// -------------------------------------------------------------------------
// QueryInfo Class :: inRange() - match check having a range
// -------------------------------------------------------------------------
IBase :: Boolean QueryInfo :: inRange(const IString &c1
,const IString &c2
,const IString &range)
{
if (c2.length() == 0)
return false;
IString matchItem, compareItem;
matchItem = chopOff(c1);
compareItem = chopOff(c2);
if ( (c1.isDigits()) && (c2.isDigits()) ) {
// compare 2 numbers
long d1=c1.asInt();
long d2=c2.asInt();
return compareIt(d1, d2, range);
}
else {
ADate *date1 = new ADate(c1);
ADate *date2 = new ADate(c2);
return compareIt(date1, date2, range);
} /* endif */
};
struct hash *makeProbeBed(char *inGff, char *outBed)
/* Convert probe location GFF file to BED. */
{
struct lineFile *lf = lineFileOpen(inGff, TRUE);
char *row[9];
struct hash *hash = newHash(16);
FILE *f = mustOpen(outBed, "w");
while (lineFileNextRowTab(lf, row, ArraySize(row)))
{
int chromIx = romanToArabicChrom(row[0], lf);
int start = lineFileNeedNum(lf, row, 3) - 1;
int end = lineFileNeedNum(lf, row, 4);
char *s = row[8];
char *probe, *orf, *note;
char *boundAt = "Bound at ";
struct tfBinding *tfbList = NULL, *tfb;
if (!startsWith("Probe ", s))
errAbort("Expecting 9th column to start with 'Probe ' line %d of %s",
lf->lineIx, lf->fileName);
probe = nextWord(&s);
orf = nextWord(&s);
chopOff(orf, ';');
note = nextWord(&s);
if (!sameWord("Note", note))
errAbort("Expecting 'note' in 9th column line %d of %s",
lf->lineIx, lf->fileName);
s = skipLeadingSpaces(s);
if (!parseQuotedString(s, s, NULL))
errAbort("Expecting quoted string in 9th column line %d of %s",
lf->lineIx, lf->fileName);
if (startsWith("Bad Probe", s))
continue;
else if (startsWith("Not bound", s))
{
/* Ok, we do nothing. */
}
else if (startsWith(boundAt, s))
{
while (s != NULL && startsWith(boundAt, s))
{
char *word, *by;
double binding;
s += strlen(boundAt);
word = nextWord(&s);
binding = atof(word);
by = nextWord(&s);
if (!sameString("by:", by))
errAbort("Expecting by: line %d of %s", lf->lineIx, lf->fileName);
while ((word = nextWord(&s)) != NULL)
{
char lastChar = 0, *e;
e = word + strlen(word) - 1;
lastChar = *e;
if (lastChar == ';' || lastChar == ',')
*e = 0;
AllocVar(tfb);
tfb->binding = binding;
tfb->tf = cloneString(word);
slAddHead(&tfbList, tfb);
if (lastChar == ';')
break;
}
s = skipLeadingSpaces(s);
}
slReverse(&tfbList);
}
else
{
errAbort("Expecting %s in note line %d of %s", boundAt,
lf->lineIx, lf->fileName);
}
fprintf(f, "chr%d\t%d\t%d\t", chromIx+1, start, end);
fprintf(f, "%s\t%d\t", orf, slCount(tfbList));
for (tfb = tfbList; tfb != NULL; tfb = tfb->next)
fprintf(f, "%s,", tfb->tf);
fprintf(f, "\t");
for (tfb = tfbList; tfb != NULL; tfb = tfb->next)
fprintf(f, "%4.3f,", tfb->binding);
fprintf(f, "\n");
hashAdd(hash, orf, NULL);
}
lineFileClose(&lf);
carefulClose(&f);
return hash;
}
