int main(int argc, char *argv[])
{
if (argc != 4)
usage();
database = argv[1];
hSetDb(database);
snpSimpleTable = argv[2];
if (!hTableExistsDb(database, snpSimpleTable))
errAbort("can't get table %s\n", snpSimpleTable);
orthoTable = argv[3];
if (!hTableExistsDb(database, orthoTable))
errAbort("can't get table %s\n", orthoTable);
outputFileHandle = mustOpen("snpOrthoJoin.tab", "w");
missingFileHandle = mustOpen("snpOrthoJoin.missing", "w");
chimpHash = getOrtho(orthoTable, "panTro2");
macaqueHash = getOrtho(orthoTable, "rheMac2");
writeResults(snpSimpleTable);
carefulClose(&outputFileHandle);
carefulClose(&missingFileHandle);
return 0;
}
int main(int argc, char *argv[])
/* Read ContigInfo into hash. */
/* Filter ContigLocusId and write to ContigLocusIdFilter. */
{
if (argc != 3)
usage();
snpDb = argv[1];
contigGroup = argv[2];
hSetDb(snpDb);
/* check for needed tables */
if(!hTableExistsDb(snpDb, "ContigLocusId"))
errAbort("no ContigLocusId table in %s\n", snpDb);
if(!hTableExistsDb(snpDb, "ContigInfo"))
errAbort("no ContigInfo table in %s\n", snpDb);
contigHash = loadContigs(contigGroup);
if (contigHash == NULL)
{
verbose(1, "couldn't get ContigInfo hash\n");
return 1;
}
filterSNPs();
createTable();
loadDatabase();
return 0;
}
int main(int argc, char *argv[])
/* hash subsnp_class and var_str from UniVariation */
/* read SNP for univar_id, lookup into univarHash */
/* store univarHash elements in snpHash */
/* read through chrN_snpTmp, rewrite with extensions to individual chrom tables */
{
struct slName *chromList, *chromPtr;
char tableName[64];
if (argc != 2)
usage();
snpDb = argv[1];
hSetDb(snpDb);
/* check for necessary tables */
if(!hTableExistsDb(snpDb, "SNP"))
errAbort("missing SNP table");
if(!hTableExistsDb(snpDb, "UniVariation"))
errAbort("missing UniVariation table");
chromList = hAllChromNamesDb(snpDb);
errorFileHandle = mustOpen("snpClassAndObserved.errors", "w");
univarHash = getUnivarHash();
snpHash = getSNPHash();
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
verbose(1, "chrom = %s\n", chromPtr->name);
processSnps(chromPtr->name);
}
carefulClose(&errorFileHandle);
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
recreateDatabaseTable(chromPtr->name);
verbose(1, "loading chrom = %s\n", chromPtr->name);
loadDatabase(chromPtr->name);
}
return 0;
}
int main(int argc, char *argv[])
/* read ContigLocFilter, writing to individual chrom tables */
{
struct hashCookie cookie;
struct hashEl *hel;
char *chromName;
if (argc != 3)
usage();
snpDb = argv[1];
contigGroup = argv[2];
hSetDb(snpDb);
/* check for needed tables */
if(!hTableExistsDb(snpDb, "ContigLocFilter"))
errAbort("no ContigLocFilter table in %s\n", snpDb);
if(!hTableExistsDb(snpDb, "ContigInfo"))
errAbort("no ContigInfo table in %s\n", snpDb);
chromHash = loadChroms(contigGroup);
if (chromHash == NULL)
{
verbose(1, "couldn't get chrom info\n");
return 1;
}
writeSplitTables();
verbose(1, "closing files...\n");
cookie = hashFirst(chromHash);
while (hel = hashNext(&cookie))
fclose(hel->val);
verbose(1, "creating tables...\n");
cookie = hashFirst(chromHash);
while ((chromName = hashNextName(&cookie)) != NULL)
createTable(chromName);
verbose(1, "loading database...\n");
cookie = hashFirst(chromHash);
while ((chromName = hashNextName(&cookie)) != NULL)
{
verbose(1, "chrom = %s\n", chromName);
loadDatabase(chromName);
}
return 0;
}
struct hash *readFasta(char *chromName)
/* read moltype from chrN_fasta into hash. */
/* Read again for random */
/* Also called to create the chrN_multi hash. */
{
char query[512];
struct sqlConnection *conn = hAllocConn();
struct sqlResult *sr;
char **row;
char fastaTableName[64];
struct hash *newChromHash = NULL;
char *adjustedChromName = cloneString(chromName);
char *randomSubstring = NULL;
newChromHash = newHash(0);
randomSubstring = strstr(chromName, "random");
