int palOutPredsInBeds(struct sqlConnection *conn, struct cart *cart,
struct bed *beds, char *table )
/* output the alignments whose names and coords match a bed*/
{
struct genePred *list = NULL;
for(; beds; beds = beds->next)
{
char where[10 * 1024];
sqlSafefFrag(where, sizeof where,
"name = '%s' and chrom='%s' and txEnd > %d and txStart <= %d",
beds->name, beds->chrom, beds->chromStart, beds->chromEnd);
struct genePredReader *reader = genePredReaderQuery( conn, table, where);
struct genePred *pred;
while ((pred = genePredReaderNext(reader)) != NULL)
slAddHead(&list, pred);
genePredReaderFree(&reader);
}
int outCount = 0;
if (list != NULL)
{
slReverse(&list);
outCount = palOutPredList( conn, cart, list);
genePredFreeList(&list);
}
return outCount;
}
static void fakePslFromGenePred(char *db, char *fileTbl, char *pslOut, char *cdsOut)
/* check a genePred */
{
struct genePredReader *gpr;
struct genePred *gp;
FILE *pslFh = mustOpen(pslOut, "w");
FILE *cdsFh = mustOpen(cdsOut, "w");
struct hash *chromHash = getChromHash(db);
if (fileExists(fileTbl))
{
gpr = genePredReaderFile(fileTbl, NULL);
}
else
{
struct sqlConnection *conn = hAllocConn(db);
gpr = genePredReaderQuery(conn, fileTbl, NULL);
hFreeConn(&conn);
}
while ((gp = genePredReaderNext(gpr)) != NULL)
{
cnvGenePred(chromHash, gp, pslFh, cdsFh);
}
genePredReaderFree(&gpr);
carefulClose(&pslFh);
carefulClose(&cdsFh);
}
struct genePred *getPredsFromBeds(char *file, char *table, char *db)
{
struct sqlConnection *conn = hAllocConn(db);
struct lineFile *lf = lineFileOpen(file, TRUE);
char *words[5000];
int wordsRead;
struct genePred *list = NULL;
while( (wordsRead = lineFileChopNext(lf, words, sizeof(words)/sizeof(char *)) ))
{
if (wordsRead != 4)
errAbort("file '%s' must be bed4. Line %d has %d fields",
file, lf->lineIx, wordsRead);
char where[10 * 1024];
sqlSafefFrag(where, sizeof where,
"name = '%s' and chrom='%s' and txStart = %d and txEnd = %d",
words[3], words[0], sqlUnsigned(words[1]), sqlUnsigned(words[2]));
//printf("table %s where %s\n",table,where);
struct genePredReader *reader = genePredReaderQuery( conn, table, where);
struct genePred *pred;
while ((pred = genePredReaderNext(reader)) != NULL)
slAddHead(&list, pred);
genePredReaderFree(&reader);
}
hFreeConn(&conn);
if (list != NULL)
slReverse(&list);
return list;
}
static void checkGenePred(char *fileTbl)
/* check a genePred file or table */
{
struct sqlConnection *conn = NULL;
struct genePredReader *gpr;
struct genePred *gp;
int iRec = 0;
if (fileExists(fileTbl))
{
gpr = genePredReaderFile(fileTbl, NULL);
}
else if (gDb != NULL)
{
conn = hAllocConn(gDb);
gpr = genePredReaderQuery(conn, fileTbl, NULL);
}
else
{
errAbort("file %s doesn't exist, must specify -db=db if this is a table", fileTbl);
}
while ((gp = genePredReaderNext(gpr)) != NULL)
{
checkAGenePred(fileTbl, ++iRec, gp);
genePredFree(&gp);
}
genePredReaderFree(&gpr);
hFreeConn(&conn);
}
struct genePred *genePredReaderLoadFile(char* gpFile, char* chrom)
/* Function that encapsulates reading a genePred file */
{
struct genePredReader *gpr = genePredReaderFile(gpFile, chrom);
struct genePred *gpList = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
return gpList;
}
struct genePred *genePredReaderLoadQuery(struct sqlConnection* conn,
char* table, char* where)
/* Function that encapsulates doing a query and loading the results */
{
struct genePredReader *gpr = genePredReaderQuery(conn, table, where);
struct genePred *gpList = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
return gpList;
}
struct genePred *genePredReaderLoadRangeQuery(struct sqlConnection* conn,
char* table, char* chrom,
int start, int end,
char* extraWhere)
/* Function that encapsulates doing a range query and loading the results */
{
struct genePredReader *gpr = genePredReaderRangeQuery(conn, table, chrom,
