struct gdfGene *wormGdfGenesInRange(char *chrom, int start, int end,
struct wormGdfCache *geneFinder)
/* Get list of genes in range according to given gene finder. */
{
char *dir = NULL;
struct gdfGene *gdfList = NULL, *gdf;
struct wormFeature *nameList, *name;
if (geneFinder == &wormSangerGdfCache)
dir = wormSangerDir();
else if (geneFinder == &wormGenieGdfCache)
dir = wormGenieDir();
else
errAbort("Unknown geneFinder line %d of %s", __LINE__, __FILE__);
nameList = wormSomeGenesInRange(chrom, start, end, dir);
for (name = nameList; name != NULL; name = name->next)
{
char *n = name->name;
if (!wormIsNamelessCluster(n))
{
gdf = wormGetSomeGdfGene(n, geneFinder);
slAddHead(&gdfList, gdf);
}
}
slFreeList(&nameList);
slReverse(&gdfList);
return gdfList;
}
DNA *wormChromPartExonsUpper(char *chromId, int start, int size)
/* Return part of a worm chromosome with exons in upper case. */
{
DNA *dna = wormChromPart(chromId, start, size);
struct wormFeature *geneFeat = wormGenesInRange(chromId, start, start+size);
struct wormFeature *feat;
for (feat = geneFeat; feat != NULL; feat = feat->next)
{
char *name = feat->name;
if (!wormIsNamelessCluster(name))
{
struct gdfGene *gene = wormGetGdfGene(name);
gdfUpcExons(gene, feat->start, dna, size, start);
gdfFreeGene(gene);
}
}
slFreeList(&geneFeat);
return dna;
}
void doMiddle()
{
char *seqName;
boolean intronsLowerCase = TRUE;
boolean intronsParenthesized = FALSE;
boolean hiliteNear = FALSE;
int startRange = 0;
int endRange = 0;
boolean gotRange = FALSE;
struct dnaSeq *cdnaSeq;
boolean isChromRange = FALSE;
DNA *dna;
char *translation = NULL;
seqName = cgiString("geneName");
seqName = trimSpaces(seqName);
if (cgiVarExists("intronsLowerCase"))
intronsLowerCase = cgiBoolean("intronsLowerCase");
if (cgiVarExists("intronsParenthesized"))
intronsParenthesized = cgiBoolean("intronsParenthesized");
if (cgiVarExists("startRange") && cgiVarExists("endRange" ))
{
startRange = cgiInt("startRange");
endRange = cgiInt("endRange");
gotRange = TRUE;
}
if (cgiVarExists("hiliteNear"))
{
hiliteNear = TRUE;
}
fprintf(stdout, "<P><TT>\n");
/* The logic here is a little complex to optimize speed.
* If we can decide what type of thing the name refers to by
* simply looking at the name we do. Otherwise we have to
* search the database in various ways until we get a hit. */
if (wormIsNamelessCluster(seqName))
{
isChromRange = TRUE;
}
else if (wormIsChromRange(seqName))
{
isChromRange = TRUE;
}
else if (getWormGeneDna(seqName, &dna, TRUE))
{
if (cgiBoolean("litLink"))
{
char nameBuf[64];
char *geneName = NULL;
char *productName = NULL;
char *coding;
int transSize;
struct wormCdnaInfo info;
printf("<H3>Information and Links for %s</H3>\n", seqName);
if (wormInfoForGene(seqName, &info))
{
if (info.description)
printf("<P>%s</P>\n", info.description);
geneName = info.gene;
productName = info.product;
}
else
{
if (wormIsGeneName(seqName))
geneName = seqName;
else if (wormGeneForOrf(seqName, nameBuf, sizeof(nameBuf)))
geneName = nameBuf;
}
coding = cloneUpperOnly(dna);
transSize = 1 + (strlen(coding)+2)/3;
translation = needMem(1+strlen(coding)/3);
dnaTranslateSome(coding, translation, transSize);
freez(&coding);
if (geneName)
{
printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=m"
"&term=C+elegans+%s&dispmax=50&relentrezdate=No+Limit\">", geneName);
printf("PubMed search on gene: </A>%s<BR>\n", geneName);
}
if (productName)
{
char *encoded = cgiEncode(productName);
printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=m"
"&term=%s&dispmax=50&relentrezdate=No+Limit\">", encoded);
printf("PubMed search on product:</A> %s<BR>\n", productName);
freeMem(encoded);
}
/* Process name to get rid of isoform letter for Proteome. */
if (geneName)
strcpy(nameBuf, geneName);
else
{
strcpy(nameBuf, seqName);
#ifdef NEVER
/* Sometimes Proteome requires the letter after the orf name
* in alt-spliced cases, sometimes it can't handle it.... */
nameLen = strlen(nameBuf);
if (wormIsOrfName(nameBuf) && isalpha(nameBuf[nameLen-1]))
{
char *dotPos = strrchr(nameBuf, '.');
if (dotPos != NULL && isdigit(dotPos[1]))
nameBuf[nameLen-1] = 0;
}
#endif /* NEVER */
}
printf("<A HREF=\"http://www.wormbase.org/db/seq/sequence?name=%s;class=Sequence\">", seqName);
printf("WormBase link on:</A> %s<BR>\n", seqName);
printf("<A HREF=\"http://www.proteome.com/databases/WormPD/reports/%s.html\">", nameBuf);
printf("Proteome link on:</A> %s<BR>\n<BR>\n", nameBuf);
printf("<A HREF=#DNA>Genomic DNA Sequence</A><BR>\n");
if (hiliteNear)
printf("<A HREF=\"#CLICKED\">Shortcut to where you clicked in gene</A><BR>");
printf("<A HREF=#protein>Translated Protein Sequence</A><BR>\n");
htmlHorizontalLine();
printf("<A NAME=DNA></A>");
printf("<H3>%s Genomic DNA sequence</H3>", seqName);
}
if (!intronsLowerCase)
tolowers(dna);
if (hiliteNear)
{
if (!gotRange)
{
double nearPos = cgiDouble("hiliteNear");
int rad = 5;
int dnaSize = strlen(dna);
long mid = (int)(dnaSize * nearPos);
startRange = mid - rad;
if (startRange < 0) startRange = 0;
endRange = mid + rad;
if (endRange >= dnaSize) endRange = dnaSize - 1;
}
}
outputSeq(dna, strlen(dna), hiliteNear, startRange, endRange, stdout);
freez(&dna);
}
else if (wormCdnaSeq(seqName, &cdnaSeq, NULL))
{
outputSeq(cdnaSeq->dna, cdnaSeq->size, FALSE, 0, 0, stdout);
}
else
{
isChromRange = TRUE;
}
if (isChromRange)
{
char *chromId;
int start, end;
char strand = '+';
int size;
if (!wormGeneRange(seqName, &chromId, &strand, &start, &end))
errAbort("Can't find %s",seqName);
size = end - start;
if (intronsLowerCase)
dna = wormChromPartExonsUpper(chromId, start, size);
else
{
dna = wormChromPart(chromId, start, size);
touppers(dna);
}
if (cgiVarExists("strand"))
strand = cgiString("strand")[0];
if (strand == '-')
reverseComplement(dna, size);
outputSeq(dna, size, FALSE, 0, 0, stdout);
}
if (translation != NULL)
{
htmlHorizontalLine();
printf("<A NAME=protein></A>");
printf("<H3>Translated Protein of %s</H3>\n", seqName);
outputSeq(translation, strlen(translation), FALSE, 0, 0, stdout);
freez(&translation);
}
fprintf(stdout, "</TT></P>\n");
}
