void outputOneRa(struct dnaSeq *seq, int start, int end, FILE *f)
/* Output one Ra record to file. */
{
fprintf(f, "orfName %s_%d_%d\n", seq->name, start, end);
fprintf(f, "txName %s\n", seq->name);
fprintf(f, "txSize %d\n", seq->size);
fprintf(f, "cdsStart %d\n", start);
fprintf(f, "cdsEnd %d\n", end);
fprintf(f, "cdsSize %d\n", end-start);
fprintf(f, "gotStart %d\n", startsWith("atg", seq->dna+start));
fprintf(f, "gotEnd %d\n", isStopCodon(seq->dna+end-3));
boolean gotKozak1 = FALSE;
if (start >= 3)
{
char c = seq->dna[start-3];
gotKozak1 = (c == 'a' || c == 'g');
}
fprintf(f, "gotKozak1 %d\n", gotKozak1);
boolean gotKozak2 = FALSE;
if (start+3 < seq->size)
gotKozak2 = (seq->dna[start+3] == 'g');
fprintf(f, "gotKozak2 %d\n", gotKozak2);
fprintf(f, "gotKozak %d\n", gotKozak1 + gotKozak2);
/* Count up upstream ATG and Kozak */
struct rbTree *upAtgRanges = rangeTreeNew(), *upKozakRanges = rangeTreeNew();
int upAtg = 0, upKozak = 0;
int i;
for (i=0; i<start; ++i)
{
if (startsWith("atg", seq->dna + i))
{
int orfEnd = findOrfEnd(seq, i);
if (orfEnd < start)
rangeTreeAdd(upAtgRanges, i, orfEnd);
++upAtg;
if (isKozak(seq->dna, seq->size, i))
{
++upKozak;
if (orfEnd < start)
rangeTreeAdd(upKozakRanges, i, orfEnd);
}
}
}
fprintf(f, "upstreamAtgCount %d\n", upAtg);
fprintf(f, "upstreamKozakCount %d\n", upKozak);
fprintf(f, "upstreamSize %d\n", rangeTreeOverlapSize(upAtgRanges, 0, start));
fprintf(f, "upstreamKozakSize %d\n", rangeTreeOverlapSize(upKozakRanges, 0, start));
fprintf(f, "\n");
/* Cluen up and go home. */
rangeTreeFree(&upAtgRanges);
rangeTreeFree(&upKozakRanges);
}
void calcUpstreams(struct dnaSeq *seq, int *upAtgCount, int *upKozakCount)
/* Count up upstream ATG and Kozak */
{
struct rbTree *upAtgRanges = rangeTreeNew(), *upKozakRanges = rangeTreeNew();
int endPos = seq->size-3;
int i;
for (i=0; i<=endPos; ++i)
{
if (startsWith("atg", seq->dna + i))
{
int orfEnd = orfEndInSeq(seq, i);
rangeTreeAdd(upAtgRanges, i, orfEnd);
if (isKozak(seq->dna, seq->size, i))
rangeTreeAdd(upKozakRanges, i, orfEnd);
}
}
setArrayCountsFromRangeTree(upAtgRanges, upAtgCount, seq->size);
setArrayCountsFromRangeTree(upKozakRanges, upKozakCount, seq->size);
rangeTreeFree(&upAtgRanges);
rangeTreeFree(&upKozakRanges);
}
