e2467a639cc1e98174ffbd9d0da399b3b75bc9ae
markd
Thu Jul 26 21:33:38 2012 -0700
highlighting by attribute functionality for GENCODE
diff --git src/hg/lib/genePredReader.c src/hg/lib/genePredReader.c
index 75d5c47..917e394 100644
--- src/hg/lib/genePredReader.c
+++ src/hg/lib/genePredReader.c
@@ -1,343 +1,309 @@
/* genePredReader - object to read genePred objects from database tables
* or files. */
#include "common.h"
#include "genePredReader.h"
#include "jksql.h"
#include "hdb.h"
#include "linefile.h"
#include "genePred.h"
#include "binRange.h"
/* Aliases for name2 field */
static char *name2Aliases[] =
{
"geneName", /* refFlat */
"proteinID", /* knownGene */
NULL
};
/* Field names in the order that they must be passed to genePredLoadExt, with
* the index and optFields flags and aliases for the fields in certain
* tables. Also default values to use. */
struct field
{
char *fld;
int fldIdx;
unsigned optFlag;
char **aliases;
char *defaultVal;
};
static struct field fieldTbl[] =
{
{"name", 0, 0, NULL, NULL},
{"chrom", 1, 0, NULL, NULL},
{"strand", 2, 0, NULL, NULL},
{"txStart", 3, 0, NULL, NULL},
{"txEnd", 4, 0, NULL, NULL},
{"cdsStart", 5, 0, NULL, NULL},
{"cdsEnd", 6, 0, NULL, NULL},
{"exonCount", 7, 0, NULL, NULL},
{"exonStarts", 8, 0, NULL, NULL},
{"exonEnds", 9, 0, NULL, NULL},
{"score", 10, genePredScoreFld, NULL, "0"},
{"name2", 11, genePredName2Fld, name2Aliases, ""},
{"cdsStartStat", 12, genePredCdsStatFld, NULL, "none"},
{"cdsEndStat", 13, genePredCdsStatFld, NULL, "none"},
{"exonFrames", 14, genePredExonFramesFld, NULL, NULL},
{NULL, 0, 0, NULL, NULL},
};
struct genePredReader
/* Object to read genePred objects from database tables or files. */
{
char *table; /* name of table or file */
/* for DB access */
unsigned optFields; /* optional fields being included from DB */
unsigned numFields;
unsigned queryCols;
struct sqlResult *sr; /* results if reading from a DB */
int rowOffset; /* offset if have a bin column */
int queryToFldMap[GENEPREDX_NUM_COLS+1]; /* map of columns in query order
* to field order, may include
* bin, hence =1 */
/* for file access */
struct lineFile *lf; /* lineFile when reading from a file */
char* chrom; /* chrom restriction for files */
};
static int optFieldsToNumFields(unsigned optFields)
/* determine the required number of columns, given the desired optional
* fields */
{
int numFields = GENEPRED_NUM_COLS;
if (optFields & genePredScoreFld)
numFields = GENEPRED_NUM_COLS+1;
if (optFields & genePredName2Fld)
numFields = GENEPRED_NUM_COLS+2;
if (optFields & genePredCdsStatFld)
numFields = GENEPRED_NUM_COLS+4; /* two columns */
if (optFields & genePredExonFramesFld)
numFields = GENEPRED_NUM_COLS+5;
return numFields;
}
static struct field* findField(char *fname)
/* search fieldTbl for the specified field */
{
int iFld, iAlias;
for (iFld = 0; fieldTbl[iFld].fld != NULL; iFld++)
{
if (sameString(fieldTbl[iFld].fld, fname))
return &(fieldTbl[iFld]);
if (fieldTbl[iFld].aliases != NULL)
{
for (iAlias = 0; fieldTbl[iFld].aliases[iAlias] != NULL; iAlias++)
{
if (sameString(fieldTbl[iFld].aliases[iAlias], fname))
return &(fieldTbl[iFld]);
}
}
}
return NULL;
}
static void buildResultFieldMap(struct genePredReader* gpr)
/* determine indices of fields for current result and fill in the mapping
* table. */
{
int iCol = 0, iFld;
char *fname;
/* initialize to not used */
for (iFld = 0; iFld < GENEPREDX_NUM_COLS+1; iFld++)
gpr->queryToFldMap[iFld] = -1;
/* build sparse field map */
while ((fname = sqlFieldName(gpr->sr)) != NULL)
{
if (sameString(fname, "bin"))
{
if (iCol != 0)
errAbort("bin column not first column in %s", gpr->table);
gpr->rowOffset = 1;
}
else
{
struct field* field = findField(fname);
if (field != NULL)
{
gpr->queryToFldMap[iCol] = field->fldIdx;
gpr->optFields |= field->optFlag;
}
}
gpr->queryCols++;
iCol++;
}
gpr->numFields = optFieldsToNumFields(gpr->optFields);
}
struct genePredReader *genePredReaderQuery(struct sqlConnection* conn,
char* table, char* where)
/* Create a new genePredReader to read from the given table in the database.
* If where is not null, it is added as a where clause. It will determine if
* extended genePred columns are in the table.