if (randomSubstring != NULL)
stripString(adjustedChromName, "_random");
safef(fastaTableName, ArraySize(fastaTableName), "%s_snpFasta", adjustedChromName);
if(!hTableExistsDb(snpDb, fastaTableName))
errAbort("can't get table %s\n", fastaTableName);
safef(query, sizeof(query), "select rsId, molType from %s", fastaTableName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
/* could check for duplicates here */
hashAdd(newChromHash, cloneString(row[0]), cloneString(row[1]));
sqlFreeResult(&sr);
hFreeConn(&conn);
return newChromHash;
}
int main(int argc, char *argv[])
/* Read chromInfo into hash. */
/* Read ContigLocusIdCondense into hash. */
/* Recreate chrN_snpTmp, adding fxn_classes. */
{
struct slName *chromList, *chromPtr;
char tableName[64];
if (argc != 2)
usage();
snpDb = argv[1];
hSetDb(snpDb);
chromList = hAllChromNamesDb(snpDb);
/* check for needed tables */
if(!hTableExistsDb(snpDb, "ContigLocusIdCondense"))
errAbort("no ContigLocusIdCondense table in %s\n", snpDb);
if(!hTableExistsDb(snpDb, "chromInfo"))
errAbort("no chromInfo table in %s\n", snpDb);
functionHash = createFunctionHash();
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
verbose(1, "chrom = %s\n", chromPtr->name);
addFunction(chromPtr->name);
}
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
safef(tableName, ArraySize(tableName), "%s_snpTmp", chromPtr->name);
if (!hTableExists(tableName)) continue;
verbose(1, "loading chrom = %s\n", chromPtr->name);
recreateDatabaseTable(chromPtr->name);
loadDatabase(chromPtr->name);
}
return 0;
}
int main(int argc, char *argv[])
{
if (argc != 4)
usage();
database = argv[1];
hSetDb(database);
snpTable = argv[2];
if (!hTableExistsDb(database, snpTable))
errAbort("can't get table %s\n", snpTable);
orthoTable = argv[3];
if (!hTableExistsDb(database, orthoTable))
errAbort("can't get table %s\n", orthoTable);
snpHash = getBaseSnpData(snpTable);
outputFileHandle = mustOpen("snpOrthoLookup.tab", "w");
writeResults(orthoTable);
carefulClose(&outputFileHandle);
return 0;
}
int main(int argc, char *argv[])
/* generate snpOrtho table from snp ortho file */
/* combine with snp table */
{
if (argc != 4)
usage();
hSetDb(argv[1]);
if (!hTableExistsDb(argv[1], argv[2]))
errAbort("can't get table %s\n", argv[2]);
if (!fileExists(argv[3]))
errAbort("can't find %s\n", argv[3]);
orthoHash = getOrtho(argv[3]);
writeResults(argv[2]);
return 0;
}
int main(int argc, char *argv[])
/* Check args and call snpMaskGenes. */
{
if (argc != 5)
usage();
database = argv[1];
if(!hDbExists(database))
errAbort("%s does not exist\n", database);
hSetDb(database);
if(!hTableExistsDb(database, "snp"))
errAbort("no snp table in %s\n", database);
chromName = argv[2];
if(hgOfficialChromName(chromName) == NULL)
errAbort("no such chromosome %s in %s\n", chromName, database);
// check that nib file exists
// or, use hNibForChrom from hdb.c
snpMaskGenes(argv[3], argv[4]);
return 0;
}
int main(int argc, char *argv[])
/* Condense ContigLocusIdFilter and write to ContigLocusIdCondense. */
{
if (argc != 2)
usage();
snpDb = argv[1];
hSetDb(snpDb);
/* check for needed tables */
if(!hTableExistsDb(snpDb, "ContigLocusIdFilter"))
errAbort("no ContigLocusIdFilter table in %s\n", snpDb);
condenseFunctionValues();
createTable();
loadDatabase();
return 0;
}
int main(int argc, char *argv[])
/* Condense SNPSubSNPLinkand write to SNPSubSNPLinkCondense. */
{
if (argc != 2)
usage();
snpDb = argv[1];
hSetDb(snpDb);
/* check for needed tables */
if(!hTableExistsDb(snpDb, "SNPSubSNPLink"))
errAbort("no SNPSubSNPLink table in %s\n", snpDb);
condenseValues();
createTable();
loadDatabase();
return 0;
}
struct genePred *getOverlappingGeneDb(struct genePred **list, char *table, char *chrom, int cStart, int cEnd, char *name, int *retOverlap, char *db)
{
/* read all genes from a table find the gene with the biggest overlap.
