5a9c106607b38401620354b237667b53332017ea braney Thu Feb 21 11:04:39 2013 -0800 change trackHubRemoveHubName to trackHubSkipName (per code review #10237) diff --git src/hg/lib/hgFind.c src/hg/lib/hgFind.c index 257f5aa..bf26778 100644 --- src/hg/lib/hgFind.c +++ src/hg/lib/hgFind.c @@ -1,3207 +1,3207 @@ /* hgFind.c - Find things in human genome annotations. */ #include "common.h" #include "regexHelper.h" #include "obscure.h" #include "hCommon.h" #include "portable.h" #include "dystring.h" #include "hash.h" #include "cheapcgi.h" #include "htmshell.h" #include "web.h" #include "jksql.h" #include "hdb.h" #include "hui.h" #include "psl.h" #include "genePred.h" #include "genePredReader.h" #include "bed.h" #include "cytoBand.h" #include "cart.h" #include "hgFind.h" #include "hgFindSpec.h" #include "snp.h" #include "refLink.h" #include "kgAlias.h" #include "kgProtAlias.h" #include "findKGAlias.h" #include "findKGProtAlias.h" #include "tigrCmrGene.h" #include "minGeneInfo.h" #include "pipeline.h" #include "hgConfig.h" #include "trix.h" #include "trackHub.h" #include "udc.h" extern struct cart *cart; char *hgAppName = ""; /* alignment tables to check when looking for mrna alignments */ static char *estTables[] = { "intronEst", "all_est", "xenoEst", NULL }; static char *estLabels[] = { "Spliced ESTs", "ESTs", "Other ESTs", NULL }; static char *mrnaTables[] = { "all_mrna", "xenoMrna", NULL }; static char *mrnaLabels[] = { "mRNAs", "Other mRNAs", NULL }; static struct dyString *hgpMatchNames = NULL; static void hgPosFree(struct hgPos **pEl) /* Free up hgPos. */ { struct hgPos *el; if ((el = *pEl) != NULL) { freeMem(el->name); freeMem(el->description); freeMem(el->browserName); freez(pEl); } } static void hgPosFreeList(struct hgPos **pList) /* Free a list of dynamically allocated hgPos's */ { struct hgPos *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; hgPosFree(&el); } *pList = NULL; } static void hgPosTableFree(struct hgPosTable **pEl) /* Free up hgPosTable. */ { struct hgPosTable *el; if ((el = *pEl) != NULL) { freeMem(el->name); hgPosFreeList(&el->posList); freez(pEl); } } static void hgPosTableFreeList(struct hgPosTable **pList) /* Free a list of dynamically allocated hgPos's */ { struct hgPosTable *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; hgPosTableFree(&el); } *pList = NULL; } static void hgPositionsFree(struct hgPositions **pEl) /* Free up hgPositions. */ { struct hgPositions *el; if ((el = *pEl) != NULL) { freeMem(el->query); freeMem(el->extraCgi); hgPosTableFreeList(&el->tableList); freez(pEl); } } #if 0 /* not used */ static void hgPositionsFreeList(struct hgPositions **pList) /* Free a list of dynamically allocated hgPos's */ { struct hgPositions *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; hgPositionsFree(&el); } *pList = NULL; } #endif #define HGPOSRANGESIZE 64 static char *hgPosBrowserRange(struct hgPos *pos, char range[HGPOSRANGESIZE]) /* Convert pos to chrN:123-456 format. If range parameter is NULL it returns * static buffer, otherwise writes and returns range. */ { static char buf[HGPOSRANGESIZE]; if (range == NULL) range = buf; safef(range, HGPOSRANGESIZE, "%s:%d-%d", pos->chrom, pos->chromStart+1, pos->chromEnd); return range; } #if 0 /* not used */ static char *getGrepIndexFile(struct hgFindSpec *hfs) /* Return grepIndex setting (may be relative to hg.conf grepIndex.default), * or NULL if the file doesn't exist. */ { char *indexFile = hgFindSpecSetting(hfs, "grepIndex"); if (indexFile == NULL) return NULL; else if (fileExists(indexFile)) return cloneString(indexFile); else if (! startsWith("/", indexFile)) { char *grepIndexRoot = cfgOption("grepIndex.default"); if (grepIndexRoot != NULL) { char absPath[1024]; safef(absPath, sizeof(absPath), "%s/%s/%s", grepIndexRoot, hGetDb(), indexFile); if (fileExists(absPath)) return cloneString(absPath); } } return NULL; } #endif #define HGFIND_MAX_KEYWORDS 16 #define HGFIND_MAX_CMDWORDS 6 static void makeCmds(char **cmds[HGFIND_MAX_KEYWORDS+1], char **keyWords, int keyCount, char *extraOptions) /* Fill in cmds, an array of command word arrays. */ { int i; for (i=0; i < keyCount; i++) { char **cmd = NULL; int j = 0; AllocArray(cmd, HGFIND_MAX_CMDWORDS); cmd[j++] = "fgrep"; cmd[j++] = "-i"; if (isNotEmpty(extraOptions)) cmd[j++] = extraOptions; cmd[j++] = keyWords[i]; cmd[j++] = NULL; if (j > HGFIND_MAX_CMDWORDS) errAbort("overflow error -- increase HGFIND_MAX_CMDWORDS."); cmds[i] = cmd; } cmds[i] = NULL; } static void freeCmds(char **cmds[], int keyCount) /* Free each element of cmds. */ { int i; for (i=0; i < keyCount; i++) { freez(&(cmds[i])); } } static boolean keyIsPrefix(char *key, char *text) /* Return TRUE only if key is at the start of some word in text. * For short keys (2 or less) it must be whole word. */ { char *s = text; int keyLen = strlen(key); while ((s = stringIn(key, s)) != NULL) { if (s == text || !isalnum(s[-1])) { if (keyLen > 2 || !isalnum(s[keyLen])) return TRUE; } s += 1; } return FALSE; } static boolean keyIsPrefixIgnoreCase(char *key, char *text) /* Case insensitive keyIsPrefix */ { boolean isPrefix; key = cloneString(key); touppers(key); text = cloneString(text); touppers(text); isPrefix = keyIsPrefix(key, text); freeMem(key); freeMem(text); return isPrefix; } static boolean allKeysPrefix(char **keys, int keyCount, char *text) /* Make sure that all keys in text are proper prefixes of a word. */ /* NOTE: this is case sensitive. To ignore case, caller must ensure that * all keys and text have been forced to the same case. */ { int i; for (i=0; i<keyCount; ++i) { if (!keyIsPrefix(keys[i], text)) return FALSE; } return TRUE; } static char *commonDescriptionWords[] = { /* List of words that are too common in mRNA descriptions to be useful. * Every year or two we might want to update this. */ "LIKE", "HUMAN", "FACTOR", "ISOFORM", "GENE", "FROM", "HYPOTHETICAL", "FAMILY", "UNKNOWN", "PA", "MEMBER", "SIMILAR", "TO", "REGION", "MUS", "MUSCULUS", "MELANOGASTER", "CAENORHABDITIS", "CHAIN", "ELEGANS", "DROSOPHILA", "COT", "NORMALIZED", "TRANSCRIPT", "FOR", "VARIANT", "FIS", "THALIANA", "ARABIDOPSIS", "PARTIAL", "LENGTH", "HUMAN", "FULL", "IMAGE", "PROTEIN", "OF", "COMPLETE", "CDNA", "CLONE", "CDS", "HOMO", "SAPIENS", "MRNA", "5", "4", "3", "2", "1", }; static char *commonProductNameWords[] = { /* List of words that are too common in productNames to be useful. * Every year or two we might want to update this. */ "MEMBER", "FAMILY", "UNKNOWN", "FOR", "PUTATIVE", "LIKE", "5", "4", "3", "2", "1", "HYPOTHETICAl", "ISOFORM", "PROTEIN", }; static boolean anyStartWith(char *prefix, char *words[], int wordCount) /* Return TRUE if any words start with prefix. */ { int i; for (i=0; i<wordCount; ++i) { if (startsWith(prefix, words[i])) return TRUE; } return FALSE; } static boolean isTooCommon(char *table, char *key) /* Return TRUE if key is too common to be useful in table */ { if (sameString(table, "description")) return anyStartWith(key, commonDescriptionWords, ArraySize(commonDescriptionWords)); else if (sameString(table, "productName")) return anyStartWith(key, commonProductNameWords, ArraySize(commonProductNameWords)); else if (sameString(table, "author")) return sameWord(key, "and"); else return FALSE; } static int removeTooCommon(char *table, char **keys, int keyCount) /* Remove keys that are too common to be meaningful. */ { int readIx, writeIx=0; for (readIx=0; readIx < keyCount; ++readIx) { if (!isTooCommon(table, keys[readIx])) { keys[writeIx] = keys[readIx]; writeIx += 1; } } return writeIx; } static struct slName *doGrepQuery(char *indexFile, char *table, char *key, char *extraOptions) /* grep -i key indexFile, return a list of ids (first word of each line). */ { struct pipeline *pl = NULL; struct slName *idList = NULL; struct lineFile *lf = NULL; char *id, *rest, *line; char *keyWords[HGFIND_MAX_KEYWORDS]; char **cmds[HGFIND_MAX_KEYWORDS+1]; /* No need to escape special chars here, it's already been done: */ char *escapedKey = cloneString(key); int keyCount; touppers(escapedKey); keyCount = chopLine(escapedKey, keyWords); keyCount = removeTooCommon(table, keyWords, keyCount); if (keyCount > 0) { if (extraOptions == NULL) extraOptions = ""; makeCmds(cmds, keyWords, keyCount, extraOptions); pl = pipelineOpen(cmds, pipelineRead | pipelineNoAbort, indexFile, NULL); lf = pipelineLineFile(pl); verbose(3, "\n***Running this fgrep command with pipeline from %s:\n*** %s\n\n", indexFile, pipelineDesc(pl)); while (lineFileNextReal(lf, &line)) { id = nextWord(&line); rest = skipLeadingSpaces(line); touppers(rest); if (allKeysPrefix(keyWords, keyCount, rest)) { struct slName *idEl = slNameNew(id); slAddHead(&idList, idEl); } } pipelineFree(&pl); /* Takes care of lf too. */ freeCmds(cmds, keyCount); if (verboseLevel() >= 3) { int count = slCount(idList); verbose(3, "*** Got %d results from %s\n\n", count, indexFile); } } freeMem(escapedKey); return idList; } static char *MrnaIDforGeneName(char *db, char *geneName) /* return mRNA ID for a gene name */ { struct sqlConnection *conn; struct sqlResult *sr = NULL; char query[256]; char **row; char *result = NULL; conn = hAllocConn(db); if (sqlTableExists(conn, "refLink")) { safef(query, sizeof(query), "SELECT mrnaAcc FROM refLink WHERE name='%s'", geneName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { result = cloneString(row[0]); } else { result = NULL; } sqlFreeResult(&sr); } hFreeConn(&conn); return result; } char *MrnaIDforProtein(char *db, char *proteinID) /* return mRNA ID for a protein */ { struct sqlConnection *conn; struct sqlResult *sr = NULL; struct dyString *query; char **row; char * result; conn = hAllocConn(db); query = newDyString(256); dyStringPrintf(query, "SELECT mrnaID FROM spMrna WHERE spID='%s'", proteinID); sr = sqlGetResult(conn, query->string); if ((row = sqlNextRow(sr)) != NULL) { result = cloneString(row[0]); } else { result = NULL; } freeDyString(&query); sqlFreeResult(&sr); hFreeConn(&conn); return result; } static boolean findKnownGeneExact(char *db, char *spec, char *geneSymbol, struct hgPositions *hgp, char *tableName) /* Look for position in Known Genes table. */ { struct sqlConnection *conn; struct sqlResult *sr = NULL; struct dyString *query; char **row; boolean ok = FALSE; struct hgPosTable *table = NULL; struct hgPos *pos = NULL; int rowOffset; char *localName; localName = spec; if (!hTableExists(db, tableName)) return FALSE; rowOffset = hOffsetPastBin(db, NULL, tableName); conn = hAllocConn(db); query = newDyString(256); dyStringPrintf(query, "SELECT chrom, txStart, txEnd, name FROM %s WHERE name='%s'", tableName, localName); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (ok == FALSE) { ok = TRUE; AllocVar(table); dyStringClear(query); dyStringPrintf(query, "%s Gene Predictions", tableName); if (hTableExists(db, "kgProtMap2")) table->description = cloneString("UCSC Genes"); else table->description = cloneString("Known Genes"); table->name = cloneString("knownGene"); slAddHead(&hgp->tableList, table); } AllocVar(pos); pos->chrom = hgOfficialChromName(db, row[0]); pos->chromStart = atoi(row[1]); pos->chromEnd = atoi(row[2]); pos->name = cloneString(geneSymbol); /* pos->browserName = cloneString(geneSymbol); highlight change */ pos->browserName = cloneString(row[3]); slAddHead(&table->posList, pos); } if (table != NULL) slReverse(&table->posList); freeDyString(&query); sqlFreeResult(&sr); hFreeConn(&conn); return ok; } static struct hgPosTable *addKnownGeneTable(char *db, struct hgPositions *hgp) /* Create new table for known genes matches, add it to hgp, and return it. */ { struct hgPosTable *table; AllocVar(table); if (hTableExists(db, "kgProtMap2")) table->description = cloneString("UCSC Genes"); else table->description = cloneString("Known Genes"); table->name = cloneString("knownGene"); slAddHead(&hgp->tableList, table); return table; } static boolean gotFullText(char *db) /* Return TRUE if we have full text index. */ { char path[PATH_LEN]; safef(path, sizeof(path), "/gbdb/%s/knownGene.ix", db); if (fileExists(path)) return TRUE; else { warn("%s doesn't exist", path); return FALSE; } } struct tsrPos /* Little helper structure tying together search result * and pos, used by addKnownGeneItems */ { struct tsrPos *next; /* Next in list. */ struct trixSearchResult *tsr; /* Basically a gene symbol */ struct hgPos *posList; /* Associated list of positions. */ }; static void addKnownGeneItems(struct hgPosTable *table, struct trixSearchResult *tsrList, struct sqlConnection *conn) /* Convert tsrList to posList, and hang posList off of table. */ { /* This code works with just two SQL queries no matter how * big the search result list is. For cases where the search * result list is big (say 100 or 1000 items) this is noticably * faster than the simpler-to-code approach that would do two * queries for each search result. We pay for this speed tweak * by having to construct a more elaborate query, and by having * to maintain a hash to connect the query results back to the * individual positions. */ struct dyString *dy = dyStringNew(0); struct trixSearchResult *tsr; struct hash *hash = hashNew(16); struct hgPos *posList = NULL, *pos; struct tsrPos *tpList = NULL, *tp; struct sqlResult *sr; char **row; int maxToReturn = 500; if (slCount(tsrList) > maxToReturn) { warn("Search terms are not very specific, only showing first %d matching UCSC Genes.", maxToReturn); tsr = slElementFromIx(tsrList, maxToReturn-1); tsr->next = NULL; } /* Make hash of all search results - one for each known gene ID. */ for (tsr = tsrList; tsr != NULL; tsr = tsr->next) { lmAllocVar(hash->lm, tp); tp->tsr = tsr; slAddHead(&tpList, tp); hashAdd(hash, tsr->itemId, tp); } /* Stream through knownGenes table and make up a pos * for each mapping of each gene matching search. */ dyStringAppend(dy, "select name,chrom,txStart,txEnd from knownGene where name in ("); for (tsr = tsrList; tsr != NULL; tsr = tsr->next) { dyStringAppendC(dy, '"'); dyStringAppend(dy, tsr->itemId); dyStringAppendC(dy, '"'); if (tsr->next != NULL) dyStringAppendC(dy, ','); } dyStringAppend(dy, ")"); sr = sqlGetResult(conn, dy->string); while ((row = sqlNextRow(sr)) != NULL) { tp = hashFindVal(hash, row[0]); if (tp == NULL) internalErr(); AllocVar(pos); pos->chrom = cloneString(row[1]); pos->chromStart = sqlUnsigned(row[2]); pos->chromEnd = sqlUnsigned(row[3]); slAddHead(&tp->posList, pos); } sqlFreeResult(&sr); /* Stream through kgXref table adding description and geneSymbol */ dyStringClear(dy); dyStringAppend(dy, "select kgID,geneSymbol,description from kgXref where kgID in ("); for (tsr = tsrList; tsr != NULL; tsr = tsr->next) { dyStringAppendC(dy, '"'); dyStringAppend(dy, tsr->itemId); dyStringAppendC(dy, '"'); if (tsr->next != NULL) dyStringAppendC(dy, ','); } dyStringAppend(dy, ")"); sr = sqlGetResult(conn, dy->string); while ((row = sqlNextRow(sr)) != NULL) { tp = hashFindVal(hash, row[0]); if (tp == NULL) internalErr(); for (pos = tp->posList; pos != NULL; pos = pos->next) { char nameBuf[256]; safef(nameBuf, sizeof(nameBuf), "%s (%s)", row[1], row[0]); pos->name = cloneString(nameBuf); pos->description = cloneString(row[2]); pos->browserName = cloneString(row[0]); } } sqlFreeResult(&sr); /* Hang all pos onto table. */ for (tp = tpList; tp != NULL; tp = tp->next) { struct hgPos *next; for (pos = tp->posList; pos != NULL; pos = next) { next = pos->next; slAddHead(&posList, pos); } } table->posList = posList; hashFree(&hash); dyStringFree(&dy); } boolean findKnownGeneFullText(char *db, char *term,struct hgPositions *hgp) /* Look for position in full text. */ { char path[PATH_LEN]; boolean gotIt = FALSE; struct trix *trix; struct trixSearchResult *tsrList; char *lowered = cloneString(term); char *keyWords[HGFIND_MAX_KEYWORDS]; int keyCount; safef(path, sizeof(path), "/gbdb/%s/knownGene.ix", db); trix = trixOpen(path); tolowers(lowered); keyCount = chopLine(lowered, keyWords); tsrList = trixSearch(trix, keyCount, keyWords, TRUE); if (tsrList != NULL) { struct hgPosTable *table = addKnownGeneTable(db, hgp); struct sqlConnection *conn = hAllocConn(db); addKnownGeneItems(table, tsrList, conn); hFreeConn(&conn); gotIt = TRUE; } freez(&lowered); trixSearchResultFreeList(&tsrList); trixClose(&trix); return gotIt; } static boolean findKnownGeneDescLike(char *db, char *spec, struct hgPositions *hgp, char *tableName) /* Look for position in gene prediction table. */ { struct sqlConnection *conn; struct sqlResult *sr = NULL; struct dyString *query; char **row; boolean ok = FALSE; struct hgPosTable *table = NULL; struct hgPos *pos = NULL; int rowOffset; char *localName; localName = spec; if (!hTableExists(db, tableName)) return FALSE; rowOffset = hOffsetPastBin(db, NULL, tableName); conn = hAllocConn(db); query = newDyString(256); dyStringPrintf(query, "SELECT chrom, txStart, txEnd, name, description FROM %s, kgXref " "WHERE description LIKE '%%%s%%' and kgId=name", tableName, localName); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (ok == FALSE) { ok = TRUE; table = addKnownGeneTable(db, hgp); } AllocVar(pos); pos->chrom = hgOfficialChromName(db, row[0]); pos->chromStart = atoi(row[1]); pos->chromEnd = atoi(row[2]); pos->name = cloneString(row[3]); pos->description = cloneString(row[4]); pos->browserName = cloneString(row[3]); slAddHead(&table->posList, pos); } if (table != NULL) slReverse(&table->posList); freeDyString(&query); sqlFreeResult(&sr); hFreeConn(&conn); return ok; } static boolean findKnownGeneLike(char *db, char *spec, struct hgPositions *hgp, char *tableName) /* Look for position in gene prediction table. */ { struct sqlConnection *conn; struct sqlResult *sr = NULL; struct dyString *query; char **row; boolean ok = FALSE; struct hgPosTable *table = NULL; struct hgPos *pos = NULL; int rowOffset; char *localName; localName = spec; if (!hTableExists(db, tableName)) return FALSE; rowOffset = hOffsetPastBin(db, NULL, tableName); conn = hAllocConn(db); query = newDyString(256); dyStringPrintf(query, "SELECT chrom, txStart, txEnd, name FROM %s " "WHERE name LIKE '%s%%'", tableName, localName); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (ok == FALSE) { ok = TRUE; table = addKnownGeneTable(db, hgp); slAddHead(&hgp->tableList, table); } AllocVar(pos); pos->chrom = hgOfficialChromName(db, row[0]); pos->chromStart = atoi(row[1]); pos->chromEnd = atoi(row[2]); pos->name = cloneString(row[3]); pos->browserName = cloneString(row[3]); slAddHead(&table->posList, pos); } if (table != NULL) slReverse(&table->posList); freeDyString(&query); sqlFreeResult(&sr); hFreeConn(&conn); return ok; } static boolean findKnownGene(char *db, char *spec, struct hgPositions *hgp, char *tableName) /* Look for position in gene prediction table. */ { char *mrnaID; if (!hTableExists(db, "knownGene")) return FALSE; if (findKnownGeneExact(db, spec, spec, hgp, tableName)) return TRUE; mrnaID = MrnaIDforProtein(db, spec); if (mrnaID == NULL) mrnaID = MrnaIDforProtein(db, spec); if (mrnaID != NULL) return (findKnownGeneExact(db, mrnaID, spec, hgp, tableName)); mrnaID = MrnaIDforGeneName(db, spec); if (mrnaID != NULL) return (findKnownGeneExact(db, mrnaID, spec, hgp, tableName)); if (findKnownGeneLike(db, spec, hgp, tableName)) return TRUE; return (findKnownGeneDescLike(db, spec, hgp, tableName)); } static char *getUiUrl(struct cart *cart) /* Get rest of UI from browser. */ { static struct dyString *dy = NULL; static char *s = NULL; if (dy == NULL) { dy = newDyString(64); if (cart != NULL) dyStringPrintf(dy, "%s=%u", cartSessionVarName(), cartSessionId(cart)); s = dy->string; } return s; } static void singlePos(struct hgPositions *hgp, char *tableDescription, char *posDescription, char *tableName, char *posName, char *browserName, char *chrom, int start, int end) /* Fill in pos for