void fillInPsls(char *pslName, struct hash *pairHash)
/* Read in psl file and save overlaps between indicated pairs
* in hash. */
{
struct lineFile *lf = pslFileOpen(pslName);
struct psl *psl;
char *pairName;
struct seqPair *pair;
struct seqOver *so;
boolean firstA;
char queryClone[128], targetClone[128];
struct hashEl *hel;
while ((psl = pslNext(lf)) != NULL)
{
fragToCloneName(psl->qName, queryClone);
fragToCloneName(psl->tName, targetClone);
pairName = makePairName(queryClone, targetClone, &firstA);
if ((pair = hashFindVal(pairHash, pairName)) != NULL)
{
so = (firstA ? &pair->a : &pair->b);
slAddHead(&so->pslList, psl);
}
else
{
pslFree(&psl);
}
}
}
void pslCut(char *cutList, char *inPsl, char *outPsl)
/* pslCut - Remove a list of clones from psl file.. */
{
struct hash *cutHash = newHash(0);
struct lineFile *lf = pslFileOpen(inPsl);
FILE *f = mustOpen(outPsl, "w");
struct psl *psl;
char cloneName[128];
int total = 0, cut = 0;
buildCutHash(cutList, cutHash);
pslWriteHead(f);
while ((psl = pslNext(lf)) != NULL)
{
fragToCloneName(psl->tName, cloneName);
if (!hashLookup(cutHash, cloneName))
{
pslTabOut(psl, f);
}
else
++cut;
++total;
pslFree(&psl);
}
printf("Cut %d of %d\n", cut, total);
}
void addCloneInfo(char *glFileName, struct hash *cloneHash, struct clonePos **pCloneList)
/* Add in clone info from one .gl file. */
{
char dir[256], chrom[128], ext[64];
struct gl gl;
struct lineFile *lf = lineFileOpen(glFileName, TRUE);
struct clonePos *clone;
char *line, *words[8];
int lineSize, wordCount;
char cloneVerName[128];
char cloneName[128];
printf("Processing %s\n", glFileName);
splitPath(glFileName, dir, chrom, ext);
while (lineFileNext(lf, &line, &lineSize))
{
wordCount = chopLine(line, words);
if (wordCount == 0)
continue;
if (wordCount != 4)
errAbort("Expecting %d words line %d of %s", 4, lf->lineIx, lf->fileName);
glStaticLoad(words, &gl);
fragToCloneVerName(gl.frag, cloneVerName);
fragToCloneName(gl.frag, cloneName);
if ((clone = hashFindVal(cloneHash, cloneName)) == NULL)
{
AllocVar(clone);
clone->name = cloneString(cloneVerName);
clone->chrom = cloneString(chrom);
clone->chromStart = gl.start;
clone->chromEnd = gl.end;
clone->faFile = cloneString("");
slAddHead(pCloneList, clone);
hashAdd(cloneHash, cloneName, clone);
}
else
{
if (!sameString(clone->chrom, chrom))
{
warn("Clone %s is on chromosomes %s and %s. Ignoring %s",
cloneName, clone->chrom, chrom, chrom);
continue;
}
if (clone->chromStart > gl.start)
clone->chromStart = gl.start;
if (clone->chromEnd < gl.end)
clone->chromEnd = gl.end;
}
}
lineFileClose(&lf);
}
struct clone *readTrans(char *fileName)
/* Read info in trans file. */
{
char cloneName[128], lastCloneName[128];
struct clone *cloneList = NULL, *clone = NULL;
struct frag *frag;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *words[8], *parts[4], *subParts[3];
int wordCount, partCount, subCount;
strcpy(lastCloneName, "");
while ((wordCount = lineFileChop(lf, words)) != 0)
{
lineFileExpectWords(lf, 3, wordCount);
partCount = chopString(words[2], "(:)", parts, ArraySize(parts));
if (partCount != 2)
errAbort("Badly formatted third field line %d of %s",
lf->lineIx, lf->fileName);
subCount = chopString(parts[1], ".", subParts, ArraySize(subParts));
if (subCount != 2)
errAbort("Badly formatted third field line %d of %s (expecting start..end)",
lf->lineIx, lf->fileName);
fragToCloneName(words[0], cloneName);
if (!sameString(cloneName, lastCloneName))
{
AllocVar(clone);
clone->name = cloneString(cloneName);
slAddHead(&cloneList, clone);
}
AllocVar(frag);
frag->name = cloneString(words[0]);
frag->ffaName = cloneString(words[1]);
frag->start = lineFileNeedNum(lf, subParts, 0) - 1;
frag->end = lineFileNeedNum(lf, subParts, 1);
slAddTail(&clone->fragList, frag);
strcpy(lastCloneName, cloneName);
}
lineFileClose(&lf);
slReverse(&cloneList);
return cloneList;
}
void agpVsMap(char *agpName, char *infoName, char *gifName)
/* agpVsMap - Plot clones in agp vs. map coordinates. */
{
struct mapPos *mapList, *mp;
struct agpFrag *agpList, *bp;
struct hash *cloneHash = newHash(14);
struct hashEl *hel;
struct cloneInfo *cloneList = NULL, *clone;
struct memGfx *mg = NULL;
int pixWidth = 600;
int pixHeight = 600;
int rulerHeight = 20;
int maxMapPos = 0, maxAgpPos = 0;
double scaleMap, scaleAgp;
Color orange, green;
mapList = readInfoFile(infoName);
agpList = readAgpFile(agpName);
for (mp = mapList; mp != NULL; mp = mp->next)
{
if (mp->phase > 0)
{
AllocVar(clone);
hel = hashAddUnique(cloneHash, mp->cloneName, clone);
clone->name = hel->name;
clone->mp = mp;
slAddHead(&cloneList, clone);
if (mp->pos > maxMapPos) maxMapPos = mp->pos;
}
}
slReverse(&cloneList);
for (bp = agpList; bp != NULL; bp = bp->next)
{
if (bp->chromStart > maxAgpPos) maxAgpPos = bp->chromStart;
}
/* Draw scatterplot on bitmap. */
mg = mgNew(pixWidth, pixHeight);
mgClearPixels(mg);
orange = mgFindColor(mg, 210, 150, 0);
green = mgFindColor(mg, 0, 200, 0);
mgDrawRuler(mg, 0, pixHeight-rulerHeight, rulerHeight, pixWidth, MG_BLACK,
mgSmallFont(), 0, maxMapPos+1);
scaleMap = (double)pixWidth/(double)(maxMapPos+1.0);
scaleAgp = (double)(pixHeight)/(double)(maxAgpPos+1.0);
for (bp = agpList; bp != NULL; bp = bp->next)
{
char cloneName[128];
fragToCloneName(bp->frag, cloneName);
clone = hashFindVal(cloneHash, cloneName);
if (clone == NULL)
warn("%s is in %s but not %s", cloneName,
agpName, infoName);
else
{
int x = round(scaleMap*clone->mp->pos);
int y = pixHeight - round(scaleAgp*bp->chromStart);
int phase = clone->mp->phase;
int back;
if (phase <= 1) back = green;
else if (phase == 2) back = orange;
else back = MG_RED;
drawPlus(mg, x, y, back);
}
}
mgSaveGif(mg, gifName);
}
