) && (chp != NULL))    	{	*chp9 = '/0';    	fprintf(outf, "%s/t%d/t%s/n", probeId, expCnt, chp);        chp = chp9;	chp++;	expCnt++;	chp9 = strstr(chp, ",");	}    row2 = sqlNextRow(sr2);    }sqlFreeResult(&sr2);hFreeConn(&conn2);fclose(outf);return(0);}

int main(int argc, char *argv[]){char *database;char *outFn;struct dnaSeq *seq;struct sqlConnection *conn2;char query2[256];struct sqlResult *sr2;char **row2;if (argc != 4) usage();database = argv[1];conn2= hAllocConn(database);outFn   = argv[2];outf    = mustOpen(outFn, "w");tgtChrom = argv[3];sqlSafef(query2, sizeof query2, "select secStr, name, chrom, chromStart, chromEnd, strand from evofold where chrom='%s'", tgtChrom);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);while (row2 != NULL)    {    secStr   	= row2[0];    id  	= row2[1];    chrom 	= row2[2];    chromStart 	= atoi(row2[3]);    chromEnd   	= atoi(row2[4]);    strand     	= *row2[5];    seq = hChromSeq(database, chrom, chromStart, chromEnd);    touppers(seq->dna);    if (strand == '-')        reverseComplement(seq->dna, seq->size);    memSwapChar(seq->dna, seq->size, 'T', 'U');    safef(javaCmd, sizeof(javaCmd),       "java -cp VARNAv3-7.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN %s -structureDBN '%s' -o evoFold/%s/%s.png",          seq->dna,  secStr, chrom, id);        fprintf(outf, "%s/n", javaCmd);    row2 = sqlNextRow(sr2);    }sqlFreeResult(&sr2);fclose(outf);hFreeConn(&conn2);return(0);}

struct pbStamp *getStampData(char *stampName)/* get data for a stamp */{struct sqlConnection *conn2;char query2[256];struct sqlResult *sr2;char **row2;struct pbStamp *pbStampPtr;int i;conn2= hAllocConn(database);safef(query2, sizeof(query2), "select * from %s.pbStamp where stampName ='%s'", database, stampName);    	sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);pbStampPtr = pbStampLoad(row2);if (row2 == NULL)    {    errAbort("%s stamp data not found.", stampName);    }sqlFreeResult(&sr2);    safef(query2, sizeof(query2), "select * from %s.%s;", database, pbStampPtr->stampTable);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);    	i=0;while (row2 != NULL)    {    tx[i] = atof(row2[0]);    ty[i] = atof(row2[1]);    i++;    row2 = sqlNextRow(sr2);    }sqlFreeResult(&sr2);hFreeConn(&conn2);return(pbStampPtr);}

int searchProteinsInSupportedGenomes(char *queryID, char **database)/* search existing genome databases to see if they contain the protein   Input: queryID   return: number of proteins found in existing genome databases   output: the last genome database is stored at *database*/{int  pbProteinCnt = {0};char *gDatabase;char *org = NULL;char cond_str[255];struct sqlConnection *conn;struct sqlConnection *connCentral;char queryCentral[256];struct sqlResult *srCentral;char **row3;char *answer;/* get all genome DBs that support PB */connCentral = hConnectCentral();sqlSafef(queryCentral, sizeof(queryCentral),      "select defaultDb.name, dbDb.organism from dbDb,defaultDb where hgPbOk=1 and defaultDb.name=dbDb.name");srCentral = sqlMustGetResult(connCentral, queryCentral);row3 = sqlNextRow(srCentral);/* go through each valid genome database that has PB */while (row3 != NULL)    {    gDatabase = row3[0];    org       = row3[1];    conn = sqlConnect(gDatabase);    sqlSafefFrag(cond_str, sizeof(cond_str), "alias='%s'", queryID);    answer = sqlGetField(gDatabase, "kgSpAlias", "count(distinct spID)", cond_str);    sqlDisconnect(&conn);    if ((answer != NULL) && (!sameWord(answer, "0")))    	{	/* increase the count only by one, because new addition of splice variants to kgSpAlias	   would give a count of 2 for both the parent and the variant, which caused the	   problem when rescale button is pressed */	if (atoi(answer) > 0) pbProteinCnt++;	*database = strdup(gDatabase);	}    row3 = sqlNextRow(srCentral);    }sqlFreeResult(&srCentral);hDisconnectCentral(&connCentral);return(pbProteinCnt);}

/* check if a locusID points to a KG mRNA */boolean checkMrna(char *locusID){    struct sqlConnection *conn, *conn2;    char query2[256];    struct sqlResult *sr2;    char **row2;    boolean result;    char cond_str[256];    char *chp;    char *gbAC;    char *gbID;    char *knownGeneID;    conn   = hAllocConn();    conn2  = hAllocConn();    result = FALSE;    sqlSafef(query2, sizeof query2, "select gbAC from %s.locus2Acc0 where locusID=%s and seqType='m';",             tempDbName, locusID);    sr2 = sqlMustGetResult(conn2, query2);    row2 = sqlNextRow(sr2);    while (row2 != NULL)    {        gbAC  	= row2[0];        gbID = strdup(gbAC);        chp = strstr(gbID, ".");        if (chp != NULL) *chp = '/0';        sqlSafefFrag(cond_str, sizeof cond_str, "name = '%s';", gbID);        knownGeneID = sqlGetField(dbName, "knownGene", "name", cond_str);        if (knownGeneID != NULL)        {            result=TRUE;            break;        }        row2 = sqlNextRow(sr2);    }    hFreeConn(&conn);    hFreeConn(&conn2);    sqlFreeResult(&sr2);    return(result);}