simple case single position. */ { struct hgPosTable *table; struct hgPos *pos; AllocVar(table); AllocVar(pos); slAddHead(&hgp->tableList, table); table->posList = pos; table->description = cloneString(tableDescription); table->name = cloneString(tableName); pos->chrom = chrom; pos->chromStart = start; pos->chromEnd = end; pos->name = cloneString(posName); pos->description = cloneString(posDescription); pos->browserName = cloneString(browserName); } static void fixSinglePos(struct hgPositions *hgp) /* Fill in posCount and if proper singlePos fields of hgp * by going through tables... */ { int posCount = 0; struct hgPosTable *table; struct hgPos *pos; for (table = hgp->tableList; table != NULL; table = table->next) { for (pos = table->posList; pos != NULL; pos = pos->next) { ++posCount; if (pos->chrom != NULL) hgp->singlePos = pos; } } if (posCount != 1) hgp->singlePos = NULL; hgp->posCount = posCount; } static char *startsWithShortHumanChromName(char *db, char *chrom) /* Return "cannonical" name of chromosome or NULL * if not a chromosome. This expects no 'chr' in name. */ { int num; char buf[64]; char c = chrom[0]; if (c == 'x' || c == 'X' || c == 'Y' || c == 'y') { safef(buf, sizeof(buf), "chr%c", toupper(c)); return hgOfficialChromName(db, buf); } if (!isdigit(chrom[0])) return NULL; num = atoi(chrom); if (num < 1 || num > 22) return NULL; safef(buf, sizeof(buf), "chr%d", num); return hgOfficialChromName(db, buf); } static struct cytoBand *loadAllBands(char *db) /* Load up all bands from database. */ { struct cytoBand *list = NULL, *el; struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; char **row; sr = sqlGetResult(conn, "select * from cytoBand"); while ((row = sqlNextRow(sr)) != NULL) { el = cytoBandLoad(row); slAddHead(&list, el); } sqlFreeResult(&sr); slReverse(&list); hFreeConn(&conn); return list; } static struct cytoBand *bandList = NULL; void hgFindChromBand(char *db, char *chromosome, char *band, int *retStart, int *retEnd) /* Return start/end of band in chromosome. */ { struct cytoBand *chrStart = NULL, *chrEnd = NULL, *cb; int start = 0, end = 500000000; boolean anyMatch; char choppedBand[64], *s, *e; if (bandList == NULL) bandList = loadAllBands(db); /* Find first band in chromosome. */ for (cb = bandList; cb != NULL; cb = cb->next) { if (sameString(cb->chrom, chromosome)) { chrStart = cb; break; } } if (chrStart == NULL) hUserAbort("Couldn't find chromosome %s in band list", chromosome); /* Find last band in chromosome. */ for (cb = chrStart->next; cb != NULL; cb = cb->next) { if (!sameString(cb->chrom, chromosome)) break; } chrEnd = cb; if (sameWord(band, "cen")) { for (cb = chrStart; cb != chrEnd; cb = cb->next) { if (cb->name[0] == 'p') start = cb->chromEnd - 500000; else if (cb->name[0] == 'q') { end = cb->chromStart + 500000; break; } } *retStart = start; *retEnd = end; return; } else if (sameWord(band, "qter")) { *retStart = *retEnd = hChromSize(db, chromosome); *retStart -= 1000000; return; } /* Look first for exact match. */ for (cb = chrStart; cb != chrEnd; cb = cb->next) { if (sameWord(cb->name, band)) { *retStart = cb->chromStart; *retEnd = cb->chromEnd; return; } } /* See if query is less specific.... */ strcpy(choppedBand, band); for (;;) { anyMatch = FALSE; for (cb = chrStart; cb != chrEnd; cb = cb->next) { if (startsWith(choppedBand, cb->name)) { if (!anyMatch) { anyMatch = TRUE; start = cb->chromStart; } end = cb->chromEnd; } } if (anyMatch) { *retStart = start; *retEnd = end; return; } s = strrchr(choppedBand, '.'); if (s == NULL) hUserAbort("Couldn't find anything like band '%s'", band); else { e = choppedBand + strlen(choppedBand) - 1; *e = 0; if (e[-1] == '.') e[-1] = 0; warn("Band %s%s is at higher resolution than data, chopping to %s%s", chromosome+3, band, chromosome+3, choppedBand); } } } boolean hgIsCytoBandName(char *db, char *spec, char **retChromName, char **retBandName) /* Return TRUE if spec is a cytological band name including chromosome short * name. Returns chromosome chrN name and band (with chromosome stripped off) */ { char *fullChromName, *shortChromName; int len; int dotCount = 0; char *s, c; /* First make sure spec is in format to be a band name. */ if ((fullChromName = startsWithShortHumanChromName(db, spec)) == NULL) return FALSE; shortChromName = skipChr(fullChromName); len = strlen(shortChromName); spec += len; c = spec[0]; if (c != 'p' && c != 'q') return FALSE; /* the mouse bands can have a letter here, A-H, searchType cytoBand * doesn't seem to use the termRegx */ if (!(isdigit(spec[1]) || (1 == countChars("ABCDEFGH", spec[1])))) return FALSE; /* Make sure rest is digits with maybe one '.' */ s = spec+2; while ((c = *s++) != 0) { if (c == '.') ++dotCount; else if (!isdigit(c)) return FALSE; } if (dotCount > 1) return FALSE; *retChromName = fullChromName; *retBandName = spec; return TRUE; } boolean hgFindCytoBand(char *db, char *spec, char **retChromName, int *retWinStart, int *retWinEnd) /* Return position associated with cytological band if spec looks to be * in that form. */ { char *bandName; if (!hgIsCytoBandName(db, spec, retChromName, &bandName)) return FALSE; hgFindChromBand(db, *retChromName, bandName, retWinStart, retWinEnd); return TRUE; } boolean findChromContigPos(char *db, char *name, char **retChromName, int *retWinStart, int *retWinEnd) /* Find position in genome of contig. Look in all chroms. * Don't alter return variables unless found. */ /* NOTE: could probably speed this up by using the chromInfo hashtable */ { struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; char **row; char query[256]; boolean foundIt = FALSE; /* In case this is a scaffold-based assembly, check for unsplit table first: */ if (sqlTableExists(conn, "gold")) { safef(query, sizeof(query), "select chrom,chromStart,chromEnd from gold where frag = '%s'", name); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { *retChromName = cloneString(row[0]); *retWinStart = atoi(row[1]); *retWinEnd = atoi(row[2]); foundIt = TRUE; } sqlFreeResult(&sr); } else { struct slName *allChroms = hAllChromNames(db); struct slName *chromPtr; for (chromPtr=allChroms; chromPtr != NULL; chromPtr=chromPtr->next) { char tableName[256]; safef(tableName, sizeof(tableName), "%s_gold", chromPtr->name); if (! sqlTableExists(conn, tableName)) continue; safef(query, sizeof(query), "select chromStart,chromEnd from %s where frag = '%s'", tableName, name); sr = sqlMustGetResult(conn, query); row = sqlNextRow(sr); if (row != NULL) { *retChromName = cloneString(chromPtr->name); *retWinStart = atoi(row[0]); *retWinEnd = atoi(row[1]); foundIt = TRUE; } sqlFreeResult(&sr); if (foundIt) break; } slNameFreeList(&allChroms); } hFreeConn(&conn); return foundIt; } #if 0 /* not used */ static boolean isAccForm(char *s) /* Returns TRUE if s is of format to be a genbank accession. */ { int len = strlen(s); if (len < 6 || len > 10) return FALSE; if (!isalpha(s[0])) return FALSE; if (!isdigit(s[len-1])) return FALSE; return TRUE; } #endif static boolean mrnaInfo(char *acc, struct sqlConnection *conn, char **mrnaType) /* Sets *mrnaType to mrna/est type for the accession */ /* Ignores returned values if parameters are NULL */ /* Return TRUE if search succeeded, else FALSE */ /* NOTE: caller must free mrnaType */ { char query[256]; struct sqlResult *sr; char **row; int ret; safef(query, sizeof(query), "select type from gbCdnaInfo where acc = '%s'", acc); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { if (mrnaType != NULL) *mrnaType = cloneString(row[0]); ret = TRUE; } else ret = FALSE; sqlFreeResult(&sr); return ret; } boolean isRefSeqAcc(char *acc) /* Return TRUE if acc looks like a RefSeq acc. */ { return regexMatchNoCase(acc, "^(N|X)M_[0-9]{6}[0-9]*$"); } static char *mrnaType(char *db, char *acc) /* Return "mrna" or "est" if acc is mRNA, otherwise NULL. Returns * NULL for refseq mRNAs */ /* for compat with older databases, just look at the seqId to * determine if it's a refseq, don't use table */ /* NOTE: caller must free returned type */ { struct sqlConnection *conn; char *type = NULL; char *ret = NULL; if (isRefSeqAcc(acc)) return NULL; conn = hAllocConn(db); if (mrnaInfo(acc, conn, &type)) ret = type; else ret = NULL; hFreeConn(&conn); return ret; } static void mrnaHtmlStart(struct hgPosTable *table, FILE *f) /* Print preamble to mrna alignment positions. */ { fprintf(f, "<H2>%s</H2>", table->description); fprintf(f, "This aligns in multiple positions. Click on a hyperlink to "); fprintf(f, "go to tracks display at a particular alignment.