*/
{
char query[1024];
struct genePredReader* gpr;
AllocVar(gpr);
gpr->table = cloneString(table);
if (where != NULL)
safef(query, sizeof(query), "select * from %s where %s", table, where);
else
safef(query, sizeof(query), "select * from %s", table);
gpr->sr = sqlGetResult(conn, query);
buildResultFieldMap(gpr);
return gpr;
}
struct genePredReader *genePredReaderRangeQuery(struct sqlConnection* conn,
char* table, char* chrom,
int start, int end,
char* extraWhere)
/* Create a new genePredReader to read a chrom range in a database table. If
* extraWhere is not null, it is added as an additional where condition. It
* will determine if extended genePred columns are in the table. */
{
struct genePredReader* gpr;
int rowOffset;
AllocVar(gpr);
gpr->table = cloneString(table);
/* non-existant table will return null */
gpr->sr = hRangeQuery(conn, table, chrom, start, end, extraWhere, &rowOffset);
if (gpr->sr != NULL)
buildResultFieldMap(gpr);
assert(gpr->rowOffset == rowOffset);
return gpr;
}
struct genePredReader *genePredReaderFile(char* gpFile, char* chrom)
/* Create a new genePredReader to read from a file. If chrom is not null,
* only this chromsome is read. The rows must contain columns in the order in
* the struct, and they must be present up to the last specfied optional
* field. Missing intermediate fields must have zero or empty columns, they
* may not be omitted. */
{
struct genePredReader* gpr;
AllocVar(gpr);
gpr->table = cloneString(gpFile);
if (chrom != NULL)
gpr->chrom = cloneString(chrom);
gpr->lf = lineFileOpen(gpFile, TRUE);
return gpr;
}
static struct genePred *queryNext(struct genePredReader* gpr)
/* read the next record from a query */
{
int iFld, iCol;
char **row = sqlNextRow(gpr->sr);
char *reorderedRow[GENEPREDX_NUM_COLS];
if (row == NULL)
return NULL;
/* fill in row defaults */
for (iFld = 0; iFld < GENEPREDX_NUM_COLS; iFld++)
reorderedRow[iFld] = fieldTbl[iFld].defaultVal;
/* reorder row */
for (iCol = 0; iCol < gpr->queryCols; iCol++)
{
iFld = gpr->queryToFldMap[iCol];
if (iFld >= 0)
reorderedRow[iFld] = row[iCol];
}
return genePredExtLoad(reorderedRow, gpr->numFields);
}
static struct genePred *fileNext(struct genePredReader* gpr)
/* read the next record from a file */
{
char *row[GENEPREDX_NUM_COLS];
int numFields;
while ((numFields = lineFileChopNextTab(gpr->lf, row, GENEPREDX_NUM_COLS)) > 0)
{
lineFileExpectAtLeast(gpr->lf, GENEPRED_NUM_COLS, numFields);
if ((gpr->chrom == NULL) || (sameString(row[1], gpr->chrom)))
return genePredExtLoad(row, numFields);
}
return NULL;
}
struct genePred *genePredReaderNext(struct genePredReader* gpr)
/* Read the next genePred, returning NULL if no more */
{
if (gpr->lf != NULL)
return fileNext(gpr);
else
return queryNext(gpr);
}
struct genePred *genePredReaderAll(struct genePredReader* gpr)
/* Read the all of genePreds */
{
struct genePred* gpList = NULL, *gp;
while ((gp = genePredReaderNext(gpr)) != NULL)
slAddHead(&gpList, gp);
slReverse(&gpList);
return gpList;
}
void genePredReaderFree(struct genePredReader** gprPtr)
/* Free the genePredRead object. */
{
struct genePredReader* gpr = *gprPtr;
if (gpr != NULL)
{
freeMem(gpr->table);
sqlFreeResult(&gpr->sr);
lineFileClose(&gpr->lf);
freeMem(gpr->chrom);
freez(gprPtr);
}
}
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;
}
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 hash *genePredToBinKeeper(char *sizeFileName, char *gpFile)
-/* read a list of genePreds and return results in hash of binKeeper structure for fast query*/
-{
-struct binKeeper *bk;
-struct genePred *gp , *gpList = NULL;
-struct lineFile *sf = lineFileOpen(sizeFileName, TRUE);
-struct hash *hash = newHash(0);
-char *chromRow[2];
-
-while (lineFileRow(sf, chromRow))
- {
- char *name = chromRow[0];
- int size = lineFileNeedNum(sf, chromRow, 1);
-
- if (hashLookup(hash, name) != NULL)
- warn("Duplicate %s, ignoring all but first\n", name);
- else
- {
- bk = binKeeperNew(0, size);
- assert(size > 1);
- hashAdd(hash, name, bk);
- }
- }
-gpList = genePredReaderLoadFile(gpFile, NULL);
-for (gp = gpList ; gp!= NULL; gp=gp->next)
- {
- bk = hashMustFindVal(hash, gp->chrom);
- binKeeperAdd(bk, gp->txStart, gp->txEnd, gp);
- }
-lineFileClose(&sf);
-return hash;
-}
-