static void display1(struct sqlConnection *conn, char *sampleId, char* colName){char query[256];struct sqlResult *sr;char **row;safef(query, sizeof(query),       "select %s from gisaidSubjInfo where EPI_ISOLATE_ID='%s'",       colName, sampleId);sr = sqlMustGetResult(conn, query);row = sqlNextRow(sr);    if (row != NULL)     {    printf("<B>%s:</B> %s<BR>/n", colName, row[0]);    fflush(stdout);    }sqlFreeResult(&sr);}

static struct genbankCds getCds(struct sqlConnection *conn, struct mappingInfo *mi)/* Get CDS, return empty genebankCds if not found or can't parse  */{char query[256];struct sqlResult *sr;struct genbankCds cds;char **row;sqlSafef(query, sizeof(query),      "select cds.name "      "from %s.gbCdnaInfo, %s.cds "      "where gbCdnaInfo.acc=/"%s/" and gbCdnaInfo.cds=cds.id",      database, database, mi->gbAcc);sr = sqlMustGetResult(conn, query);row = sqlNextRow(sr);if ((row == NULL) || !genbankCdsParse(row[0], &cds))    ZeroVar(&cds);  /* can't get or parse cds */sqlFreeResult(&sr);return cds;}

static struct psl *loadAlign(struct sqlConnection *conn, struct mappingInfo *mi, int start)/* load a psl that must exist */{char rootTable[256], table[256], query[256];boolean hasBin;struct sqlResult *sr;char **row;struct psl *psl;if (mi->suffix == NULL)    safef(rootTable, sizeof(rootTable), "%s%sAli", mi->tblPre, mi->geneSet);else    safef(rootTable, sizeof(rootTable), "%s%sAli%s", mi->tblPre, mi->geneSet,mi->suffix);hFindSplitTable(database, seqName, rootTable, table, &hasBin);sqlSafef(query, sizeof(query), "select * from %s where qName = '%s' and tStart = %d",      table, mi->pg->name, start);sr = sqlMustGetResult(conn, query);row = sqlNextRow(sr);psl = pslLoad(row+hasBin);sqlFreeResult(&sr);return psl;}

int main(int argc, char *argv[]){struct sqlConnection *conn; char query[512];struct sqlResult *sr;char **row;char *dataBase;char *chp;char *chp9;char *feature, *xrefStr;char *Dbxref;char *DbxrefEnd = NULL;char *rgdGeneId;char *rest = NULL;FILE *outf;char *outfileName;boolean more;if (argc != 3) usage();dataBase    = argv[1];outfileName = argv[2];outf = mustOpen(outfileName, "w");conn= hAllocConn(dataBase);	sqlSafef(query, sizeof query,"select feature, rgdId from rgdGeneRaw0 where feature = 'gene'");sr = sqlMustGetResult(conn, query);row = sqlNextRow(sr);while (row != NULL)    {    feature 	= row[0];    xrefStr     = row[1];    Dbxref = row[1];    chp9 = strstr(xrefStr, ";");    if (chp9 != NULL)     	{	*chp9 = '/0';	DbxrefEnd = chp9;	}    chp = Dbxref;    /* get start of "RGD:" */    chp = strstr(chp, ",");    chp ++;    rgdGeneId = chp;        /* check if there are other references beside the RGD: entry */    more = FALSE;    chp = strstr(rgdGeneId, ",");    if (chp != NULL)     	{	more = TRUE;	*chp = '/0';        chp++;	rest = chp;	}    if (more)    	{	chp9 = strstr(rest, ",");	while (chp9 != NULL)	    {	    *chp9 = '/0';	    fprintf(outf, "%s/t%s/n", rgdGeneId, chp); fflush(stdout);	    if (DbxrefEnd == chp9)	    	{		/* if end is reached, break */		break;		}	    else	    	{		/* keep looking for next entry */		chp9++;		chp = chp9;		chp9 = strstr(chp, ",");		}	    }		/* print last entry */	fprintf(outf, "%s/t%s/n", rgdGeneId, chp); fflush(stdout);	}        row = sqlNextRow(sr);    }sqlFreeResult(&sr);hFreeConn(&conn);fclose(outf);return(0);}

int getSuperfamilies2(char *proteinID)/* getSuperfamilies2() superceed getSuperfamilies() starting from hg16,    it gets Superfamily data of a protein    from ensemblXref3, sfAssign, and sfDes from the proteinsXXXXXX database,   and placed them in arrays to be used by doSuperfamily().*/{struct sqlConnection *conn, *conn2, *conn3;char query[MAXNAMELEN], query2[MAXNAMELEN];struct sqlResult *sr, *sr2;char **row, **row2;char cond_str[255];char *sfID, *seqID, *sfDesc,  *region;int  done;int j;char *chp, *chp2;int  sfCnt;int  int_start, int_end;if (!hTableExists(protDbName, "sfAssign")) return(0);if (!hTableExists(protDbName, "ensemblXref3")) return(0);conn  = hAllocConn(database);conn2 = hAllocConn(database);conn3 = hAllocConn(database);sqlSafef(query2, sizeof(query),     "select distinct sfID, seqID from %s.ensemblXref3 x, %s.sfAssign a where (swissAcc='%s' or tremblAcc='%s') and seqID=x.protein and protein != '' and evalue <= 0.02",      protDbName, protDbName, proteinID, proteinID);sr2  = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);sfCnt=0;    while (row2 != NULL)    {          sfID = row2[0];    seqID= row2[1];        sqlSafef(query, sizeof(query),     	  "select region from %s.sfAssign where sfID='%s' and seqID='%s' and evalue <=0.02", 	  protDbName, sfID, seqID);    sr = sqlMustGetResult(conn, query);    row = sqlNextRow(sr);        while (row != NULL)    	{        	region   = row[0];    		for (j=0; j<sfCnt; j++)	    {	    if (sfId[j] == atoi(sfID)) goto skip;	    }		sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s;", sfID);    	sfDesc = sqlGetField(protDbName, "sfDes", "description", cond_str);    	/* !!! refine logic here later to be defensive against illegal syntax */    	chp = region;    	done = 0;    	while (!done)	    {	    chp2  = strstr(chp, "-");	    *chp2 = '/0';	    chp2++;	    sscanf(chp, "%d", &int_start);		    chp = chp2;	    chp2  = strstr(chp, ",");	    if (chp2 != NULL) 	    	{	    	*chp2 = '/0';	    	}	    else	    	{	    	done = 1;		}	    chp2++;	    sscanf(chp, "%d", &int_end); 	    sfId[sfCnt]    = atoi(sfID);	    sfStart[sfCnt] = int_start;	    sfEnd[sfCnt]   = int_end;	    strncpy(superfam_name[sfCnt], sfDesc, MAXNAMELEN-1);	    sfCnt++;	    chp = chp2;	    }skip:    	row = sqlNextRow(sr);    	}    sqlFreeResult(&sr);    row2 = sqlNextRow(sr2);    }	sqlFreeResult(&sr2);hFreeConn(&conn);hFreeConn(&conn2);hFreeConn(&conn3);//.........这里部分代码省略.........