<BR>"); fprintf(f, "<PRE>"); fprintf(f, " SIZE IDENTITY CHROMOSOME STRAND START END cDNA START END TOTAL\n"); fprintf(f, "------------------------------------------------------------------------------\n"); } static void mrnaHtmlEnd(struct hgPosTable *table, FILE *f) /* Print end to mrna alignment positions. */ { fprintf(f, "</PRE>"); } static void mrnaHtmlOnePos(struct hgPosTable *table, struct hgPos *pos, FILE *f) /* Print one mrna alignment position. */ { fprintf(f, "%s", pos->description); } #ifdef OLD static void makeGbTrackTableName(char *db, char *tableName, size_t tnSize, char *base) /* Now we have to watch out for scaffold-based browsers where * the track is all_{mrna,est} not {mrna,est}. */ { char splitTable[256]; safef(splitTable, sizeof(splitTable), "%s_%s", hDefaultChrom(db), base); if (hTableExists(db, splitTable)) safef(tableName, tnSize, "%s", base); else safef(tableName, tnSize, "all_%s", base); } #endif /* OLD */ char *hCarefulTrackOpenVis(char *db, char *trackName) /* If track is already in full mode, return full; otherwise, return * hTrackOpenVis. */ { char *vis = cart ? cartOptionalString(cart, trackName) : NULL; if (vis && sameString(vis, "full")) return "full"; else return hTrackOpenVis(db, trackName); } static struct psl *getPslFromTable(struct sqlConnection *conn, char *db, char *table, char *acc) /* If table exists, return PSL for each row with qName = acc. */ { struct psl *pslList = NULL; if (sqlTableExists(conn, table)) { int rowOffset = hOffsetPastBin(db, NULL, table); char query[256]; safef(query, sizeof(query), "select * from %s where qName = '%s'", table, acc); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct psl *psl = pslLoad(row+rowOffset); slAddHead(&pslList, psl); } slReverse(&pslList); sqlFreeResult(&sr); } return pslList; } static void addPslResultToHgp(struct hgPositions *hgp, char *db, char *tableName, char *shortLabel, char *acc, struct psl *pslList) /* Create an hgPosTable for the given psl search results, and add it to hgp->tableList. */ { if (pslList == NULL) return; struct hgPosTable *table; struct dyString *dy = newDyString(1024); struct psl *psl; char hgAppCombiner = (strchr(hgAppName, '?')) ? '&' : '?'; char *ui = getUiUrl(cart); AllocVar(table); table->htmlStart = mrnaHtmlStart; table->htmlEnd = mrnaHtmlEnd; table->htmlOnePos = mrnaHtmlOnePos; slAddHead(&hgp->tableList, table); dyStringPrintf(dy, "%s Alignments in %s", acc, shortLabel); table->description = cloneString(dy->string); table->name = cloneString(tableName); char *trackName = hGetTrackForTable(db, table->name); slSort(&pslList, pslCmpScore); for (psl = pslList; psl != NULL; psl = psl->next) { struct hgPos *pos; dyStringClear(dy); AllocVar(pos); pos->chrom = hgOfficialChromName(db, psl->tName); pos->chromStart = psl->tStart; pos->chromEnd = psl->tEnd; pos->name = cloneString(psl->qName); pos->browserName = cloneString(psl->qName); dyStringPrintf(dy, "<A HREF=\"%s%cposition=%s&%s=%s", hgAppName, hgAppCombiner, hgPosBrowserRange(pos, NULL), trackName, hCarefulTrackOpenVis(db, trackName)); if (ui != NULL) dyStringPrintf(dy, "&%s", ui); dyStringPrintf(dy, "%s\">", hgp->extraCgi); dyStringPrintf(dy, "%5d %5.1f%% %9s %s %9d %9d %8s %5d %5d %5d</A>", psl->match + psl->misMatch + psl->repMatch + psl->nCount, 100.0 - pslCalcMilliBad(psl, TRUE) * 0.1, skipChr(psl->tName), psl->strand, psl->tStart + 1, psl->tEnd, psl->qName, psl->qStart+1, psl->qEnd, psl->qSize); dyStringPrintf(dy, "\n"); pos->description = cloneString(dy->string); slAddHead(&table->posList, pos); } slReverse(&table->posList); freeDyString(&dy); } static boolean findMrnaPos(char *db, char *acc, struct hgPositions *hgp) /* Find MRNA or EST position(s) from accession number. * Look to see if it's an mRNA or EST. Fill in hgp and return * TRUE if it is, otherwise return FALSE. */ /* NOTE: this excludes RefSeq mrna's, as they are currently * handled in findRefGenes(), which is called later in the main function */ { if (!hTableExists(db, "gbCdnaInfo")) return FALSE; char *type = mrnaType(db, acc); if (isEmpty(type)) /* this excludes refseq mrna's, and accessions with * invalid column type in mrna table (refseq's and ests) */ return FALSE; char lowerType[16]; struct sqlConnection *conn = hAllocConn(db); char **tables, **labels, *tableName; boolean gotResults = FALSE; safecpy(lowerType, sizeof(lowerType), type); tolowers(lowerType); if (sameWord(lowerType, "mrna")) { tables = mrnaTables; labels = mrnaLabels; } else if (sameWord(lowerType, "est")) { tables = estTables; labels = estLabels; } else return FALSE; while ((tableName = *tables++) != NULL) { char *label = *labels++; struct psl *pslList = NULL; if (sameString(tableName, "intronEst") && !sqlTableExists(conn, tableName)) { struct slName *c, *chromList = hChromList(db); char splitTable[HDB_MAX_TABLE_STRING]; for (c = chromList; c != NULL; c = c->next) { safef(splitTable, sizeof(splitTable), "%s_%s", c->name, tableName); struct psl *chrPslList = getPslFromTable(conn, db, splitTable, acc); if (pslList == NULL) pslList = chrPslList; else slCat(pslList, chrPslList); } } else pslList = getPslFromTable(conn, db, tableName, acc); if (pslList == NULL) continue; gotResults = TRUE; addPslResultToHgp(hgp, db, tableName, label, acc, pslList); if (!sameString(tableName, "intronEst")) /* for speed -- found proper table, so don't need to look farther */ break; } hFreeConn(&conn); return gotResults; } static char *getGenbankGrepIndex(char *db, struct hgFindSpec *hfs, char *table, char *suffix) /* If hg.conf has a grepIndex.genbank setting, hfs has a (placeholder) * grepIndex setting, and we can access the index file for table, then * return the filename; else return NULL. */ /* Special case for genbank: Mark completely specifies the root in * hg.conf, so hfs's grepIndex setting value is ignored -- it is used * only to enable grep indexing. So we have multiple ways to turn this * off if necessary: remove hg.conf setting (takes out all dbs), * remove hgFindSpec setting (takes out one db at a time), or remove * a file (takes out one table at a time). */ { char *grepIndexRoot = cfgOption("grepIndex.genbank"); char *hfsSetting = hgFindSpecSetting(hfs, "grepIndex"); if (grepIndexRoot != NULL && hfsSetting != NULL) { char buf[1024]; safef(buf, sizeof(buf), "%s/%s/%s.%s", grepIndexRoot, db, table, suffix); if (fileExists(buf)) return cloneString(buf); } return NULL; } static struct slName *genbankGrepQuery(char *indexFile, char *table, char *key) /* grep -i key indexFile, return a list of ids (first word of each line). */ { char *extraOptions = ""; if (sameString(table, "author")) extraOptions = "-w"; return doGrepQuery(indexFile, table, key, extraOptions); } static struct slName *genbankSqlFuzzyQuery(struct sqlConnection *conn, char *table, char *key) /* Perform a fuzzy sql search for %key% in table.name; return list of * corresponding table.id's. */ { struct slName *idList = NULL, *idEl = NULL; if (!isTooCommon(table, key)) { struct sqlResult *sr; char **row; char query[256]; safef(query, sizeof(query), "select id,name from %s where name like '%%%s%%'", table, key); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { touppers(row[1]); if (keyIsPrefix(key, row[1])) { idEl = newSlName(row[0]); slAddHead(&idList, idEl); } } sqlFreeResult(&sr); } return idList; } static boolean gotAllGenbankGrepIndexFiles(char *db, struct hgFindSpec *hfs, char *tables[], int tableCount) /* Return TRUE if all tables have a readable genbank index file. */ { int i; for (i=0; i < tableCount; i++) if (! getGenbankGrepIndex(db, hfs, tables[i], "idName")) return FALSE; return TRUE;; } static void findHitsToTables(char *db, struct hgFindSpec *hfs, char *key, char *tables[], int tableCount, struct hash **retHash, struct slName **retList) /* Return all unique accessions that match any table. */ { struct slName *list = NULL, *el; struct hash *hash = newHash(0); struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr; char **row; char query[256]; char *field; int i; for (i = 0; i<tableCount; ++i) { struct slName *idList = NULL, *idEl; char *grepIndexFile = NULL; /* I'm doing this query in two steps in C rather than * in one step in SQL just because it somehow is much * faster this way (like 100x faster) when using mySQL. */ field = tables[i]; if (!hTableExists(db, field)) continue; if ((grepIndexFile = getGenbankGrepIndex(db, hfs, field, "idName")) != NULL) idList = genbankGrepQuery(grepIndexFile, field, key); else idList = genbankSqlFuzzyQuery(conn, field, key); for (idEl = idList; idEl != NULL; idEl = idEl->next) { /* don't check srcDb to exclude refseq for compat with older tables */ safef(query, sizeof(query), "select acc, organism from gbCdnaInfo where %s = %s " " and type = 'mRNA'", field, idEl->name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *acc = row[0]; /* will use this later to distinguish xeno mrna */ int organismID = sqlUnsigned(row[1]); if (!isRefSeqAcc(acc) && !hashLookup(hash, acc)) { el = newSlName(acc); slAddHead(&list, el); hashAddInt(hash, acc, organismID); } } sqlFreeResult(&sr); } slFreeList(&idList); } hFreeConn(&conn); slReverse(&list); *retList = list; *retHash = hash; } static void andHits(struct hash *aHash, struct slName *aList, struct hash *bHash, struct slName *bList, struct hash **retHash, struct slName **retList) /* Return hash/list that is intersection of lists a and b. */ { struct slName *list = NULL, *el, *newEl; struct hash *hash = newHash(0); for (el = aList; el != NULL; el = el->next) { char *name = el->name; int organismID = hashIntValDefault(bHash, name, -1); if (organismID >= 0 && !hashLookup(hash, name)) { newEl = newSlName(name); slAddHead(&list, newEl); hashAddInt(hash, name, organismID); } } *retHash = hash; *retList = list; } static void mrnaKeysHtmlOnePos(struct hgPosTable *table, struct hgPos *pos, FILE *f) { fprintf(f, "%s", pos->description); } static boolean mrnaAligns(struct sqlConnection *conn, char *table, char *acc) /* Return TRUE if accession is in the designated alignment table (for speed, * this assumes that we've already checked that the table exists) */ { char query[256]; safef(query, sizeof(query), "select count(*) from %s where qName = '%s'", table, acc); return (sqlQuickNum(conn, query) > 0); } static int addMrnaPositionTable(char *db, struct hgPositions *hgp, struct slName **pAccList, struct hash *accOrgHash, struct cart *cart, struct sqlConnection *conn, char *hgAppName, boolean aligns, boolean isXeno) /* Generate table of positions that match criteria. * Add to hgp if any found. Return number found */ { struct hgPosTable *table = NULL; struct hgPos *pos = NULL; struct slName *el = NULL; struct slName *elToFree = NULL; struct dyString *dy = newDyString(256); char query[512]; char description[512]; char product[256]; char organism[128]; char *ui = getUiUrl(cart); char *acc = NULL; int organismID = hOrganismID(hgp->database); /* id from mrna organism table */ int alignCount = 0; char hgAppCombiner = (strchr(hgAppName, '?')) ? '&' : '?'; char *mrnaTable = isXeno ? "xenoMrna" : "all_mrna"; boolean mrnaTableExists = hTableExists(hgp->database, mrnaTable); AllocVar(table); /* Examine all accessions to see if they fit criteria for * this table. Add all matching to the position