Cache the list of genes to so we only read it once */
struct genePred *el = NULL, *bestMatch = NULL, *gp = NULL;
int overlap = 0 , bestOverlap = 0, i;
int *eFrames;
if (list == NULL)
return NULL;
if (*list == NULL)
{
struct genePred *gpList = NULL;
struct sqlConnection *conn = sqlConnect(db);
struct genePredReader *gpr = NULL;
if (!hTableExistsDb(db,table))
table = altTable;
if (!hTableExistsDb(db,table))
{
verbose(2,"no table %s in %s\n",table, db);
return NULL;
}
gpr = genePredReaderQuery(conn, table, NULL);
verbose(1,"Loading Predictions from %s in %s\n",table, db);
gpList = genePredReaderAll(gpr);
if (gpList != NULL)
{
hashAdd(geneListHash, db, gpList);
*list = gpList;
}
sqlDisconnect(&conn);
}
for (el = *list; el != NULL; el = el->next)
{
if (chrom != NULL && el->chrom != NULL)
{
overlap = 0;
if ( sameString(chrom, el->chrom))
{
for (i = 0 ; i<(el->exonCount); i++)
{
overlap += positiveRangeIntersection(cStart,cEnd, el->exonStarts[i], el->exonEnds[i]) ;
}
if (overlap > 20 && sameString(name, el->name))
{
bestMatch = el;
bestOverlap = overlap;
*retOverlap = bestOverlap;
}
if (overlap > bestOverlap)
{
bestMatch = el;
bestOverlap = overlap;
*retOverlap = bestOverlap;
}
}
}
}
if (bestMatch != NULL)
{
/* Allocate genePred and fill in values. */
AllocVar(gp);
gp->name = cloneString(bestMatch->name);
gp->chrom = cloneString(bestMatch->chrom);
gp->strand[1] = bestMatch->strand[1];
gp->strand[0] = bestMatch->strand[0];
gp->txStart = bestMatch->txStart;
gp->txEnd = bestMatch->txEnd;
gp->cdsStart = bestMatch->cdsStart;
gp->cdsEnd = bestMatch->cdsEnd;
gp->exonCount = bestMatch->exonCount;
AllocArray(gp->exonStarts, bestMatch->exonCount);
AllocArray(gp->exonEnds, bestMatch->exonCount);
for (i=0; i<bestMatch->exonCount; ++i)
{
gp->exonStarts[i] = bestMatch->exonStarts[i] ;
gp->exonEnds[i] = bestMatch->exonEnds[i] ;
}
gp->optFields = bestMatch->optFields;
gp->id = bestMatch->id;
if (bestMatch->optFields & genePredName2Fld)
gp->name2 = cloneString(bestMatch->name2);
else
gp->name2 = NULL;
if (bestMatch->optFields & genePredCdsStatFld)
{
gp->cdsStartStat = bestMatch->cdsStartStat;
gp->cdsEndStat = bestMatch->cdsEndStat;
}
if (bestMatch->optFields & genePredExonFramesFld)
{
gp->exonFrames = AllocArray(eFrames, bestMatch->exonCount);
for (i = 0; i < bestMatch->exonCount; i++)
gp->exonFrames[i] = bestMatch->exonFrames[i];
}
eFrames = gp->exonFrames;
}
return gp;
}
void doMiddle(struct cart *theCart)
/* Set up pretty web display. */
{
struct sqlConnection *conn, *conn2;
struct sqlConnection *connCentral = hConnectCentral();
char query[256], query2[256];
struct sqlResult *sr, *sr2;
char **row, **row2;
char buf[128];
char *answer;
char *database;
char *genome, *genomeDesc;
char *kgID, *chrom, *txStart, *txEnd;
int iCnt = 1;
cart = theCart;
cartWebStart(theCart, database, "UCSC Known Genes List \n");
getDbAndGenome(cart, &database, &genome, oldVars);
if (!hTableExistsDb(database, "knownGene"))
{
printf("<br>Database %s currently does not have UCSC Known Genes.", database);
cartWebEnd();
return;
}
sprintf(query, "select description from dbDb where name = '%s'", database);
genomeDesc = strdup(sqlQuickQuery(connCentral, query, buf, sizeof(buf)));
hDisconnectCentral(&connCentral);
printf("<H2>%s Genome (%s Assembly)</H2>\n", genome, genomeDesc);
conn = hAllocConn(database);
conn2= hAllocConn(database);
sprintf(query2,"select kgID from %s.kgXref order by geneSymbol;",
database);
/* use the following for quck testing */
/*sprintf(query2,"select kgID, geneSymbol, description, spID, refseq from %s.kgXref order by geneSymbol limit 10;", database);
*/
sr2 = sqlMustGetResult(conn2, query2);
row2 = sqlNextRow(sr2);
while (row2 != NULL)
{
kgID = row2[0];
sprintf(query,"select chrom, txSTart, txEnd from %s.knownGene where name='%s'", database, kgID);
sr = sqlMustGetResult(conn, query);
row = sqlNextRow(sr);
chrom = row[0];
txStart = row[1];
txEnd = row[2];
printf("<A href=\"/cgi-bin/hgGene?db=%s&hgg_gene=%s",
database, kgID);
printf("&hgg_chrom=%s&hgg_start=%s&hgg_end=%s\">", chrom, txStart, txEnd);
printf("%d</A><BR>\n", iCnt);
iCnt++;
if ((iCnt % 1000) == 0) fflush(stdout);
sqlFreeResult(&sr);
row2 = sqlNextRow(sr2);
}
sqlFreeResult(&sr2);
cartWebEnd();
}