int getSuperfamilies(char *proteinID)/* preserved here for previous older genomes.   Newer genomes should be using getSuperfamilies2(). 6/16/04 Fan*/{struct sqlConnection *conn, *conn2;char query[MAXNAMELEN];struct sqlResult *sr;char **row;char cond_str[255];char *genomeID, *seqID, *modelID, *eValue, *sfID, *sfDesc;char *region;int  done;char *ensPep;char *transcriptName;char *chp, *chp2;int  ii = 0;int  int_start, int_end;   if (!hTableExists(database, "sfAssign")) return(0); conn  = hAllocConn(database);conn2 = hAllocConn(database);if (hTableExists(database, "ensemblXref3"))     {	    /* use ensemblXref3 for Ensembl data release after ensembl34d */    sqlSafefFrag(cond_str, sizeof(cond_str), "tremblAcc='%s'", proteinID);    ensPep = sqlGetField(database, "ensemblXref3", "protein", cond_str);    if (ensPep == NULL)	{   	sqlSafefFrag(cond_str, sizeof(cond_str), "swissAcc='%s'", proteinID);   	ensPep = sqlGetField(database, "ensemblXref3", "protein", cond_str);	if (ensPep == NULL) return(0);	}    }else    {    if (! (hTableExists(database, "ensemblXref") || hTableExists(database, "ensTranscript") ) )       return(0);        /* two steps query needed because the recent Ensembl gene_xref 11/2003 table does not have        valid translation_name */    sqlSafefFrag(cond_str, sizeof(cond_str), "external_name='%s'", protDisplayID);    transcriptName = sqlGetField(database, "ensGeneXref", "transcript_name", cond_str);    if (transcriptName == NULL)        {        return(0);         }    else        {        sqlSafefFrag(cond_str, sizeof(cond_str), "transcript_name='%s';", transcriptName);        ensPep = sqlGetField(database, "ensTranscript", "translation_name", cond_str);        if (ensPep == NULL) 	    {	    hFreeConn(&conn);    	    return(0);     	    }    	}    }ensPepName = ensPep;sqlSafef(query, sizeof(query), "select * from %s.sfAssign where seqID='%s' and evalue <= 0.02;", database, ensPep);sr = sqlMustGetResult(conn, query);row = sqlNextRow(sr);if (row == NULL) return(0);    while (row != NULL)    {          genomeID = row[0];    seqID    = row[1];    modelID  = row[2];    region   = row[3];    eValue   = row[4];    sfID     = row[5];    /* sfDesc   = row[6]; */    /* !!! the recent Suprefamily sfAssign table does not have valid sf description */    sqlSafefFrag(cond_str, sizeof(cond_str), "id=%s;", sfID);    sfDesc = sqlGetField(database, "sfDes", "description", cond_str);    /* !!! refine logic here later to be defensive against illegal syntax */    chp = region;    done = 0;    while (!done)	{	chp2  = strstr(chp, "-");	*chp2 = '/0';	chp2++;	sscanf(chp, "%d", &int_start);				chp = chp2;	chp2  = strstr(chp, ",");	if (chp2 != NULL) //.........这里部分代码省略.........

int main(int argc, char *argv[]){struct sqlConnection *conn, *conn2, *conn3;char query[256], query2[256];struct sqlResult *sr, *sr2;char **row, **row2;    char *chp;FILE *o1;char *locusID;	/* LocusLink ID */char *gbAC;		/* GenBank accession.version */char *giNCBI;	/* NCBI gi for the protein record associated with the CDS */char *seqType;	/* sequence type m=mRNA g=genomic u=undefined */char *proteinAC;	/* protein accession.version */char *taxID;	/* tax id */    char *locusID2;	/* LocusLink ID */char *refAC;	/* Refseq accession.version */char *giNCBI2;	/* NCBI gi for the protein record associated with the CDS */char *revStatus;	/* review status */char *proteinAC2;	/* protein accession.version */char *taxID2;	/* tax id */char *dbName; if (argc != 2) usage();dbName = argv[1];conn = hAllocConn(dbName);conn2= hAllocConn(dbName);conn3= hAllocConn(dbName);o1 = fopen("j.dat", "w");    sqlSafef(query2, sizeof query2, "select * from %sTemp.locus2Ref0;", dbName);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);while (row2 != NULL)    {    locusID2 	= row2[0];    refAC 	= row2[1];    giNCBI2 	= row2[2];    revStatus 	= row2[3];    proteinAC2 	= row2[4];    taxID2 	= row2[5];		    sqlSafef(query, sizeof query, "select * from %sTemp.locus2Acc0 where locusID=%s and seqType='m';", dbName, locusID2);    sr = sqlMustGetResult(conn, query);    row = sqlNextRow(sr);    while (row != NULL)    	{	locusID 	= row[0];	gbAC 		= row[1];	giNCBI 		= row[2];	seqType 	= row[3];	proteinAC 	= row[4];	taxID 		= row[5];	chp = strstr(gbAC, ".");	if (chp != NULL) *chp = '/0';    				chp = strstr(refAC, ".");	if (chp != NULL) *chp = '/0';    				fprintf(o1, "%s/t%s/n", gbAC, refAC);				row = sqlNextRow(sr);	}    row2 = sqlNextRow(sr2);    }		fclose(o1);hFreeConn(&conn);hFreeConn(&conn2);sqlFreeResult(&sr2);mustSystem("cat j.dat|sort|uniq >mrnaRefseq.tab");printf("mrnaRefseq.tab created./n");mustSystem("rm j.dat");return(0);}