list, and * remove from the accession list */ for (el = *pAccList; el != NULL; el = el->next) { freez(&elToFree); acc = el->name; /* check if item matches xeno criterion */ if (hTableExists(db, "gbStatus")) { safef(query, sizeof(query), "select (orgCat = 'native' && srcDb != 'RefSeq') from gbStatus where acc = '%s'", acc); /* redmine #3301 */ if (isXeno == sqlQuickNum(conn, query)) continue; } else { int itemOrganismID = hashIntVal(accOrgHash, acc); if (isXeno == (itemOrganismID == organismID)) continue; } /* check if item matches alignment criterion */ if (aligns != (mrnaTableExists && mrnaAligns(conn, mrnaTable, acc))) continue; /* item fits criteria, so enter in table */ AllocVar(pos); slAddHead(&table->posList, pos); pos->name = cloneString(acc); pos->browserName = cloneString(acc); dyStringClear(dy); if (aligns) { dyStringPrintf(dy, "<A HREF=\"%s%cposition=%s", hgAppName, hgAppCombiner, acc); } else { /* display mRNA details page -- need to add dummy CGI variables*/ dyStringPrintf(dy, "<A HREF=\"%s%cg=%s&i=%s&c=0&o=0&l=0&r=0", hgcName(), hgAppCombiner, mrnaTable, acc); } if (ui != NULL) dyStringPrintf(dy, "&%s", ui); dyStringPrintf(dy, "%s\">", hgp->extraCgi); dyStringPrintf(dy, "%s</A>", acc); /* print description for item, or lacking that, the product name */ safef(description, sizeof(description), "%s", "n/a"); safef(query, sizeof(query), "select description.name from gbCdnaInfo,description" " where gbCdnaInfo.acc = '%s' and gbCdnaInfo.description = description.id", acc); sqlQuickQuery(conn, query, description, sizeof(description)); if (sameString(description, "n/a")) { /* look for product name */ safef(query, sizeof(query), "select productName.name from gbCdnaInfo,productName" " where gbCdnaInfo.acc = '%s' and gbCdnaInfo.productName = productName.id", acc); sqlQuickQuery(conn, query, product, sizeof(product)); if (!sameString(product, "n/a")) { /* get organism name */ safef(query, sizeof(query), "select organism.name from gbCdnaInfo,organism" " where gbCdnaInfo.acc = '%s' and gbCdnaInfo.organism = organism.id", acc); *organism = 0; sqlQuickQuery(conn, query, organism, sizeof(organism)); safef(description, sizeof(description), "%s%s%s", *organism ? organism : "", *organism ? ", " : "", product); } } if (!sameString(description, "n/a")) /* print description if it has been loaded */ dyStringPrintf(dy, " - %s", description); dyStringPrintf(dy, "\n"); pos->description = cloneString(dy->string); /* remove processed element from accession list */ slRemoveEl(pAccList, el); elToFree = el; } /* fill in table and add to hgp only if it contains results */ alignCount = slCount(table->posList); if (alignCount > 0) { char *organism = hOrganism(hgp->database); /* dbDb organism column */ char title[256]; slReverse(&table->posList); safef(title, sizeof(title), "%s%s %sligned mRNA Search Results", isXeno ? "Non-" : "", organism, aligns ? "A" : "Una"); freeMem(organism); table->description = cloneString(title); table->name = cloneString(mrnaTable); table->htmlOnePos = mrnaKeysHtmlOnePos; slAddHead(&hgp->tableList, table); } freeDyString(&dy); return alignCount; } static boolean findMrnaKeys(char *db, struct hgFindSpec *hfs, char *keys, struct hgPositions *hgp) /* Find mRNA that has keyword in one of its fields. */ { int alignCount; static char *tables[] = { "productName", "geneName", "author", "tissue", "cell", "description", "development", }; struct hash *allKeysHash = NULL; struct slName *allKeysList = NULL; struct sqlConnection *conn = hAllocConn(db); boolean found = FALSE; /* If we can use grep to search all tables, then use piped grep to * implement implicit "AND" of multiple keys. */ if (gotAllGenbankGrepIndexFiles(db, hfs, tables, ArraySize(tables))) { findHitsToTables(db, hfs, keys, tables, ArraySize(tables), &allKeysHash, &allKeysList); } else { struct hash *oneKeyHash = NULL; struct slName *oneKeyList = NULL; struct hash *andedHash = NULL; struct slName *andedList = NULL; char *words[32]; char buf[512]; int wordCount; int i; safef(buf, sizeof(buf), "%s", keys); wordCount = chopLine(buf, words); if (wordCount == 0) return FALSE; found = TRUE; for (i=0; i<wordCount; ++i) { findHitsToTables(db, hfs, words[i], tables, ArraySize(tables), &oneKeyHash, &oneKeyList); if (allKeysHash == NULL) { allKeysHash = oneKeyHash; oneKeyHash = NULL; allKeysList = oneKeyList; oneKeyList = NULL; } else { andHits(oneKeyHash, oneKeyList, allKeysHash, allKeysList, &andedHash, &andedList); freeHash(&oneKeyHash); slFreeList(&oneKeyList); freeHash(&allKeysHash); slFreeList(&allKeysList); allKeysHash = andedHash; andedHash = NULL; allKeysList = andedList; andedList = NULL; } } } if (allKeysList == NULL) return FALSE; /* generate position lists and add to hgp */ /* organism aligning */ alignCount = addMrnaPositionTable(db, hgp, &allKeysList, allKeysHash, cart, conn, hgAppName, TRUE, FALSE); /* organism non-aligning */ addMrnaPositionTable(db, hgp, &allKeysList, allKeysHash, cart, conn, hgAppName, FALSE, FALSE); /* xeno aligning */ /* NOTE: to suppress display of xeno mrna's in non-model organisms * (RT 801 and 687), uncommented the following... * add to display list only if there is a scarcity of items * already listed as aligning (low number of own mRna's for this organism) */ if (alignCount < 20) addMrnaPositionTable(db, hgp, &allKeysList, allKeysHash, cart, conn, hgAppName, TRUE, TRUE); hashFree(&allKeysHash); hFreeConn(&conn); return(found); } static boolean isUnsignedInt(char *s) /* Return TRUE if s is in format to be an unsigned int. */ { int size=0; char c; while ((c = *s++) != 0) { if (++size > 10 || !isdigit(c)) return FALSE; } return TRUE; } #if 0 /* not used */ static void findAffyProbe(char *spec, struct hgPositions *hgp) /* Look up affy probes. */ { } #endif int findKgGenesByAlias(char *db, char *spec, struct hgPositions *hgp) /* Look up Known Genes using the gene Alias table, kgAlias. */ { struct sqlConnection *conn = hAllocConn(db); struct sqlConnection *conn2 = hAllocConn(db); struct sqlResult *sr = NULL; struct dyString *ds = newDyString(256); char **row; struct hgPosTable *table = NULL; struct hgPos *pos; struct genePred *gp; char *answer, cond_str[256]; char *desc; struct kgAlias *kaList = NULL, *kl; boolean gotKgAlias = sqlTableExists(conn, "kgAlias"); int kgFound = 0; if (gotKgAlias) { /* get a linked list of kgAlias (kgID/alias pair) nodes that match * the spec using "Fuzzy" mode*/ kaList = findKGAlias(db, spec, "P"); } if (kaList != NULL) { struct hash *hash = newHash(8); kgFound = 1; AllocVar(table); slAddHead(&hgp->tableList, table); table->description = cloneString("Known Genes"); table->name = cloneString("knownGene"); for (kl = kaList; kl != NULL; kl = kl->next) { /* Don't return duplicate mrna accessions */ if (hashFindVal(hash, kl->kgID)) { hashAdd(hash, kl->kgID, kl); continue; } hashAdd(hash, kl->kgID, kl); dyStringClear(ds); dyStringPrintf(ds, "select * from knownGene where name = '%s'", kl->kgID); sr = sqlGetResult(conn, ds->string); while ((row = sqlNextRow(sr)) != NULL) { gp = genePredLoad(row); AllocVar(pos); slAddHead(&table->posList, pos); pos->name = cloneString(kl->alias); #if UNUSED pos->browserName = cloneString(kl->alias); // highlight change #endif pos->browserName = cloneString(kl->kgID); safef(cond_str, sizeof(cond_str), "kgID = '%s'", kl->kgID); answer = sqlGetField(db, "kgXref", "description", cond_str); if (answer != NULL) { desc = answer; } else { desc = kl->alias; } dyStringClear(ds); dyStringPrintf(ds, "(%s) %s", kl->kgID, desc); pos->description = cloneString(ds->string); pos->chrom = hgOfficialChromName(db, gp->chrom); pos->chromStart = gp->txStart; pos->chromEnd = gp->txEnd; genePredFree(&gp); } sqlFreeResult(&sr); } kgAliasFreeList(&kaList); freeHash(&hash); } freeDyString(&ds); hFreeConn(&conn); hFreeConn(&conn2); return(kgFound); } int findKgGenesByProtAlias(char *db, char *spec, struct hgPositions *hgp) /* Look up Known Genes using the protein alias table, kgProtAlias. */ { struct sqlConnection *conn = hAllocConn(db); struct sqlConnection *conn2 = hAllocConn(db); struct sqlResult *sr = NULL; struct dyString *ds = newDyString(256); char **row; struct hgPosTable *table = NULL; struct hgPos *pos; struct genePred *gp; char *answer, cond_str[256]; char *desc; struct kgProtAlias *kpaList = NULL, *kl; boolean gotKgProtAlias = sqlTableExists(conn, "kgProtAlias"); int kgFound = 0; if (gotKgProtAlias) { /* get a link list of kgProtAlias (kgID, displayID, and alias) nodes that match the query spec using "Fuzzy" search mode*/ kpaList = findKGProtAlias(db, spec, "P"); } if (kpaList != NULL) { struct hash *hash = newHash(8); kgFound = 1; AllocVar(table); slAddHead(&hgp->tableList, table); table->description = cloneString("Known Genes"); table->name = cloneString("knownGene"); for (kl = kpaList; kl != NULL; kl = kl->next) { /* Don't return duplicate mrna accessions */ if (hashFindVal(hash, kl->kgID)) { hashAdd(hash, kl->kgID, kl); continue; } hashAdd(hash, kl->kgID, kl); dyStringClear(ds); dyStringPrintf(ds, "select * from knownGene where name = '%s'", kl->kgID); sr = sqlGetResult(conn, ds->string); while ((row = sqlNextRow(sr)) != NULL) { gp = genePredLoad(row); AllocVar(pos); slAddHead(&table->posList, pos); pos->name = cloneString(kl->alias); /* pos->browserName = cloneString(kl->alias); highlight change */ pos->browserName = cloneString(kl->kgID); safef(cond_str, sizeof(cond_str), "kgID = '%s'", kl->kgID); answer = sqlGetField(db, "kgXref", "description", cond_str); if (answer != NULL) { desc = answer; } else { desc = kl->alias; } dyStringClear(ds); dyStringPrintf(ds, "(%s) %s", kl->displayID, desc); pos->description = cloneString(ds->string); pos->chrom = hgOfficialChromName(db, gp->chrom); pos->chromStart = gp->txStart; pos->chromEnd = gp->txEnd; genePredFree(&gp); } sqlFreeResult(&sr); } kgProtAliasFreeList(&kpaList); freeHash(&hash); } freeDyString(&ds); hFreeConn(&conn); hFreeConn(&conn2); return(kgFound); } static