struct pgo *readC2g(char *fileName)
/* Read a C2g file into memory. */
{
FILE *f = mustOpen(fileName, "r");
struct pgo *list = NULL, *el;
char lineBuf[128];
char *words[4];
int wordCount;
int lineCount = 0;
while (fgets(lineBuf, sizeof(lineBuf), f) != NULL)
{
++lineCount;
wordCount = chopLine(lineBuf, words);
if (wordCount == 0)
continue; /* Ignore blank lines. */
if (wordCount != 3)
{
errAbort("Strange line starting with %s line %d of %s",
words[0], lineCount, fileName);
}
AllocVar(el);
if (!wormParseChromRange(words[0], &el->chrom, &el->start, &el->end))
errAbort("Bad chromosome range line %d of %s", lineCount, fileName);
el->strand = words[1][0];
el->gene = cloneString(words[2]);
slAddHead(&list, el);
}
slReverse(&list);
return list;
}
boolean wormIsChromRange(char *in)
/* Check to see if the input is formatted correctly to be
* a range of a chromosome. */
{
char *chromId;
int start, end;
boolean ok;
ok = wormParseChromRange(in, &chromId, &start, &end);
return ok;
}
void doMiddle()
/* Write middle part of .html. */
{
DNA *targetDna;
char *chrom;
int tStart, tEnd;
struct xaAli *xa;
int bothStart, bothEnd;
char cbCosmidName[256];
char *s;
/* Get input variables from CGI. */
char *qOrganism = cgiString("qOrganism");
char *tOrganism = cgiString("tOrganism");
char *query = cgiString("query");
char *target = cgiString("target");
char *strandString = cgiString("strand");
char strand = strandString[0];
boolean showSym = cgiBoolean("symbols");
boolean gotClickPos = cgiVarExists("clickPos");
double clickPos;
if (gotClickPos) clickPos = cgiDouble("clickPos");
strcpy(cbCosmidName, query);
if ((s = strrchr(cbCosmidName, '.')) != NULL)
*s = 0;
/* Get xaAli. */
xa = getOneXaAli(qOrganism, query);
printf("<H2>Alignment of <I>C. briggsae</I> %s:%d-%d and <I>C. elegans</I> %s</H2>\n",
cbCosmidName, xa->qStart, xa->qEnd, target);
htmlParagraph("<I>C. briggsae</I> appears on top. Coding regions in <I>C. elegans</I> are in upper case.");
/* Get display window. */
if (!wormParseChromRange(target, &chrom, &tStart, &tEnd))
errAbort("Target %s isn't formatted correctly", target);
/* Figure out intersection of display window and xeno-alignment */
bothStart = max(xa->tStart, tStart);
bothEnd = min(xa->tEnd, tEnd);
/* Get upper-cased-exon target DNA. */
targetDna = wormChromPartExonsUpper(chrom, bothStart, bothEnd - bothStart);
upcCorresponding(targetDna, bothEnd - bothStart, xa->tSym, bothStart - xa->tStart);
printf("<TT><PRE>");
showTargetRange(xa, bothStart - xa->tStart, bothEnd-bothStart, strand, showSym);
printf("</TT></PRE>");
}
static boolean findAltSpliceRange(char *name, struct snof *snof, FILE *f,
char **retChrom, int *retStart, int *retEnd, char *retStrand)
/* Return range of chromosome covered by a gene and all of it's isoforms. */
{
char baseName[64];
char bName[64];
int snIx, maxIx;
int start = 0x7fffffff;
int end = -start;
char lineBuf[128];
char *words[3];
int wordCount;
int baseNameSize;
strcpy(baseName, name);
makeIsoformBaseName(baseName);
baseNameSize = strlen(baseName);
if (!snofFindFirstStartingWith(snof, baseName, baseNameSize, &snIx))
return FALSE;
maxIx = snofElementCount(snof);
for (;snIx < maxIx; ++snIx)
{
long offset;
char *geneName;
snofNameOffsetAtIx(snof, snIx, &geneName, &offset);
if (strncmp(geneName, baseName, baseNameSize) != 0)
break;
strcpy(bName, geneName);
makeIsoformBaseName(bName);
if (sameString(baseName, bName))
{
int s, e;
fseek(f, offset, SEEK_SET);
mustGetLine(f, lineBuf, sizeof(lineBuf));
wordCount = chopLine(lineBuf, words);
assert(wordCount == 3);
wormParseChromRange(words[0], retChrom, &s, &e);
*retStrand = words[1][0];
if (start > s)
start = s;
if (end < e)
end = e;
}
}
*retStart = start;
*retEnd = end;
return TRUE;
}
boolean wormGeneRange(char *name, char **retChrom, char *retStrand, int *retStart, int *retEnd)
/* Return chromosome position of a chrom range, gene, ORF, cosmid, or nameless cluster. */
{
static struct snof *c2gSnof = NULL, *c2cSnof = NULL;
static FILE *c2gFile = NULL, *c2cFile = NULL;
long offset;
char fileName[512];
struct slName *syn = NULL;
boolean ok;
if (wormIsChromRange(name))
{
*retStrand = '.';
return wormParseChromRange(name, retChrom, retStart, retEnd);
}
getDirs();
/* Translate biologist type name to cosmid.N name */
if (wormIsGeneName(name))
{
syn = wormGeneToOrfNames(name);
if (syn != NULL)
{
name = syn->name;
}
}
if (wormFixupOrfName(name)) /* See if ORF, and if so make nice. */
{
if (c2gSnof == NULL)
{
sprintf(fileName, "%sc2g", featDir);
c2gSnof = snofMustOpen(fileName);
sprintf(fileName, "%sc2g", featDir);
c2gFile = mustOpen(fileName, "rb");
}
ok = findAltSpliceRange(name, c2gSnof, c2gFile, retChrom, retStart, retEnd, retStrand);
}
else /* Lets say it's a cosmid. */
{
char lineBuf[128];
char *words[3];
int wordCount;
touppers(name);
if (c2cSnof == NULL)
{
sprintf(fileName, "%sc2c", featDir);
c2cSnof = snofMustOpen(fileName);
sprintf(fileName, "%sc2c", featDir);
c2cFile = mustOpen(fileName, "rb");
}
if (!snofFindOffset(c2cSnof, name, &offset) )
return FALSE;
fseek(c2cFile, offset, SEEK_SET);
mustGetLine(c2cFile, lineBuf, sizeof(lineBuf));
wordCount = chopLine(lineBuf, words);
assert(wordCount == 3);
assert(strcmp(words[2], name) == 0);
assert(wormIsChromRange(words[0]));
*retStrand = words[1][0];
ok = wormParseChromRange(words[0], retChrom, retStart, retEnd);
}
slFreeList(&syn);
return ok;
}