void processAlign(char *kgTempDb, char *spDb, char *alignID, int cdsCnt, FILE *outf){struct sqlConnection *conn2, *conn3, *conn4;char query2[256], query3[256];struct sqlResult *sr2, *sr3;char **row2, **row3;char *score;char *chrom;char *protAcc;char *mrnaID;char *ranking;int  protDbId;char condStr[255];int  i;char *chp;char *isCurated;conn2= hAllocConn(kgTempDb);conn3= hAllocConn(kgTempDb);conn4= hAllocConn(kgTempDb);sqlSafef(query2, sizeof(query2), "select * from %s.kgCandidate where alignID='%s'", kgTempDb, alignID);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);while (row2 != NULL)    {    mrnaID = row2[0];    chrom = row2[1];    ranking = row2[11];        /* check if it is a composite mrnaID */    /* if yes, select from entries with both protein and mrna specified */    if (alignID[0] == 'U')     	{	chp = strstr(row2[0], "_");	*chp = '/0';	protAcc = row2[0];	chp ++;	mrnaID = chp;    	sqlSafef(query3, sizeof(query3),     	      "select protAcc, score from %s.protMrnaScore where mrnaAcc='%s' and protAcc='%s'",	      kgTempDb, mrnaID, protAcc);	}    else    	{    	sqlSafef(query3, sizeof(query3),     	      "select protAcc, score from %s.protMrnaScore where mrnaAcc='%s' order by score desc",	      kgTempDb, mrnaID);	}	    sr3  = sqlMustGetResult(conn3, query3);    row3 = sqlNextRow(sr3);	          while(row3 != NULL)        {	protAcc = row3[0];	score   = row3[1];	chp = strstr(protAcc, "-");	if (chp == NULL)	    {            sqlSafefFrag(condStr, sizeof(condStr), "acc='%s'", protAcc);	    isCurated = sqlGetField(spDb, "info", "isCurated", condStr);	    if (sameWord(isCurated, "1"))	    	{		protDbId = 1;		}	    else	    	{		protDbId = 2;		}	    }   	else	    {	    protDbId = 4;	    }	    	fprintf(outf, "%s:", chrom);	for (i=0; i<cdsCnt; i++) fprintf(outf, "%s", cdsBloc[i]);	fprintf(outf, "/t%s/t%d/t%8s/t%s/t%s/t%s/n", 		ranking, protDbId, score, mrnaID, protAcc, alignID);	/* for composite type, process just one record */         if (alignID[0] == 'U') break; 	row3 = sqlNextRow(sr3);	}    sqlFreeResult(&sr3);    row2 = sqlNextRow(sr2);    }sqlFreeResult(&sr2);hFreeConn(&conn2);hFreeConn(&conn3);hFreeConn(&conn4);}

int main(int argc, char *argv[]){struct sqlConnection *conn2, *conn3, *conn4;char query2[256], query3[256], query4[256];struct sqlResult *sr2, *sr3, *sr4;char **row2, **row3, **row4;char *aaSeq;char *accession;char *desc;FILE *outFile;char *outFileName;char *tableName;char *interProId;int  maxLen, len;char *maxAcc = NULL;char *start, *end;char *maxStart=NULL, *maxEnd=NULL, *maxDesc = NULL;if (argc != 3) usage();tableName    = argv[1];outFileName  = argv[2];   outFile = mustOpen(outFileName, "w");conn2 = hAllocConn();conn3 = hAllocConn();conn4 = hAllocConn();	/* loop over all InterPro entry for the specific InterPro xref table for this organism */sprintf(query2, "select distinct interProId from proteome.%s", tableName);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);while (row2 != NULL)    {    interProId  = row2[0];        /* get all start/end positions of this InterPro domain */     sprintf(query3,     "select accession, start, end, description from proteome.%s where interProId='%s'",     tableName, interProId);    sr3 = sqlMustGetResult(conn3, query3);    row3 = sqlNextRow(sr3);    maxLen = 0;    while (row3 != NULL)	{   	accession = row3[0];       	start     = row3[1];	         end       = row3[2];  	desc      = row3[3];	len = atoi(end) - atoi(start) + 1;		/* remember the max len, so far */	if (len > maxLen)	    {	    maxLen   = len;	    maxAcc   = cloneString(accession);	    maxStart = cloneString(start);	    maxEnd   = cloneString(end);	    maxDesc  = cloneString(desc);	    }	    	row3 = sqlNextRow(sr3);	}    sqlFreeResult(&sr3);        /* fetch the corresponding AA sequence of the domain having the max length */    sprintf(query4, "select substring(val, %s, %d) from uniProt.protein where acc='%s'",    	    maxStart, maxLen, maxAcc);    sr4 = sqlMustGetResult(conn4, query4);    row4 = sqlNextRow(sr4);    if (row4 == NULL)    	{	fprintf(stderr, "%s %s missing, exiting .../n", maxAcc, interProId);	exit(1);	}    else    	{	aaSeq = row4[0];	if (maxLen >= 18)	    {	    fprintf(outFile, ">%s %s/n", interProId, maxDesc);	    fprintf(outFile, "%s/n", aaSeq);fflush(stdout);	    }	}    sqlFreeResult(&sr4);	           row2 = sqlNextRow(sr2);    }sqlFreeResult(&sr2);hFreeConn(&conn2);hFreeConn(&conn3);hFreeConn(&conn4);fclose(outFile);return(0);}

