void makeNewExpTable(char *oldTable, struct maMedSpec *medList, char *newTable)
/* Create new expTable in hgFixed that is very similar
* to oldExpTable, but with rows defined by medList. */
{
struct maMedSpec *med;
struct expRecord *oldExp, newExp;
struct sqlConnection *conn = sqlConnect("hgFixed");
FILE *f = hgCreateTabFile(tabDir, newTable);
char query[256], **row;
struct sqlResult *sr;
int curId = 0;
for (med = medList; med != NULL; med = med->next)
{
/* Load expression record from old table of first
* thing in median. */
sqlSafef(query, sizeof(query),
"select * from %s where id = %d", oldTable, med->ids[0]);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
errAbort("Can't find id %d in %s\n", med->ids[0], oldTable);
oldExp = expRecordLoad(row);
sqlFreeResult(&sr);
if (oldExp->numExtras < 3)
errAbort("Can only deal with old tables with 3 extras or more");
/* Create new expression record, mostly just a shallow copy of old. */
newExp = *oldExp;
newExp.id = curId;
++curId;
newExp.name = newExp.description = med->name;
newExp.extras[2] = med->group;
/* Save new one, free old one. */
expRecordTabOut(&newExp, f);
expRecordFree(&oldExp);
}
if (doLoad)
{
expRecordCreateTable(conn, newTable);
hgLoadTabFile(conn, tabDir, newTable, &f);
hgRemoveTabFile(tabDir, newTable);
}
sqlDisconnect(&conn);
}
void affyPslAndAtlasToBedOld(char *pslFile, char *atlasFile, char *bedOut, char *expRecOut)
/** Main function that does all the work for old-style*/
{
struct hash *bedHash = NULL;
struct affyAtlas *aaList=NULL, *aa=NULL;
struct expRecord *erList=NULL, *er=NULL;
struct bed *bedList=NULL, *bed=NULL;
int expCount = 0;
FILE *erOut = NULL, *bOut=NULL;
warn("loading atlas file");
aaList = affyAtlasLoadAll(atlasFile);
expCount = countExperiments(aaList);
warn("creating list of beds from alignments");
bedList = createBedsFromPsls(pslFile, expCount);
warn("creating hash from list of beds");
bedHash = createBedHash(bedList);
warn("appending experiments to beds in hash");
appendExperiments(bedHash, aaList, &erList);
warn("Running sanity Checks");
checkAllBeds(&bedList, expCount);
warn("%d beds were missing experiments." , missingExpsCount);
warn("%d beds had no experiments.", noExpCount);
warn("Calculating average intensities");
convertIntensitiesToRatios(bedList);
calculateAverages(bedList);
warn("writing expRecords out");
erOut = mustOpen(expRecOut, "w");
for(er = erList; er != NULL; er = er->next)
expRecordTabOut(er, erOut);
carefulClose(&erOut);
warn("writing beds out");
bOut = mustOpen(bedOut, "w");
for(bed = bedList; bed != NULL; bed = bed->next)
bedTabOutN(bed, 15, bOut);
carefulClose(&bOut);
warn("cleaning up..");
freeHash(&bedHash);
bedFreeList(&bedList);
warn("Done.");
}
int main(int argc, char *argv[])
{
struct hash *pslHash = newHash(5);
struct hash *bedHash = newHash(5);
struct expRecord *erList = NULL, *er=NULL;
int i;
FILE *erOut = NULL;
if(argc <4)
usage();
warn("Reading in psls...");
readInPslHash(pslHash, argv[1]);
warn("Creating beds...");
createBeds(bedHash, pslHash, argv[4], (argc-4));
warn("Appending Experiements...");
for(i=4; i < argc; i++)
{
printf("%d,",i-4);
fflush(stdout);
appendNewExperiment(argv[i], bedHash, pslHash,&erList, (i-4));
}
warn("\tDone.");
warn("Writing to files...");
erOut = mustOpen(argv[2],"w");
bedOut= mustOpen(argv[3],"w");
for(er = erList; er != NULL; er = er->next)
{
expRecordTabOut(er, erOut);
}
hashTraverseVals(bedHash, averageValues);
hashTraverseVals(bedHash, bedHashOutput);
carefulClose(&erOut);
carefulClose(&bedOut);
freeHash(&pslHash);
freeHash(&bedHash);
warn("Finished.");
return 0;
}
