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"); }
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; }