static void gadPrint(struct section *section, 	struct sqlConnection *conn, char *geneId)/* Print out GAD section. */{int refPrinted = 0;boolean showCompleteGadList;char condStr[256];char query[256];struct sqlResult *sr;char **row;struct dyString *currentCgiUrl;char *upperDisease;char *url = cloneString("http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=gene=");char *itemName;if (url != NULL && url[0] != 0)    {    safef(condStr, sizeof(condStr),     "k.kgId='%s' and k.geneSymbol = g.geneSymbol", geneId);    itemName = sqlGetField(database, "kgXref k, gadAll g", "k.geneSymbol", condStr);    showCompleteGadList = FALSE;    if (cgiOptionalString("showAllRef") != NULL)    	{        if (sameWord(cgiOptionalString("showAllRef"), "Y") ||	    sameWord(cgiOptionalString("showAllRef"), "y") )	    {	    showCompleteGadList = TRUE;	    }	}    currentCgiUrl = cgiUrlString();       printf("<B>Genetic Association Database: ");    printf("<A HREF=/"%s'%s'/" target=_blank>", url, itemName);    printf("%s</B></A>/n", itemName);    printf("<BR><B>CDC HuGE Published Literature:  ");    printf("<A HREF=/"%s%s%s/" target=_blank>",            "http://hugenavigator.net/HuGENavigator/searchSummary.do?firstQuery=",           itemName, 	   "&publitSearchType=now&whichContinue=firststart&check=n&dbType=publit&Mysubmit=go");    printf("%s</B></A>/n", itemName);    /* List diseases associated with the gene */    safef(query, sizeof(query),    "select distinct broadPhen from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",    itemName);    sr = sqlMustGetResult(conn, query);    row = sqlNextRow(sr);        if (row != NULL)     	{	upperDisease = replaceChars(row[0], "'", "''");	touppers(upperDisease);	printf("<BR><B>Positive Disease Associations:  </B>");	printf("<A HREF=/"%s%s%s%s%s/" target=_blank>",	"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",	cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");	printf("%s</B></A>/n", row[0]);        row = sqlNextRow(sr);    	}    while (row != NULL)        {	upperDisease = replaceChars(row[0], "'", "''");	touppers(upperDisease);	printf(", <A HREF=/"%s%s%s%s%s/" target=_blank>",	"http://geneticassociationdb.nih.gov/cgi-bin/tableview.cgi?table=allview&cond=upper(DISEASE)%20like%20'%25",	cgiEncode(upperDisease), "%25'%20AND%20upper(GENE)%20%20like%20'%25", itemName, "%25'");	printf("%s</B></A>/n", row[0]);        row = sqlNextRow(sr);	}    sqlFreeResult(&sr);    refPrinted = 0;    safef(query, sizeof(query),        "select broadPhen,reference,title,journal, pubMed, conclusion from gadAll where geneSymbol='%s' and association = 'Y' order by broadPhen",       itemName);    sr = sqlMustGetResult(conn, query);    row = sqlNextRow(sr);        if (row != NULL) printf("<BR><B>Related Studies: </B><OL>");    while (row != NULL)        {        printf("<LI><B>%s </B>", row[0]);	printf("<br>%s, %s, %s./n", row[1], row[2], row[3]);	if (!sameWord(row[4], ""))	    {	    printf(" [PubMed ");	    printf("<A HREF=/"%s%s%s'/" target=_blank>",	    "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=",	    row[4],"&query_hl=1&itool=genome.ucsc.edu");	    printf("%s</B></A>]/n", row[4]);	    }	printf("<br><i>%s</i>/n", row[5]);		printf("</LI>/n");        refPrinted++;//.........这里部分代码省略.........

void gsidMsa(char *database, char *table, char *baseAcc, int startPos, char *outWigFn, char *outConsFn){struct sqlConnection *conn2; char query2[256];struct sqlResult *sr2;char **row2;FILE *outf, *outf2;char base;int ii;int i = 0;int j,jj,k;int seqCnt = 0;int max, kmax, kmax2;conn2= hAllocConn(database);outf = mustOpen(outWigFn, "w");	sqlSafef(query2, sizeof query2, "select seq from %s.%s where id='%s'", database, table, baseAcc);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);baseGenomeSeq = cloneString(row2[0]);baseSeqLen=strlen(baseGenomeSeq);sqlFreeResult(&sr2);sqlSafef(query2, sizeof query2, "select * from %s.%s", database, table);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);ii=0;while (row2 != NULL)    {    strcpy(seqId[ii], row2[0]);    strcpy(seq[ii], row2[1]);        ii++;    row2 = sqlNextRow(sr2);    }seqCnt = ii;sqlFreeResult(&sr2);hFreeConn(&conn2);/* print header */fprintf(outf, "browser position chr1:1-9000/n");fprintf(outf, "track type=wiggle_0/n");fprintf(outf, "variableStep chrom=chr1/n");jj=0;for (j=0; j<baseSeqLen; j++)    {    for (k=0; k<MAXBASE; k++)    	cnt[i][k] = 0;        for (i=0; i<seqCnt; i++)	{	for (k=0; k<MAXBASE; k++)	    {	    base = toupper(seq[i][j]);	    if (base == refBase[k]) 		{		cnt[j][k]++;		}	    }	}     max  = 0;    kmax = 0;    kmax2= 0;    for (k=0; k<MAXBASE; k++)	{	if (cnt[j][k] > max) 	    {	    max = cnt[j][k];	    	    /* keep track of the 2nd hightest */	    kmax2 = kmax;	    kmax = k;	    }	}    consensusSeq[j] = refBase[kmax];    if (refBase[kmax] == '-')	{        consensusSeq2[j] = refBase2[kmax2];	}    else	{        consensusSeq2[j] = refBase[kmax];	}    aliSeq[j] = refBase[kmax];    identity[j] = (float)max/(float)seqCnt;    if (baseGenomeSeq[j] != '-')	{        fprintf(outf, "%d %f/n", startPos+jj, identity[j]);	jj++;//.........这里部分代码省略.........

