void affyPslAndAtlasToBedNew(char *pslFile, char *atlasFile, char *bedOut,
char *expRecOut)
/** Main function that does all the work for new-style*/
{
struct lineFile *lf = lineFileOpen(atlasFile, TRUE);
char *line, *name;
int i, wordCount, expCount;
char **row;
double *data, median;
double invMedian, ratio, logRatio;
char *affyId;
struct hash *hash = newHash(17);
struct psl *psl;
struct bed *bed;
FILE *f = NULL;
int dataCount = 0, pslCount = 0, bedCount = 0;
int minExpVal = 20;
/* Open Atlas file and use first line to create experiment table. */
if (!lineFileNextReal(lf, &line))
errAbort("%s is empty", lf->fileName);
if (startsWith("Affy", line))
line += 4;
if (line[0] != '\t')
errAbort("%s doesn't seem to be a new format atlas file", lf->fileName);
expCount = lineToExp(line+1, expRecOut);
if (expCount <= 0)
errAbort("No experiments in %s it seems", lf->fileName);
warn("%d experiments\n", expCount);
f = mustOpen(bedOut, "w");
/* Build up a hash keyed by affyID with an int array of data
* for value. Do output in short case. */
AllocArray(row, expCount);
while (lineFileNextReal(lf, &line))
{
affyId = nextWord(&line);
wordCount = chopByWhite(line, row, expCount);
if (wordCount != expCount)
errAbort("Expecting %d data points, got %d line %d of %s",
expCount, wordCount, lf->lineIx, lf->fileName);
if (hashLookup(hash, affyId))
{
warn("Duplicate %s, skipping all but first.", affyId);
continue;
}
AllocArray(data, expCount);
for (i=0; i<expCount; ++i)
{
data[i] = atof(row[i]);
if (data[i] < minExpVal)
data[i] = minExpVal;
}
median = findPositiveMedian(data, expCount, minExpVal);
if (median >= 0)
{
invMedian = 1.0/median;
for (i=0; i<expCount; ++i)
{
double val = data[i];
val = safeLog2(invMedian*val);
data[i] = val;
}
if (shortOut)
shortDataOut(f, affyId, expCount, data);
else
hashAdd(hash, affyId, data);
}
data = NULL;
++dataCount;
}
lineFileClose(&lf);
warn("%d rows of expression data\n", dataCount);
/* Stream through psl file, converting it to bed with expression data. */
if (!shortOut)
{
lf = pslFileOpen(pslFile);
while ((psl = pslNext(lf)) != NULL)
{
++pslCount;
/* get probe id from sequence name */
name=parseNameFromHgc(psl->qName);
data = hashFindVal(hash, name);
if (data != NULL)
{
struct bed *bed = bedFromPsl(psl);
bed->expCount = expCount;
AllocArray(bed->expIds, expCount);
AllocArray(bed->expScores, expCount);
for (i=0; i<expCount; ++i)
{
bed->expScores[i] = data[i];
bed->expIds[i] = i;
}
bedTabOutN(bed, 15, f);
++bedCount;
bedFree(&bed);
}
pslFree(&psl);
}
warn("%d records in %s", pslCount, pslFile);
warn("%d records written to %s", bedCount, bedOut);
}
lineFileClose(&lf);
carefulClose(&f);
}
void hgGnfMicroarray(char *expTable, char *dataTable, char *atlasFile)
/** Main function that does all the work for new-style*/
{
struct lineFile *lf = lineFileOpen(atlasFile, TRUE);
char *line;
int i, wordCount, expCount;
char **row;
float *data;
char *affyId;
struct hash *hash = newHash(17);
FILE *f = NULL;
int dataCount = 0;
/* Open Atlas file and use first line to create experiment table. */
if (!lineFileNextReal(lf, &line))
errAbort("%s is empty", lf->fileName);
if (startsWith("Affy", line))
line += 4;
if (startsWith("Gene Name", line))
line += 9;
if (line[0] != '\t')
errAbort("%s doesn't seem to be a new format atlas file", lf->fileName);
expCount = lineToExpTable(line+1, expTable);
if (expCount <= 0)
errAbort("No experiments in %s it seems", lf->fileName);
warn("%d experiments\n", expCount);
f = hgCreateTabFile(tabDir, dataTable);
AllocArray(row, expCount);
AllocArray(data, expCount);
while (lineFileNextReal(lf, &line))
{
affyId = nextWord(&line);
wordCount = chopByWhite(line, row, expCount);
if (wordCount != expCount)
errAbort("Expecting %d data points, got %d line %d of %s",
expCount, wordCount, lf->lineIx, lf->fileName);
if (chopName != NULL)
{
char *e = stringIn(chopName, affyId);
if (e != NULL)
*e = 0;
}
if (hashLookup(hash, affyId))
{
warn("Duplicate %s, skipping all but first.", affyId);
continue;
}
for (i=0; i<expCount; ++i)
{
data[i] = sqlFloat(row[i]);
}
shortDataOut(f, affyId, expCount, data);
++dataCount;
if (limit != 0 && dataCount >= limit)
break;
}
lineFileClose(&lf);
if (doLoad)
{
struct sqlConnection *conn = sqlConnect(database);
expDataCreateTable(conn, dataTable);
hgLoadTabFile(conn, tabDir, dataTable, &f);
hgRemoveTabFile(tabDir, dataTable);
sqlDisconnect(&conn);
}
}