struct altGraphX *agFromAlignments(char *db, struct ggMrnaAli *maList, struct dnaSeq *seq, struct sqlConnection *conn,
int chromStart, int chromEnd, FILE *out )
/** Custer overlaps from maList into altGraphX structure. */
{
struct altGraphX *ag = NULL, *agList = NULL;
struct ggMrnaCluster *mcList=NULL, *mc=NULL;
struct ggMrnaInput *ci = NULL;
struct geneGraph *gg = NULL;
static int count = 0;
ci = ggMrnaInputFromAlignments(maList, seq);
mcList = ggClusterMrna(ci);
if(mcList == NULL)
{
freeGgMrnaInput(&ci);
return NULL;
}
clusterCount++;
for(mc = mcList; mc != NULL; mc = mc->next)
{
if(optionExists("consensus"))
{
gg = ggGraphConsensusCluster(db, mc, ci, tissLibHash, !optionExists("skipTissues"));
}
else
gg = ggGraphCluster(db, mc,ci);
assert(checkEvidenceMatrix(gg));
ag = ggToAltGraphX(gg);
if(ag != NULL)
{
char name[256];
freez(&ag->name);
safef(name, sizeof(name), "%s.%d", ag->tName, count++);
ag->name = cloneString(name);
/* Convert back to genomic coordinates. */
altGraphXoffset(ag, chromStart);
/* Sort vertices so that they are chromosomal order */
altGraphXVertPosSort(ag);
/* write to file */
binKeeperAdd(agxSeenBin, ag->tStart, ag->tEnd, ag);
slAddHead(&agList, ag);
}
}
/* Sometimes get nested, partial transcripts. Want to filter
those out. */
for(ag = agList; ag != NULL; ag = ag->next)
{
if(!agxIsRedundant(ag))
altGraphXTabOut(ag, out);
}
/* genoSeq and maList are freed with ci and gg */
ggFreeMrnaClusterList(&mcList);
freeGgMrnaInput(&ci);
freeGeneGraph(&gg);
return agList;
}
void smallTest()
/* Test out stuff. */
{
struct ggMrnaCluster *mc = makeTestInput();
struct geneGraph *gg;
static struct ggMrnaInput dummyCi;
uglyf("Initial input\n");
dumpMc(mc);
uglyf("\n");
gg = ggGraphCluster(mc, &dummyCi);
traverseGeneGraph(gg, mc->tStart, mc->tEnd, dumpGgAliInfo);
errAbort("Done testing");
}
void constraintsForBac(char *bacAcc, char *outDir)
/* Generate a set of constraint files for bac. */
{
struct ggMrnaInput *ci = ggGetMrnaForBac(bacAcc);
struct ggMrnaCluster *mc, *mcList = ggClusterMrna(ci);
struct geneGraph *gg;
uglyf("Got %d clusters\n", slCount(mcList));
for (mc = mcList; mc != NULL; mc = mc->next)
{
uglyf("Initial input\n");
dumpMc(mc);
uglyf("\n");
gg = ggGraphCluster(mc, ci);
uglyf("Constraints\n");
traverseGeneGraph(gg, mc->tStart, mc->tEnd, dumpGgAliInfo);
uglyf("\n\n");
}
}