int main(int argc, char *argv[]){struct sqlConnection *conn2, *conn3, *conn4;char query2[256], query3[256], query4[256];struct sqlResult *sr2, *sr3, *sr4;char **row2, **row3, **row4;FILE *o3;char *chp;char *proteinDataDate;int maxlen = {0};int len;char *bioentry_id;char *biodatabase_id;char *display_id;char *accession;char *division;char *biosequence_str;  char *desc, *desc2;char *genenames = NULL;char *ontology_term_id;char *qualifier_value;if (argc != 2) usage();proteinDataDate = argv[1];conn2= hAllocConn();conn3= hAllocConn();conn4= hAllocConn();    o3 = fopen("allPep.tab", "w");    sqlSafef(query3, sizeof query3, "select * from biosql%s.bioentry;", proteinDataDate);sr3 = sqlMustGetResult(conn3, query3);row3 = sqlNextRow(sr3);	      while (row3 != NULL)    {    bioentry_id 	= row3[0];    biodatabase_id  = row3[1];    display_id 	= row3[2];    accession 	= row3[3];            division 	= row3[5];    	    sqlSafef(query2, sizeof query2, "select * from biosql%s.biosequence where bioentry_id='%s';", 	           proteinDataDate, bioentry_id);    sr2 = sqlMustGetResult(conn2, query2);    row2 = sqlNextRow(sr2);    if (row2 != NULL)	{ 	biosequence_str = row2[4];			len = strlen(biosequence_str);	if (maxlen < len) maxlen = len;	}		    sqlSafef(query4, sizeof query4,	    "select * from biosql%s.bioentry_qualifier_value where bioentry_id='%s';",	    proteinDataDate, bioentry_id);        genenames="";    desc  = "";    desc2 = "";	    sr4  = sqlMustGetResult(conn4, query4);    row4 = sqlNextRow(sr4);    if (row4 != NULL)	{	ontology_term_id= row4[1];	qualifier_value = row4[2];	if (strcmp(ontology_term_id, "10") == 0)	    {	    desc = qualifier_value;	    }	chp = strstr(desc, "(");	if (chp != NULL)	    {	    chp--;	    *chp = '/0';	    chp++;	    desc2 = chp;	    }	}    fprintf(o3, "%s/t%s/t%s/t%s/t%s/t%s/t%s/t%s/t%s/n",       		bioentry_id,   		biodatabase_id,    		display_id,    		accession,    		division,		genenames,		desc,		desc2,//.........这里部分代码省略.........

//.........这里部分代码省略........./*	if we are not doing a summary (== return all data) and *	we are not creating a bed list, then obey the limit requested *	It will be zero if they really want everything. */if (!summaryOnly && !createBedList)    dataLimit = maxBedElements;spans = newHash(0);	/*	a listing of all spans found here	*/resetStats(&wigStatsAcc);	/*	zero everything	*//*	Are the constraints going to interfere with our span search ? */if (constraints)    {    char *c = cloneString(constraints);    tolowers(c);    if (stringIn("span",c))	bewareConstraints = TRUE;    }if (bewareConstraints)    snprintf(query, sizeof(query),	"SELECT span from %s where chrom = '%s' AND %s group by span",	table, chromName, constraints );else    snprintf(query, sizeof(query),	"SELECT span from %s where chrom = '%s' group by span",	table, chromName );/*	Survey the spans to see what the story is here */sr = sqlMustGetResult(conn,query);while ((row = sqlNextRow(sr)) != NULL){    unsigned span = sqlUnsigned(row[0]);    ++rowCount;    snprintf(spanName, sizeof(spanName), "%u", span);    el = hashLookup(spans, spanName);    if ( el == NULL)	{	if (span > mostSpan) mostSpan = span;	if (span < leastSpan) leastSpan = span;	++spanCount;	hashAddInt(spans, spanName, span);	}    }sqlFreeResult(&sr);/*	Now, using that span list, go through each span, fetching data	*/cookie = hashFirst(spans);while ((! reachedDataLimit) && (el = hashNext(&cookie)) != NULL)    {    if ((struct wiggleStats **)NULL != wsList)	returnStats(&wigStatsAcc,wsList,chromName,winStart,winEnd,span);    resetStats(&wigStatsAcc);    if (bewareConstraints)	{	snprintf(whereSpan, sizeof(whereSpan), "((span = %s) AND %s)", el->name,	    constraints);

