struct bed *bedIntronsFromAgx(struct altGraphX *ag)
/* Produce an intron bed for every intron in the altGraphx. */
{
struct bed *bed = NULL, *bedList = NULL;
int i,j;
int count =0;
int vCount = ag->vertexCount;
bool **em = altGraphXCreateEdgeMatrix(ag);
for(i=0; i<vCount; i++)
{
for(j=0; j<vCount; j++)
{
if(em[i][j] && altGraphXEdgeVertexType(ag, i, j) == ggSJ)
{
bed = bedForEdge(ag, em, i, j, count++);
if(bed != NULL)
slAddHead(&bedList, bed);
}
}
}
altGraphXFreeEdgeMatrix(&em, vCount);
slReverse(&bedList);
return bedList;
}
void lookForAltSplicing(char *db, struct altGraphX *ag, struct altSpliceSite **aSpliceList,
int *altSpliceSites, int *altSpliceLoci, int *totalSpliceSites)
/* Walk throught the altGraphX graph and look for evidence of altSplicing. */
{
struct altSpliceSite *notAlt = NULL, *notAltList = NULL;
bool **em = altGraphXCreateEdgeMatrix(ag);
int vCount = ag->vertexCount;
unsigned char *vTypes = ag->vTypes;
int altSpliceSitesOrig = *altSpliceSites;
int i,j,k;
int altCount = 0;
occassionalDot();
totalLoci++;
for(i=0; i<vCount; i++)
{
struct altSpliceSite *aSplice = NULL;
for(j=0; j<vCount; j++)
{
if(em[i][j] && areConsSplice(em, vCount, vTypes,i,j) &&
(agxEvCount(ag, i,j) >= minConfidence))
{
for(k=j+1; k<vCount; k++)
{
if(em[i][k] && areConsSplice(em, vCount, vTypes, i, k) &&
(agxEvCount(ag, i,k) >= minConfidence))
{
totalSplices++;
if(aSplice == NULL)
{
splicedLoci++;
aSplice = initASplice(ag, em, i, j, k);
(*altSpliceSites)++;
}
else
addSpliceSite(ag, em, aSplice, k);
}
}
}
/* Only want non alt-spliced exons for our controls. Some of
these checks are historical and probably redundant....*/
if(em[i][j] &&
rowSum(em[i], ag->vTypes, ag->vertexCount) == 1 &&
rowSum(em[j], ag->vTypes, ag->vertexCount) == 1 &&
colSum(em, ag->vTypes, ag->vertexCount, j) == 1 &&
colSum(em, ag->vTypes, ag->vertexCount, j) == 1 &&
altGraphXEdgeVertexType(ag, i, j) == ggExon &&
areHard(ag, i, j) &&
areConstitutive(ag, em, i, j))
{
notAlt = initASplice(ag, em, i, j, j);
if(altRegion != NULL)
outputControlExonBeds(ag, i, j);
slAddHead(¬AltList, notAlt);
}
}
if(aSplice != NULL)
{
if(altLogFile)
fprintf(altLogFile, "%s\n", ag->name);
slAddHead(aSpliceList, aSplice);
}
/* If we have a simple splice classfy it and log it. */
if(aSplice != NULL && aSplice->altCount == 2)
{
altTotalCount++;
fixOtherStrand(aSplice);
logSpliceType(aSplice->spliceTypes[1], abs(aSplice->altBpEnds[1] - aSplice->altBpStarts[1]));
if(aSplice->spliceTypes[1] == alt3Prime && (aSplice->altBpEnds[1] - aSplice->altBpStarts[1] == 3))
reportThreeBpBed(aSplice);
if(doSScores)
fillInSscores(db, aSplice, 1);
if(RData != NULL)
{
outputForR(aSplice, 1, RData);
}
}
/* Otherwise log it as altOther. Start at 1 as 0->1 is the first
* splice, 1->2 is the first alt spliced.*/
else if(aSplice != NULL)
{
for(altCount=1; altCount<aSplice->altCount; altCount++)
{
altTotalCount++;
altOtherCount++;
}
}
}
for(notAlt = notAltList; notAlt != NULL; notAlt = notAlt->next)
{
if(doSScores)
fillInSscores(db, notAlt, 1);
if(RData != NULL)
{
fixOtherStrand(notAlt);
outputForR(notAlt, 1, RDataCont);
}
}
if(*altSpliceSites != altSpliceSitesOrig)
(*altSpliceLoci)++;
altGraphXFreeEdgeMatrix(&em, vCount);
}