void txgAnalyze(char *inTxg, char *dnaPath, char *outFile)
/* txgAnalyze - Analyse transcription graph for alt exons, alt 3', alt 5',
* retained introns, alternative promoters, etc.. */
{
struct lineFile *lf = lineFileOpen(inTxg, TRUE);
FILE *f = mustOpen(outFile, "w");
char *row[TXGRAPH_NUM_COLS];
struct nibTwoCache *ntc = nibTwoCacheNew(dnaPath);
struct dnaSeq *chrom = NULL;
while (lineFileRow(lf, row))
{
struct txGraph *txg = txGraphLoad(row);
if (chrom == NULL || !sameString(chrom->name, txg->tName))
{
dnaSeqFree(&chrom);
chrom = nibTwoCacheSeq(ntc, txg->tName);
verbose(2, "Loaded %s into %s\n", txg->tName, chrom->name);
}
struct range *exonsWithIntrons = retainedIntrons(txg, f);
cassetteExons(txg, f);
altThreePrime(txg, exonsWithIntrons, f);
altFivePrime(txg, exonsWithIntrons, f);
altPromoter(txg, f);
strangeSplices(txg, chrom, f);
bleedsIntoIntrons(txg, f);
refSeparateButJoined(txg, f);
if (fConst != NULL)
constExons(txg, fConst);
slFreeList(&exonsWithIntrons);
txGraphFree(&txg);
}
carefulClose(&f);
}
void txgToAgx(char *inTxg, char *outAgx)
/* txgToAgx - Convert from txg (txGraph) format to agx (altGraphX). */
{
struct lineFile *lf = lineFileOpen(inTxg, TRUE);
char *row[TXGRAPH_NUM_COLS];
FILE *f = mustOpen(outAgx, "w");
while (lineFileRow(lf, row))
{
struct txGraph *txg = txGraphLoad(row);
verbose(2, "loaded txGraph %s\n", txg->name);
struct altGraphX *agx = txGraphToAltGraphX(txg);
altGraphXTabOut(agx, f);
altGraphXFree(&agx);
txGraphFree(&txg);
}
carefulClose(&f);
}