int spanInUse(struct sqlConnection *conn, char *table, char *chrom,	int winStart, int winEnd, struct cart *cart)/*	determine span used during hgTracks display, *	winEnd == 0 means whole chrom	*/{struct sqlResult *sr;char query[256];char **row;float basesPerPixel = 0.0;int spanInUse = 0;struct hashCookie cookie;int insideWidth;int minSpan = BIGNUM;int maxSpan = 0;int spanCount = 0;struct hash *spans = newHash(0);	/*	list of spans in this table */struct hashEl *el;int insideX = hgDefaultGfxBorder;int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH ));boolean withLeftLabels = cartUsualBoolean(cart, "leftLabels", TRUE);/*	winEnd less than 1 (i.e. == 0), we need to find this chrom size	*/if (winEnd < 1)    {    safef(query, ArraySize(query),	"SELECT size from chromInfo where chrom = '%s'", chrom);    sr = sqlMustGetResult(conn,query);    if ((row = sqlNextRow(sr)) == NULL)	errAbort("spanInUse: query failed: '%s'/n", query);    winEnd = sqlUnsigned(row[0]);    sqlFreeResult(&sr);    if (winEnd < 1)	errAbort("spanInUse: failed to find valid chrom size via query: '%s'/n", query);    }/*	This is a time expensive query, *	~3 to 6 seconds on large chroms full of data	*/safef(query, ArraySize(query),    "SELECT span from %s where chrom = '%s' group by span", table, chrom);sr = sqlMustGetResult(conn,query);while ((row = sqlNextRow(sr)) != NULL)    {       char spanName[128];    unsigned span = sqlUnsigned(row[0]);    safef(spanName, ArraySize(spanName), "%u", span);    el = hashLookup(spans, spanName);    if ( el == NULL)	{	if (span > maxSpan) maxSpan = span;	if (span < minSpan) minSpan = span;	++spanCount;	hashAddInt(spans, spanName, span);	}    }sqlFreeResult(&sr);spanInUse = minSpan;if (withLeftLabels)	insideX += hgDefaultLeftLabelWidth + hgDefaultGfxBorder;insideWidth = pixWidth - insideX - hgDefaultGfxBorder;basesPerPixel = (winEnd - winStart) / insideWidth;cookie = hashFirst(spans);while ((el = hashNext(&cookie)) != NULL)    {    int span = sqlSigned(el->name);        if ((float) span <= basesPerPixel) 	spanInUse = span;    }return spanInUse;}	/*	int spanInUse()	*/

int main(int argc, char *argv[]){    struct sqlConnection *conn, *conn2;    char query2[256];    struct sqlResult *sr2;    char **row2;    char cond_str[255];    char *proteinDatabaseName;    FILE *o1, *o2, *o3;    FILE *fh[23];    char temp_str[1000];;    char *accession;    char *aaSeq;    char *chp;    int i, j, len;    int ihi, ilow;    char *answer;    char *protDisplayId;    int aaResCnt[30];    char aaAlphabet[30];    int aaResFound;    float fvalue1, fvalue2;    float p1, p2;    int icnt, jcnt;    char *taxon;    char *database;    int sortedCnt;    if (argc != 4) usage();    strcpy(aaAlphabet, "WCMHYNFIDQKRTVPGEASLXZB");    proteinDatabaseName = argv[1];    taxon = argv[2];    database = argv[3];    o2 = mustOpen("pbResAvgStd.tab", "w");    for (i=0; i<20; i++)    {        safef(temp_str, sizeof(temp_str), "%c.txt", aaAlphabet[i]);        fh[i] = mustOpen(temp_str, "w");    }    conn  = hAllocConn(hDefaultDb());    conn2 = hAllocConn(hDefaultDb());    safef(query2, sizeof(query2), "select proteinID from %s.knownGene;", database);    sr2 = sqlMustGetResult(conn2, query2);    row2 = sqlNextRow(sr2);    icnt = 0;    jcnt = 0;    for (j=0; j<MAXRES; j++)    {        sumJ[j] = 0;    }    while (row2 != NULL)    {        protDisplayId = row2[0];        safef(cond_str, sizeof(cond_str),  "val='%s'", protDisplayId);        accession = sqlGetField(proteinDatabaseName, "displayId", "acc", cond_str);        if (accession == NULL)        {            safef(cond_str, sizeof(cond_str),  "acc='%s'", protDisplayId);            accession = sqlGetField(proteinDatabaseName, "displayId", "acc", cond_str);            if (accession == NULL)            {                verbose(2, "'%s' not found./n", protDisplayId);                goto skip;            }        }        safef(cond_str, sizeof(cond_str),  "accession='%s'", accession);        answer = sqlGetField("proteins040115", "spXref2", "biodatabaseID", cond_str);        if (answer == NULL)        {            /* this protein might be a variant splice protein, and then it won't be in spXref2 */            goto skip;        }        if (answer[0] != '1')        {            /* printf("%s not in SWISS-PROT/n", protDisplayId);fflush(stdout); */            goto skip;        }        safef(cond_str, sizeof(cond_str),  "acc='%s'", accession);        aaSeq = sqlGetField(proteinDatabaseName, "protein", "val", cond_str);        if (aaSeq == NULL)        {            printf("Can't find peptide sequence for %s, exiting .../n", protDisplayId);            fflush(stdout);            exit(1);        }        len  = strlen(aaSeq);        if (len < 100) goto skip;//.........这里部分代码省略.........

static void sequencePrint(struct section *section, 	struct sqlConnection *conn, char *subjId)/* Print out Sequence section. */{char query[256];struct sqlResult *sr;char **row;char *seq, *seqId;int i, l;char *chp;printf("<B>DNA Sequences</B><BR>");sqlSafef(query, sizeof(query),       "select dnaSeqId, seq from gisaidXref, dnaSeq where subjId = '%s' and id = dnaSeqId order by dnaSeqId", subjId);sr = sqlMustGetResult(conn, query);row = sqlNextRow(sr);if (row == NULL) printf("<BR>Not available.<BR><BR>");while (row != NULL)     {    seqId    = row[0];    seq	     = row[1];    l =strlen(seq);    hPrintf("<A NAME=/"%s/">/n", seqId);    hPrintf("<pre>/n");    hPrintf("%c%s", '>', seqId);    hPrintf("%s%s", ":", subjId);    chp = seq;    for (i=0; i<l; i++)	{	if ((i%50) == 0) hPrintf("/n");	hPrintf("%c", *chp);	chp++;	}    hPrintf("</pre>");    fflush(stdout);        row = sqlNextRow(sr);    }sqlFreeResult(&sr);printf("<B>Protein Sequences</B><BR>");sqlSafef(query, sizeof(query),       "select aaSeqId, seq from gisaidXref, aaSeq where subjId = '%s' and aaSeqId = id order by aaSeqId", subjId);sr = sqlMustGetResult(conn, query);row = sqlNextRow(sr);if (row == NULL) printf("<BR>Not available.<BR>");    while (row != NULL)     {    seqId    = row[0];    seq	     = row[1];    l =strlen(seq);    hPrintf("<A NAME=/"%s/">/n", seqId);    hPrintf("<pre>/n");    hPrintf("%c%s", '>', seqId);    hPrintf("%s%s", ":", subjId);    //hPrintf("<A NAME=/"%s/">/n", seqId);    //hPrintf("><A HREF=/"../cgi-bin/pbGsid?proteinID=%s/"", seqId);    //hPrintf("%c%s", '>', seqId);    //hPrintf("</A>");    //hPrintf("%c%s", ':', subjId);    chp = seq;    for (i=0; i<l; i++)	{	if ((i%50) == 0) hPrintf("/n");	hPrintf("%c", *chp);	chp++;	}    hPrintf("</pre>");    fflush(stdout);        row = sqlNextRow(sr);    }sqlFreeResult(&sr);return;}