start, end, extraWhere);
struct genePred *gpList = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
return gpList;
}
static void printCcdsHgGeneUrl(struct sqlConnection *conn, char *ccdsId, char* kgId)
/* output a URL to hgGene for a ccds */
{
char where[128];
struct genePredReader *gpr;
struct genePred *ccdsGene = NULL, *kgGene = NULL;
/* get ccds genePred to get location */
sqlSafefFrag(where, sizeof(where), "chrom = '%s' and name = '%s'", seqName, ccdsId);
gpr = genePredReaderQuery(conn, "ccdsGene", where);
ccdsGene = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
if (ccdsGene == NULL)
errAbort("%s not found in ccdsGene table for chrom %s", ccdsId, seqName);
else if (ccdsGene->next != NULL)
errAbort("multiple %s rows found in ccdsGene table for chrom %s", ccdsId, seqName);
/* get KG genePred, as need exact location for link */
sqlSafefFrag(where, sizeof(where), "name = '%s' and strand = '%s'", kgId,
ccdsGene->strand);
gpr = genePredReaderRangeQuery(conn, "knownGene", seqName,
ccdsGene->txStart, ccdsGene->txEnd, where);
kgGene = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
if (kgGene == NULL)
errAbort("%s not found in knownGene table for chrom %s", kgId, seqName);
else if (kgGene->next != NULL)
errAbort("multiple %s rows found in knownGene table for chrom %s", kgId, seqName);
printf("../cgi-bin/hgGene?%s&%s=%s&%s=%s&%s=%s&%s=%d&%s=%d",
cartSidUrlString(cart),
"db", database,
"hgg_gene", kgId,
"hgg_chrom", seqName,
"hgg_start", kgGene->txStart,
"hgg_end", kgGene->txEnd);
genePredFree(&ccdsGene);
genePredFree(&kgGene);
}
static void loadGenes(struct orgGenes *genes, char *genePredFile)
/* load genePred file into object */
{
struct genePredReader *gpr = genePredReaderFile(genePredFile, NULL);
struct genePred *gp;
while ((gp = genePredReaderNext(gpr)) != NULL)
{
if ((gp->optFields & genePredExonFramesFld) == 0)
genePredAddExonFrames(gp);
loadGene(genes, gp);
}
genePredReaderFree(&gpr);
}
static void getGeneAnns(struct sqlConnection *conn, struct hash *refSeqVerInfoTbl, char *outFile)
/* get request genePred annotations from database */
{
struct genePredReader *gpr = genePredReaderQuery(conn, "refGene", NULL);
FILE *fh = mustOpen(outFile, "w");
struct genePred *gp;
while ((gp = genePredReaderNext(gpr)) != NULL)
{
processGenePred(fh, refSeqVerInfoTbl, gp);
genePredFree(&gp);
}
carefulClose(&fh);
genePredReaderFree(&gpr);
}
static void genePredHisto(char *what, char *gpFile, char *outFile)
/* get data for generating histograms from a genePred file. */
{
struct genePredReader *gpr = genePredReaderFile(gpFile, NULL);
histoFuncType histoFunc = getHistoFunc(what);
struct genePred *gp;
FILE *outFh = mustOpen(outFile, "w");
while ((gp = genePredReaderNext(gpr)) != NULL)
{
histoFunc(gp, outFh);
genePredFree(&gp);
}
carefulClose(&outFh);
genePredReaderFree(&gpr);
}
/* load one or more genePreds from the database */
struct genePred *getPredsForName(char *name, char *geneTable, char *db)
{
struct sqlConnection *conn = hAllocConn(db);
struct genePred *list = NULL;
char splitTable[HDB_MAX_TABLE_STRING];
struct genePred *gene;
boolean hasBin;
struct genePredReader *reader;
boolean found = hFindSplitTable(db, NULL, geneTable,
splitTable, &hasBin);
if (!found)
errAbort("can't find table %s\n", geneTable);
char extra[2048];
if (onlyChrom != NULL)
safef(extra, sizeof extra, "name='%s' and chrom='%s'", name, onlyChrom);
else
safef(extra, sizeof extra, "name='%s'", name);
reader = genePredReaderQuery( conn, splitTable, extra);
while ((gene = genePredReaderNext(reader)) != NULL)
{
verbose(2, "got gene %s\n",gene->name);
slAddHead(&list, gene);
}
if (list == NULL)
errAbort("no genePred for gene %s in %s\n",name, geneTable);
slReverse(&list);
genePredReaderFree(&reader);
hFreeConn(&conn);
return list;
}