void addRefLinks(struct sqlConnection *conn, struct dyString *query, struct refLink **pList) /* Query database and add returned refLinks to head of list. */ { struct sqlResult *sr = sqlGetResult(conn, query->string); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct refLink *rl = refLinkLoad(row); slAddHead(pList, rl); } sqlFreeResult(&sr); } static void addRefLinkAccs(struct sqlConnection *conn, struct slName *accList, struct refLink **pList) /* Query database and add returned refLinks to head of list. */ { struct slName *accEl = NULL; struct sqlResult *sr = NULL; char **row = NULL; char query[256]; for (accEl = accList; accEl != NULL; accEl = accEl->next) { safef(query, sizeof(query), "select * from refLink where mrnaAcc = '%s'", accEl->name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct refLink *rl = refLinkLoad(row); slAddHead(pList, rl); } sqlFreeResult(&sr); } } static boolean findRefGenes(char *db, struct hgFindSpec *hfs, char *spec, struct hgPositions *hgp) /* Look up refSeq genes in table. */ { struct sqlConnection *conn = hAllocConn(db); struct dyString *ds = newDyString(256); struct refLink *rlList = NULL, *rl; boolean gotRefLink = hTableExists(db, "refLink"); boolean found = FALSE; char *specNoVersion = cloneString(spec); (void) chopPrefix(specNoVersion); if (gotRefLink) { if (startsWith("NM_", specNoVersion) || startsWith("NR_", specNoVersion) || startsWith("XM_", specNoVersion)) { dyStringPrintf(ds, "select * from refLink where mrnaAcc = '%s'", specNoVersion); addRefLinks(conn, ds, &rlList); } else if (startsWith("NP_", specNoVersion) || startsWith("XP_", specNoVersion)) { dyStringPrintf(ds, "select * from refLink where protAcc = '%s'", specNoVersion); addRefLinks(conn, ds, &rlList); } else if (isUnsignedInt(specNoVersion)) { dyStringPrintf(ds, "select * from refLink where locusLinkId = %s", specNoVersion); addRefLinks(conn, ds, &rlList); dyStringClear(ds); dyStringPrintf(ds, "select * from refLink where omimId = %s", specNoVersion); addRefLinks(conn, ds, &rlList); } else { char *indexFile = getGenbankGrepIndex(db, hfs, "refLink", "mrnaAccProduct"); dyStringPrintf(ds, "select * from refLink where name like '%s%%'", specNoVersion); addRefLinks(conn, ds, &rlList); if (indexFile != NULL) { struct slName *accList = doGrepQuery(indexFile, "refLink", specNoVersion, NULL); addRefLinkAccs(conn, accList, &rlList); } else { dyStringClear(ds); dyStringPrintf(ds, "select * from refLink where product like '%%%s%%'", specNoVersion); addRefLinks(conn, ds, &rlList); } } } if (rlList != NULL) { struct hgPosTable *table = NULL; struct hash *hash = newHash(8); for (rl = rlList; rl != NULL; rl = rl->next) { char where[64]; struct genePredReader *gpr; struct genePred *gp; /* Don't return duplicate mrna accessions */ if (hashFindVal(hash, rl->mrnaAcc)) { hashAdd(hash, rl->mrnaAcc, rl); continue; } hashAdd(hash, rl->mrnaAcc, rl); safef(where, sizeof where, "name = '%s'", rl->mrnaAcc); gpr = genePredReaderQuery(conn, hfs->searchTable, where); while ((gp = genePredReaderNext(gpr)) != NULL) { struct hgPos *pos = NULL; AllocVar(pos); if (table == NULL) { char desc[256]; AllocVar(table); table->name = cloneString(hfs->searchTable); if (startsWith("xeno", hfs->searchTable)) safef(desc, sizeof(desc), "Non-%s RefSeq Genes", hOrganism(db)); else safef(desc, sizeof(desc), "RefSeq Genes"); table->description = cloneString(desc); slAddHead(&hgp->tableList, table); } slAddHead(&table->posList, pos); pos->name = cloneString(rl->name); pos->browserName = cloneString(rl->mrnaAcc); dyStringClear(ds); dyStringPrintf(ds, "(%s) %s", rl->mrnaAcc, rl->product); pos->description = cloneString(ds->string); pos->chrom = hgOfficialChromName(db, gp->chrom); pos->chromStart = gp->txStart; pos->chromEnd = gp->txEnd; genePredFree(&gp); found = TRUE; } genePredReaderFree(&gpr); } refLinkFreeList(&rlList); freeHash(&hash); } freeDyString(&ds); hFreeConn(&conn); return(found); } /* Lowe lab additions */ static void addTigrCmrGenes(struct sqlConnection *conn, struct dyString *query, struct tigrCmrGene **pList) /* Query database and add returned tigrCmrGenes to head of list. */ { struct sqlResult *sr = sqlGetResult(conn, query->string); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct tigrCmrGene *rl = tigrCmrGeneLoad(row); slAddHead(pList, rl); } sqlFreeResult(&sr); } static void findTigrGenes(char *db, char *spec, struct hgPositions *hgp) /* Look up TIGR and Genbank genes from keyword */ { struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; struct dyString *ds = newDyString(256); char **row; struct hgPosTable *table = NULL; struct hgPos *pos; struct bed *bed; struct tigrCmrGene *tigrList = NULL, *tigr; /* struct minGeneInfo *gbList = NULL, *gb; */ boolean gotTIGRkeys = sqlTableExists(conn, "tigrCmrORFsInfo"); if (gotTIGRkeys) { dyStringPrintf(ds, "select * from tigrCmrORFsInfo where tigrCommon like '%%%s%%'", spec); addTigrCmrGenes(conn, ds, &tigrList); dyStringClear(ds); dyStringPrintf(ds, "select * from tigrCmrORFsInfo where tigrMainRole like '%%%s%%'", spec); addTigrCmrGenes(conn, ds, &tigrList); dyStringClear(ds); dyStringPrintf(ds, "select * from tigrCmrORFsInfo where tigrSubRole like '%%%s%%'", spec); addTigrCmrGenes(conn, ds, &tigrList); dyStringClear(ds); } if (tigrList != NULL) { struct hash *hash = newHash(8); AllocVar(table); slAddHead(&hgp->tableList, table); table->description = cloneString("TIGR CMR Genes"); table->name = cloneString("tigrORFsCmr"); for (tigr = tigrList; tigr != NULL; tigr = tigr->next) { /* Don't return duplicate TIGR CMR accessions */ if (hashFindVal(hash, tigr->name)) { hashAdd(hash, tigr->name, tigr); continue; } hashAdd(hash, tigr->name, tigr); dyStringClear(ds); dyStringPrintf(ds, "select * from tigrCmrORFs where name = '%s'", tigr->name); sr = sqlGetResult(conn, ds->string); while ((row = sqlNextRow(sr)) != NULL) { bed = bedLoadN(row+1,6); AllocVar(pos); slAddHead(&table->posList, pos); pos->name = cloneString(tigr->name); pos->browserName = cloneString(tigr->name); dyStringClear(ds); dyStringPrintf(ds, "%s; %s; %s", tigr->tigrCommon, tigr->tigrMainRole, tigr->tigrSubRole); pos->description = cloneString(ds->string); pos->chrom = hgOfficialChromName(db, bed->chrom); pos->chromStart = bed->chromStart; pos->chromEnd = bed->chromEnd; bedFree(&bed); } sqlFreeResult(&sr); } tigrCmrGeneFreeList(&tigrList); freeHash(&hash); } freeDyString(&ds); hFreeConn(&conn); } /* End of Lowe Lab stuff */ static boolean findGenePredPattern(char *db, char *pattern, struct hgPositions *hgp, char *tableName, struct hgPosTable *table) /* Look for position pattern in gene prediction table. */ { struct sqlConnection *conn; struct sqlResult *sr = NULL; struct dyString *query; char **row; boolean ok = FALSE; struct hgPos *pos = NULL; int rowOffset; char *localName; localName = pattern; if (!hTableExists(db, tableName)) return FALSE; rowOffset = hOffsetPastBin(db, NULL, tableName); conn = hAllocConn(db); query = newDyString(256); dyStringPrintf(query, "SELECT chrom, txStart, txEnd, name FROM %s WHERE name LIKE '%s'", tableName, pattern); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { if (ok == FALSE) { ok = TRUE; if (table == NULL) { AllocVar(table); dyStringClear(query); dyStringPrintf(query, "%s Gene Predictions", tableName); table->description = cloneString(query->string); table->name = cloneString(tableName); slAddHead(&hgp->tableList, table); } } AllocVar(pos); pos->chrom = hgOfficialChromName(db, row[0]); pos->chromStart = atoi(row[1]); pos->chromEnd = atoi(row[2]); pos->name = cloneString(row[3]); pos->browserName = cloneString(row[3]); slAddHead(&table->posList, pos); } if (table != NULL) slReverse(&table->posList); freeDyString(&query); sqlFreeResult(&sr); hFreeConn(&conn); return ok; } static void addUniqYeastGene(char *db, struct hash *uniqHash, struct sqlConnection *conn, char *query, struct hgPositions *hgp, char *geneTable, struct hgPosTable **pTable) /* Execute query which returns a single row, and add genes. */ { struct sqlResult *sr = sqlGetResult(conn, query); char **row; struct hgPosTable *table = *pTable; while ((row = sqlNextRow(sr)) != NULL) { char *id = row[0]; if (!hashLookup(uniqHash, id)) { hashAdd(uniqHash, id, NULL); if (table == NULL) { AllocVar(table); table->name = geneTable; table->description = "Genes from Sacchromyces Genome Database"; slAddHead(&hgp->tableList, table); *pTable = table; } findGenePredPattern(db, id, hgp, geneTable, table); } } sqlFreeResult(&sr); } static boolean findYeastGenes(char *db, char *pattern, struct hgPositions *hgp) /* Scan yeast-specific tables. */ { struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr; char **row, query[256]; struct hgPosTable *table = NULL; boolean found = FALSE; if (hTableExists(db, "sgdGene")) { struct hash *uniqHash = newHash(0); boolean gotNames = FALSE, gotDescriptions = FALSE; safef(query, sizeof(query), "select name from sgdGene where name = '%s'", pattern); addUniqYeastGene(db, uniqHash, conn, query, hgp, "sgdGene", &table); if (hTableExists(db, "sgdToName")) { gotNames = TRUE; safef(query, sizeof(query), "select name from sgdToName where value like '%s%%'", pattern); addUniqYeastGene(db, uniqHash, conn, query, hgp, "sgdGene", &table); } if (hTableExists(db, "sgdDescription")) { gotDescriptions = TRUE; safef(query, sizeof(query), "select name from sgdDescription where description like '%%%s%%'", pattern); addUniqYeastGene(db, uniqHash, conn, query, hgp, "sgdGene", &table); } hashFree(&uniqHash); /* Add descriptions to table. */ if (table != NULL) { struct hgPos *pos; for (pos = table->posList; pos != NULL; pos = pos->next) { struct dyString *dy = newDyString(1024); if (gotNames) { safef(query, sizeof(query), "select value from sgdToName where name = '%s'", pos->name); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) dyStringPrintf(dy, "(%s) ", row[0]); sqlFreeResult(&sr); } if (gotDescriptions) { safef(query, sizeof(query), "select description from sgdDescription where name = '%s'", pos->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) dyStringPrintf(dy, "%s", row[0]); sqlFreeResult(&sr); } if (dy->stringSize > 0) pos->description = cloneString(dy->string); dyStringFree(&dy); } found = TRUE; } } hFreeConn(&conn); return(found); } static void hgPositionsHtml(char *db, struct hgPositions *hgp, FILE *f, boolean useWeb, char *hgAppName, struct cart *cart) /* Write out hgp table as HTML to file. */ { struct hgPosTable *table; struct hgPos *pos; char *desc; char range[HGPOSRANGESIZE]; char *ui = getUiUrl(cart); char *extraCgi = hgp->extraCgi; char hgAppCombiner = (strchr(hgAppName, '?')) ? '&' : '?'; boolean containerDivPrinted = FALSE; if (useWeb) webStart(cart, db, "Select Position"); for (table = hgp->tableList; table != NULL; table = table->next) { if (table->posList != NULL) { char *parent = hGetParent(db, table->name); char *trackName = hGetTrackForTable(db, table->name); if (trackName == NULL) errAbort("no track for table \"%s\" found via a findSpec", table->name); // wish we had searchName char *vis = hCarefulTrackOpenVis(db, trackName); boolean excludeTable = FALSE; if(!containerDivPrinted) { fprintf(f, "<div id='hgFindResults'>\n"); containerDivPrinted = TRUE; } if (table->htmlStart) table->htmlStart(table, f); else fprintf(f, "<H2>%s</H2><PRE>\n", table->description); for (pos = table->posList; pos != NULL; pos = pos->next) { if (table->htmlOnePos) table->htmlOnePos(table, pos, f); else { char *matches = excludeTable ? "" : pos->browserName; char *encMatches = cgiEncode(matches); hgPosBrowserRange(pos, range); fprintf(f, "<A HREF=\"%s%cposition=%s", hgAppName, hgAppCombiner, range); if (ui != NULL) fprintf(f, "&%s", ui); fprintf(f, "%s&", extraCgi); fprintf(f, "%s=%s&", trackName, vis); // this is magic to tell the browser to make the // composite and this subTrack visible if (parent) { fprintf(f, "%s_sel=1&", trackName); fprintf(f, "%s_sel=1&", parent); } fprintf(f, "hgFind.matches=%s,\">", encMatches); htmTextOut(f, pos->name); fprintf(f, " at %s</A>", range); desc = pos->description; if (desc) { fprintf(f, " - "); htmTextOut(f, desc); } fprintf(f, "\n"); freeMem(encMatches); } } if (table->htmlEnd) table->htmlEnd(table, f); else fprintf(f, "</PRE>\n"); } } if(containerDivPrinted) fprintf(f, "</div>\n"); if (useWeb) webEnd(); } static struct hgPositions *genomePos(char *db, char *spec, char **retChromName, int *retWinStart, int *retWinEnd, struct cart *cart, boolean showAlias, boolean useWeb, char *hgAppName) /* Search for positions in genome that match user query. * Return an hgp if the query results in a unique position. * Otherwise display list of positions, put # of positions in retWinStart, * and return NULL. */ { struct hgPositions *hgp = NULL; char *terms[16]; int termCount = 0; int i = 0; boolean multiTerm = FALSE; char *chrom = NULL; int start = BIGNUM; int end = 0; termCount = chopByChar(cloneString(spec), ';', terms, ArraySize(terms)); multiTerm = (termCount > 1); for (i = 0; i < termCount; i++) { trimSpaces(terms[i]); if (isEmpty(terms[i])) continue; hgp = hgPositionsFind(db, terms[i], "", hgAppName, cart, multiTerm); if (hgp == NULL || hgp->posCount == 0) { hgPositionsFree(&hgp); warn("Sorry, couldn't locate %s in genome database\n", htmlEncode(terms[i])); if (multiTerm) hUserAbort("%s not uniquely determined -- " "can't do multi-position search.", terms[i]); *retWinStart = 0; return NULL; } if ((hgp->singlePos != NULL) && (!showAlias || !hgp->useAlias)) { if (chrom != NULL && !sameString(chrom, hgp->singlePos->chrom)) hUserAbort("Sites occur on different chromosomes: %s, %s.", chrom, hgp->singlePos->chrom); chrom = hgp->singlePos->chrom; if (hgp->singlePos->chromStart < start) start = hgp->singlePos->chromStart; if (hgp->singlePos->chromEnd > end) end = hgp->singlePos->chromEnd; } else { hgPositionsHtml(db, hgp, stdout, useWeb, hgAppName, cart); if (multiTerm && hgp->posCount != 1) hUserAbort("%s not uniquely determined (%d locations) -- " "can't do multi-position search.", terms[i], hgp->posCount); *retWinStart = hgp->posCount; hgp = NULL; break; } } if (hgp != NULL) { *retChromName = chrom; *retWinStart = start; *retWinEnd = end; } return hgp; } struct hgPositions *findGenomePos(char *db, char *spec, char **retChromName, int *retWinStart, int *retWinEnd, struct cart *cart) /* Search for positions in genome that match user query. * Return an hgp if the query results in a unique position. * Otherwise display list of positions, put # of positions in retWinStart, * and return NULL. */ { return genomePos(db, spec, retChromName, retWinStart, retWinEnd, cart, TRUE, FALSE, "hgTracks"); } struct hgPositions *findGenomePosWeb(char *db, char *spec, char **retChromName, int *retWinStart, int *retWinEnd, struct cart *cart, boolean useWeb, char *hgAppName) /* Search for positions in genome that match user query. * Use the web library to print out HTML headers if necessary, and use * hgAppName when forming URLs (instead of "hgTracks"). * Return an hgp if the query results in a unique position. * Otherwise display list of positions, put # of positions in retWinStart, * and return NULL. */ { struct hgPositions *hgp; if (useWeb) webPushErrHandlers(); hgp = genomePos(db, spec, retChromName, retWinStart, retWinEnd, cart, TRUE, useWeb, hgAppName); if (useWeb) webPopErrHandlers(); return hgp; } #if 0 /* not used */ static void noRelative(boolean relativeFlag, int relStart, int relEnd, char *table) { if (relativeFlag) hUserAbort("Sorry, range spec (\":%d-%d\") is not supported for %s.", relStart+1, relEnd, table); } #endif static boolean searchSpecial(char *db, struct hgFindSpec *hfs, char *term, struct hgPositions *hgp, boolean relativeFlag, int relStart, int relEnd, boolean *retFound) /* Handle searchTypes for which we have special code. Return true if * we have special code. Set retFind according to whether we find term. */ { boolean isSpecial = TRUE; boolean found = FALSE; char *upcTerm = cloneString(term); touppers(upcTerm); if (sameString(hfs->searchType, "knownGene")) { if (gotFullText(db)) found = findKnownGeneFullText(db, term, hgp); else /* NOTE, in a few months (say by April 1 2006) get rid of else -JK */ { if (!found && hTableExists(db, "kgAlias")) found = findKgGenesByAlias(db, term, hgp); if (!found && hTableExists(db, "kgProtAlias")) found = findKgGenesByProtAlias(db, term, hgp); if (!found) found = findKnownGene(db, term, hgp, hfs->searchTable); } } else if (sameString(hfs->searchType, "refGene")) { found = findRefGenes(db, hfs, term, hgp); } else if (sameString(hfs->searchType, "cytoBand")) { char *chrom; int start, end; found = hgFindCytoBand(db, term, &chrom, &start, &end); if (found) singlePos(hgp, hfs->searchDescription, NULL, hfs->searchTable, term, term, chrom, start, end); } else if (sameString(hfs->searchType, "gold")) { char *chrom; int start, end; found = findChromContigPos(db, term, &chrom, &start, &end); if (found) { if (relativeFlag) { end = start + relEnd; start = start + relStart; } singlePos(hgp, hfs->searchDescription, NULL, hfs->searchTable, term, term, chrom, start, end); } } else if (sameString(hfs->searchType, "mrnaAcc")) { found = findMrnaPos(db, term, hgp); } else if (sameString(hfs->searchType, "mrnaKeyword")) { found = findMrnaKeys(db, hfs, upcTerm, hgp); } else if (sameString(hfs->searchType, "sgdGene")) { found = findYeastGenes(db, term, hgp); } else { isSpecial = FALSE; } *retFound = found; freeMem(upcTerm); return(isSpecial); } static struct slPair *getXrefTerms(char *db, struct hgFindSpec *hfs, char *term) /* Search xrefTable for xrefQuery with term. Return all matching names. */ { struct slPair *xrefList = NULL, *xrefPtr = NULL; struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; char **row; char buf[512]; boolean isFuzzy = sameWord(hfs->searchMethod, "fuzzy"); safef(buf, sizeof(buf), hfs->xrefQuery, hfs->xrefTable, term); sr = sqlGetResult(conn, buf); while ((row = sqlNextRow(sr)) != NULL) { if (!isFuzzy || keyIsPrefixIgnoreCase(term, row[1])) { xrefPtr = slPairNew(cloneString(row[1]), cloneString(row[0])); slAddHead(&xrefList, xrefPtr); } } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&xrefList); if (xrefList == NULL && hgFindSpecSetting(hfs, "searchBoth") != NULL) xrefList = slPairNew(cloneString(""), cloneString(term)); return(xrefList); } int vatruncatef(char *buf, int size, char *format, va_list args) /* Like vasafef, but truncates the formatted string instead of barfing on * overflow. */ { char *truncStr = " [truncated]"; int sz = vsnprintf(buf, size, format, args); /* note that some version return -1 if too small */ if ((sz < 0) || (sz >= size)) strncpy(buf + size - 1 - strlen(truncStr), truncStr, strlen(truncStr)); buf[size-1] = 0; return sz; } void truncatef(char *buf, int size, char *format, ...) /* Like safef, but truncates the formatted string instead of barfing on * overflow. */ { int sz; va_list args; va_start(args, format); sz = vatruncatef(buf, size, format, args); va_end(args); } static boolean doQuery(char *db, struct hgFindSpec *hfs, char *xrefTerm, char *term, struct hgPositions *hgp, boolean relativeFlag, int relStart, int relEnd, boolean multiTerm) /* Perform a query as specified in hfs, assuming table existence has been * checked and xref'ing has been taken care of. */ { struct slName *tableList = hSplitTableNames(db, hfs->searchTable); struct slName *tPtr = NULL; struct hgPosTable *table = NULL; struct hgPos *pos = NULL; struct sqlConnection *conn = hAllocConn(db); struct sqlResult *sr = NULL; char **row = NULL; char *termPrefix = hgFindSpecSetting(hfs, "termPrefix"); char *paddingStr = hgFindSpecSetting(hfs, "padding"); int padding = isEmpty(paddingStr) ? 