int main(int argc, char *argv[]){struct sqlConnection *conn, *conn2, *conn3;char query[256], query2[256], query3[256];struct sqlResult *sr, *sr2, *sr3;char **row, **row2, **row3;char *r1, *r2, *r3, *r4;FILE *o1;char *proteinDataDate;char *bio_dblink_id;char *source_bioentry_id;char *dbxref_id;char *bioentry_id;char *biodatabase_id;char *display_id;char *accession;char *entry_version;char *division;     char *dbxref_id3;char *dbname;char *extAC;if (argc != 2) usage();proteinDataDate = argv[1];o1 = fopen("temp_spXref2.dat", "w");conn = hAllocConn();conn2= hAllocConn();conn3= hAllocConn();sprintf(query2,"select * from biosql%s.bioentry;", proteinDataDate);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);while (row2 != NULL)    {    bioentry_id 	= row2[0];        biodatabase_id 	= row2[1];     display_id		= row2[2];         accession		= row2[3];          entry_version	= row2[4];      division		= row2[5];			           sprintf(query, "select * from biosql%s.bioentry_direct_links where source_bioentry_id='%s';",	    proteinDataDate, bioentry_id);    sr = sqlMustGetResult(conn, query);    row = sqlNextRow(sr);    while (row != NULL)    	{    	bio_dblink_id = row[0];    	source_bioentry_id = row[1];   	dbxref_id = row[2];            sprintf(query3, "select * from biosql%s.dbxref where dbxref_id=%s;",		proteinDataDate, dbxref_id);	sr3  = sqlMustGetResult(conn3, query3);    	row3 = sqlNextRow(sr3);	dbxref_id3 	= row3[0];	dbname 		= row3[1];	extAC 		= row3[2];				fprintf(o1, "%s/t%s/t%s/t%s/t%s/t%s/t%s/n", accession, display_id, division,		    dbname, extAC,bioentry_id,biodatabase_id);			    	sqlFreeResult(&sr3);	row = sqlNextRow(sr);	}   sqlFreeResult(&sr);   row2 = sqlNextRow(sr2);   }fclose(o1);sqlFreeResult(&sr2);hFreeConn(&conn);hFreeConn(&conn2);hFreeConn(&conn3);system("cat temp_spXref2.dat | sort |uniq > spXref2.tab");system("rm temp_spXref2.dat");return(0);}

int main(int argc, char *argv[]){struct sqlConnection *conn, *conn2, *conn3;char query[256], query2[256], query3[256];struct sqlResult *sr, *sr2, *sr3;char **row, **row2, **row3;char *chp;FILE *o1, *o2;char *locusID;	/* LocusLink ID */char *gbAC;		/* GenBank accession.version */char *locusID2;	/* LocusLink ID */char *refAC;	/* Refseq accession.version */char *dbName; char cond_str[200];char *kgID;char *mapID;char *desc;if (argc != 2) usage();dbName = argv[1];conn = hAllocConn(dbName);conn2= hAllocConn(dbName);conn3= hAllocConn(dbName);o1 = fopen("j.dat",  "w");o2 = fopen("jj.dat", "w");    sprintf(query2,"select * from %sTemp.locus2Ref0;", dbName);sr2 = sqlMustGetResult(conn2, query2);row2 = sqlNextRow(sr2);while (row2 != NULL)    {    locusID2 	= row2[0];    refAC 	= row2[1];        sprintf(query, "select * from %sTemp.locus2Acc0 where locusID=%s and seqType='m';", 		   dbName, locusID2);    sr = sqlMustGetResult(conn, query);    row = sqlNextRow(sr);    while (row != NULL)    	{	locusID 	= row[0];	gbAC 		= row[1];		chp = strstr(gbAC, ".");	if (chp != NULL) *chp = '/0';	chp = strstr(refAC, ".");	if (chp != NULL) *chp = '/0';    	sprintf(cond_str, "name='%s'", gbAC);        kgID = sqlGetField(dbName, "knownGene", "name", cond_str);	if (kgID != NULL)	    {            sprintf(query3, "select * from %sTemp.keggList where locusID = '%s'", dbName, locusID);            sr3 = sqlGetResult(conn3, query3);            while ((row3 = sqlNextRow(sr3)) != NULL)                {                mapID   = row3[1];		desc    = row3[2];		fprintf(o1, "%s/t%s/t%s/n", kgID, locusID, mapID);		fprintf(o2, "%s/t%s/n", mapID, desc);		row3 = sqlNextRow(sr3);                }            sqlFreeResult(&sr3);	    }	row = sqlNextRow(sr);	}    row2 = sqlNextRow(sr2);    }sqlFreeResult(&sr2);fclose(o1);fclose(o2);hFreeConn(&conn);hFreeConn(&conn2);mustSystem("cat j.dat|sort|uniq >keggPathway.tab");mustSystem("cat jj.dat|sort|uniq >keggMapDesc.tab");mustSystem("rm j.dat");mustSystem("rm jj.dat");return(0);}