struct evidence *evidenceForEdge(struct altGraphX *ag, int v1, int v2)
/* Return the evidence associated with this edge. */
{
int edgeNum = altGraphXGetEdgeNum(ag, v1, v2);
struct evidence *ev = slElementFromIx(ag->evidence, edgeNum);
return ev;
}
int agxEvCount(struct altGraphX *ag, int v1, int v2)
/* Return the number of ESTs supporting this edge. */
{
int edgeNum = altGraphXGetEdgeNum(ag, v1, v2);
struct evidence *ev = slElementFromIx(ag->evidence, edgeNum);
return ev->evCount;
}
void outputControlExonBeds(struct altGraphX *ag, int v1, int v2)
{
int *vPos = ag->vPositions;
struct bed bedUp, bedDown, bedAlt;
struct evidence *ev = slElementFromIx(ag->evidence, altGraphXGetEdgeNum(ag, v1, v2));
/* Make sure that this edge has enough support
that we believe it. */
if(ev->evCount >= minControlConf)
{
/* Initialize some beds for reporting. */
bedUp.chrom = bedDown.chrom = bedAlt.chrom = ag->tName;
bedUp.name = bedDown.name = bedAlt.name = ag->name;
bedUp.score = bedDown.score = bedAlt.score = altControl;
safef(bedUp.strand, sizeof(bedUp.strand), "%s", ag->strand);
safef(bedDown.strand, sizeof(bedDown.strand), "%s", ag->strand);
safef(bedAlt.strand, sizeof(bedDown.strand), "%s", ag->strand);
/* Alt spliced region. */
bedAlt.chromStart = vPos[v1];
bedAlt.chromEnd = vPos[v2];
/* Upstream/down stream */
if(sameString(ag->strand, "+"))
{
bedUp.chromStart = vPos[v1] - flankingSize;
bedUp.chromEnd = vPos[v1];
bedDown.chromStart = vPos[v2];
bedDown.chromEnd = vPos[v2] + flankingSize;
}
else
{
bedDown.chromStart = vPos[v1] - flankingSize;
bedDown.chromEnd = vPos[v1];
bedUp.chromStart = vPos[v2];
bedUp.chromEnd = vPos[v2] + flankingSize;
}
bedOutputN(&bedAlt, 6, altRegion, '\t','\n');
bedOutputN(&bedUp, 6, upStream100, '\t', '\n');
bedOutputN(&bedDown, 6, downStream100, '\t', '\n');
}
}
boolean isRetainIntron(struct altGraphX *ag, bool **em, int vs, int ve1, int ve2,
int *altBpStart, int *altBpEnd)
/* return TRUE if retained intron.
Looking for pattern:
hs-->he---->hs--->he
\---------------/
Use edgesInArea() to investigate that encompasses the common hard
end and common hard start. Should only be 4 edges in area defined by
splicing.
eseses
012345
0
1 + +
2 +
3 +
4
5
*/
{
unsigned char *vTypes = ag->vTypes;
int i=0;
int numAltVerts = 4;
/* Quick check. */
if(vTypes[vs] != ggHardStart || vTypes[ve1] != ggHardEnd || vTypes[ve2] != ggHardEnd)
return FALSE;
if(em[vs][ve1] && em[vs][ve2])
{
/* Try to find a hard start that connects ve1 and ve2. */
for(i=0; i<ag->vertexCount; i++)
{
if(vTypes[i] == ggHardStart && em[ve1][i] && em[i][ve2] &&
edgesInArea(ag,em,ve2-1,vs+1) == numAltVerts)
{
int *vPos = ag->vPositions;
struct bed bedAlt;
/* Initialize some beds for reporting. */
bedAlt.chrom = ag->tName;
bedAlt.name = ag->name;
bedAlt.score = altRetInt;
safef(bedAlt.strand, sizeof(bedAlt.strand), "%s", ag->strand);
/* Alt spliced region. */
bedAlt.chromStart = vPos[ve1];
bedAlt.chromEnd = vPos[i];
if(optionExists("printRetIntAccs"))
{
int incEdge = altGraphXGetEdgeNum(ag, vs, ve2);
int exEdge = altGraphXGetEdgeNum(ag, ve1, i);
struct evidence *ev= slElementFromIx(ag->evidence, incEdge);
int i;
fprintf(stdout, "RETINT\t%s\t%d\t", ag->name,ev->evCount);
for(i = 0; i < ev->evCount; i++)
{
fprintf(stdout, "%s,", ag->mrnaRefs[ev->mrnaIds[i]]);
}
fprintf(stdout, "\t");
ev= slElementFromIx(ag->evidence, exEdge);
fprintf(stdout, "%d\t", ev->evCount);
for(i = 0; i < ev->evCount; i++)
{
fprintf(stdout, "%s,", ag->mrnaRefs[ev->mrnaIds[i]]);
}
fprintf(stdout, "\n");
}
/* Upstream/down stream */
if(altRegion != NULL)
{
bedOutputN(&bedAlt, 6, altRegion, '\t','\n');
}
*altBpStart = ve1;
*altBpEnd = i;
return TRUE;
}
}
}
return FALSE;
}
struct bed *bedForEdge(struct altGraphX *ag, bool **em, int v1, int v2, int edgeCount)
{
int i;
char buff[256];
int *vPos = ag->vPositions;
int vCount = ag->vertexCount;
int pos1=0, pos2=BIGNUM;
int ev1=0, ev2=0;
struct bed *bed = NULL;
boolean found1 = FALSE, found2 = FALSE;
/* Find first exon. */
for(i=0; i<vCount; i++)
{
if(em[i][v1] && altGraphXEdgeVertexType(ag, i, v1) == ggExon)
{
int edgeNum = altGraphXGetEdgeNum(ag, i, v1);
struct evidence *ev = slElementFromIx(ag->evidence, edgeNum);
if(ev->evCount > ev1)
{
found1 = TRUE;
ev1 = ev->evCount;
pos1 = vPos[i];
}
}
}
/* Find second exon. */
for(i=0; i<vCount; i++)
{
if(em[v2][i] && altGraphXEdgeVertexType(ag, v2, i) == ggExon)
{
int edgeNum = altGraphXGetEdgeNum(ag, v2, i);
struct evidence *ev = slElementFromIx(ag->evidence, edgeNum);
if(ev->evCount > ev2)
{
found2 = TRUE;
ev2 = ev->evCount;
pos2 = vPos[i];
}
}
}
if(found1 && found2)
{
AllocVar(bed);
safef(buff, sizeof(buff), "%s.%d", ag->name, edgeCount);
bed->name = cloneString(buff);
safef(bed->strand, sizeof(bed->strand), "%s", ag->strand);
bed->chrom = cloneString(ag->tName);
bed->chromStart = bed->thickStart = pos1;
bed->chromEnd = bed->thickEnd = pos2;
bed->score = (ev1 + ev2)/2;
AllocArray(bed->chromStarts, 2);
AllocArray(bed->blockSizes, 2);
bed->blockCount = 2;
bed->chromStarts[0] = pos1 - bed->chromStart;
bed->chromStarts[1] = vPos[v2] - bed->chromStart;
bed->blockSizes[0] = vPos[v1] - pos1;
bed->blockSizes[1] = pos2 - vPos[v2];
}
return bed;
}