0 : atoi(paddingStr); boolean found = FALSE; char *description = NULL; char buf[2048]; if (isNotEmpty(termPrefix) && startsWith(termPrefix, term)) term += strlen(termPrefix); if (isEmpty(term)) return(FALSE); if (isNotEmpty(hfs->searchDescription)) truncatef(buf, sizeof(buf), "%s", hfs->searchDescription); else safef(buf, sizeof(buf), "%s", hfs->searchTable); description = cloneString(buf); if (hgp->tableList != NULL && sameString(hgp->tableList->name, hfs->searchTable) && sameString(hgp->tableList->description, description)) table = hgp->tableList; for (tPtr = tableList; tPtr != NULL; tPtr = tPtr->next) { safef(buf, sizeof(buf), hfs->query, tPtr->name, term); sr = sqlGetResult(conn, buf); while ((row = sqlNextRow(sr)) != NULL) { if(table == NULL) { AllocVar(table); table->description = description; table->name = cloneString(hfs->searchTable); slAddHead(&hgp->tableList, table); } found = TRUE; AllocVar(pos); pos->chrom = cloneString(row[0]); pos->chromStart = atoi(row[1]); pos->chromEnd = atoi(row[2]); if (isNotEmpty(xrefTerm)) truncatef(buf, sizeof(buf), xrefTerm); else safef(buf, sizeof(buf), "%s%s", termPrefix ? termPrefix : "", row[3]); pos->name = cloneString(buf); pos->browserName = cloneString(row[3]); if (isNotEmpty(xrefTerm)) { safef(buf, sizeof(buf), "(%s%s)", termPrefix ? termPrefix : "", row[3]); pos->description = cloneString(buf); } if (relativeFlag && (pos->chromStart + relEnd) <= pos->chromEnd) { pos->chromEnd = pos->chromStart + relEnd; pos->chromStart = pos->chromStart + relStart; } else if (padding > 0 && !multiTerm) { int chromSize = hChromSize(db, pos->chrom); pos->chromStart -= padding; pos->chromEnd += padding; if (pos->chromStart < 0) pos->chromStart = 0; if (pos->chromEnd > chromSize) pos->chromEnd = chromSize; } slAddHead(&table->posList, pos); } } if (table != NULL) slReverse(&table->posList); sqlFreeResult(&sr); hFreeConn(&conn); slFreeList(&tableList); return(found); } boolean hgFindUsingSpec(char *db, struct hgFindSpec *hfs, char *term, struct hgPositions *hgp, boolean relativeFlag, int relStart, int relEnd, boolean multiTerm) /* Perform the search described by hfs on term. If successful, put results * in hgp and return TRUE. (If not, don't modify hgp.) */ { struct slPair *xrefList = NULL, *xrefPtr = NULL; boolean found = FALSE; if (hfs == NULL || term == NULL || hgp == NULL) errAbort("NULL passed to hgFindUsingSpec.\n"); if (strlen(term)<2 && ! (sameString(hfs->searchName, "knownGene") || sameString(hfs->searchName, "flyBaseGeneSymbolOneLetter"))) return FALSE; if (isNotEmpty(hfs->termRegex) && ! regexMatchNoCase(term, hfs->termRegex)) return(FALSE); if (! hTableOrSplitExists(db, hfs->searchTable)) return(FALSE); if (isNotEmpty(hfs->searchType) && searchSpecial(db, hfs, term, hgp, relativeFlag, relStart, relEnd, &found)) return(found); if (isNotEmpty(hfs->xrefTable)) { struct sqlConnection *conn = hAllocConn(db); boolean exists = sqlTableExists(conn, hfs->xrefTable); hFreeConn(&conn); if (! exists) return(FALSE); xrefList = getXrefTerms(db, hfs, term); } else xrefList = slPairNew(cloneString(""), cloneString(term)); for (xrefPtr = xrefList; xrefPtr != NULL; xrefPtr = xrefPtr->next) { found |= doQuery(db, hfs, xrefPtr->name, (char *)xrefPtr->val, hgp, relativeFlag, relStart, relEnd, multiTerm); } slPairFreeValsAndList(&xrefList); return(found); } /* Support these formats for range specifiers. Note the ()'s around chrom, * start and end portions for substring retrieval: */ char *canonicalRangeExp = "^([[:alnum:]._\\-]+)" "[[:space:]]*:[[:space:]]*" "([-0-9,]+)" "[[:space:]]*-[[:space:]]*" "([0-9,]+)$"; char *gbrowserRangeExp = "^([[:alnum:]._\\-]+)" "[[:space:]]*:[[:space:]]*" "([0-9,]+)" "[[:space:]]*\\.\\.[[:space:]]*" "([0-9,]+)$"; char *lengthRangeExp = "^([[:alnum:]._\\-]+)" "[[:space:]]*:[[:space:]]*" "([0-9,]+)" //"[[:space:]]*\\^[[:space:]]*" "[[:space:]]*\\+[[:space:]]*" "([0-9,]+)$"; char *bedRangeExp = "^([[:alnum:]._\\-]+)" "[[:space:]]+" "([0-9,]+)" "[[:space:]]+" "([0-9,]+)$"; char *sqlRangeExp = "^([[:alnum:]._\\-]+)" "[[:space:]]*\\|[[:space:]]*" "([0-9,]+)" "[[:space:]]*\\|[[:space:]]*" "([0-9,]+)$"; char *singleBaseExp = "^([[:alnum:]._\\-]+)" "[[:space:]]*:[[:space:]]*" "([0-9,]+)$"; static void collapseSamePos(struct hgPositions *hgp) /* If all positions in all tables in hgp are the same position, then * trim all but the first table/pos. */ { struct hgPosTable *firstTable = NULL, *table; struct hgPos *firstPos = NULL, *pos; char *chrom = NULL; int start=0, end=0; for (table = hgp->tableList; table != NULL; table = table->next) { for (pos = table->posList; pos != NULL; pos = pos->next) { if (pos->chrom != NULL) { if (chrom == NULL) { chrom = pos->chrom; start = pos->chromStart; end = pos->chromEnd; firstTable = table; firstPos = pos; } else if (! (sameString(chrom, pos->chrom) && start == pos->chromStart && end == pos->chromEnd)) return; } } } if (firstPos) { hgp->tableList = firstTable; hgp->tableList->posList = firstPos; hgPosTableFreeList(&(hgp->tableList->next)); hgPosFreeList(&(hgp->tableList->posList->next)); } } static boolean searchKnownCanonical(char *db, char *term, struct hgPositions *hgp) /* Look for term in kgXref.geneSymbol, and if found, put knownCanonical coords and * knownGene.name in hgp. */ { boolean foundIt = FALSE; struct sqlConnection *conn = hAllocConn(db); if (sqlTableExists(conn, "knownGene") && sqlTableExists(conn, "knownCanonical") && sqlTableExists(conn, "kgXref")) { char query[512]; safef(query, sizeof(query), "select chrom,chromStart,chromEnd,kgID from knownCanonical,kgXref " "where kgXref.geneSymbol = '%s' and kgXref.kgId = knownCanonical.transcript;", term); struct sqlResult *sr = sqlGetResult(conn, query); char **row; if ((row = sqlNextRow(sr)) != NULL) { singlePos(hgp, "UCSC Genes", term, "knownGene", row[3], row[3], cloneString(row[0]), atoi(row[1]), atoi(row[2])); foundIt = TRUE; } sqlFreeResult(&sr); } hFreeConn(&conn); return foundIt; } static struct hgFindSpec *hfsFind(struct hgFindSpec *list, char *name) /* Return first element of list that matches name. */ { struct hgFindSpec *el; for (el = list; el != NULL; el = el->next) if (sameString(name, el->searchName)) return el; return NULL; } static boolean singleSearch(char *db, char *term, struct cart *cart, struct hgPositions *hgp) /* If a search type is specified in the CGI line (not cart), perform that search. * If the search is successful, fill in hgp as a single-pos result and return TRUE. */ { char *search = cgiOptionalString("singleSearch"); if (search == NULL) return FALSE; cartRemove(cart, "singleSearch"); boolean foundIt = FALSE; if (sameString(search, "knownCanonical")) foundIt = searchKnownCanonical(db, term, hgp); else { struct hgFindSpec *shortList = NULL, *longList = NULL; hgFindSpecGetAllSpecs(db, &shortList, &longList); struct hgFindSpec *hfs = hfsFind(shortList, search); if (hfs == NULL) hfs = hfsFind(longList, search); if (hfs != NULL) foundIt = hgFindUsingSpec(db, hfs, term, hgp, FALSE, 0,0, FALSE); else warn("Unrecognized singleSearch=%s in URL", search); } if (foundIt) { fixSinglePos(hgp); if (cart != NULL) cartSetString(cart, "hgFind.matches", hgp->tableList->posList->browserName); } return foundIt; } struct hgPositions *hgPositionsFind(char *db, char *term, char *extraCgi, char *hgAppNameIn, struct cart *cart, boolean multiTerm) /* Return table of positions that match term or NULL if none such. */ { struct hgPositions *hgp = NULL, *hgpItem = NULL; regmatch_t substrs[4]; boolean canonicalSpec = FALSE; boolean gbrowserSpec = FALSE; boolean lengthSpec = FALSE; boolean singleBaseSpec = FALSE; boolean relativeFlag = FALSE; int relStart = 0, relEnd = 0; hgAppName = hgAppNameIn; AllocVar(hgp); hgp->useAlias = FALSE; term = trimSpaces(term); if(isEmpty(term)) return hgp; hgp->query = cloneString(term); hgp->database = db; if (extraCgi == NULL) extraCgi = ""; hgp->extraCgi = cloneString(extraCgi); if (singleSearch(db, term, cart, hgp)) return hgp; /* Allow any search term to end with a :Start-End range -- also support stuff * pasted in from BED (chrom start end) or SQL query (chrom | start | end). * If found, strip it off and remember the start and end. */ char *originalTerm = term; if ((canonicalSpec = regexMatchSubstrNoCase(term, canonicalRangeExp, substrs, ArraySize(substrs))) || (gbrowserSpec = regexMatchSubstrNoCase(term, gbrowserRangeExp, substrs, ArraySize(substrs))) || (lengthSpec = regexMatchSubstrNoCase(term, lengthRangeExp, substrs, ArraySize(substrs))) || regexMatchSubstrNoCase(term, bedRangeExp, substrs, ArraySize(substrs)) || (singleBaseSpec = regexMatchSubstrNoCase(term, singleBaseExp, substrs, ArraySize(substrs))) || regexMatchSubstrNoCase(term, sqlRangeExp, substrs, ArraySize(substrs))) { term = cloneString(term); /* Since we got a match, substrs[1] is the chrom/term, [2] is relStart, * [3] is relEnd. ([0] is all.) */ term[substrs[1].rm_eo] = 0; eraseTrailingSpaces(term); term[substrs[2].rm_eo] = 0; relStart = atoi(stripCommas(term+substrs[2].rm_so)); term[substrs[3].rm_eo] = 0; if (singleBaseSpec) { relEnd = relStart; relStart--; } else relEnd = atoi(stripCommas(term+substrs[3].rm_so)); if (canonicalSpec || gbrowserSpec || lengthSpec) relStart--; if (lengthSpec) relEnd += relStart; if (relStart > relEnd) { int tmp = relStart; relStart = relEnd; relEnd = tmp; } relativeFlag = TRUE; } term = sqlEscapeString(term); if (hgOfficialChromName(db, term) != NULL) { char *chrom; int start, end; hgParseChromRange(db, term, &chrom, &start, &end); if (relativeFlag) { int chromSize = end; end = start + relEnd; start = start + relStart; if (end > chromSize) end = chromSize; if (start < 0) start = 0; } singlePos(hgp, "Chromosome Range", NULL, "chromInfo", originalTerm, "", chrom, start, end); } else { struct hgFindSpec *shortList = NULL, *longList = NULL; struct hgFindSpec *hfs; boolean done = FALSE; // Disable singleBaseSpec for any term that is not hgOfficialChromName // because that mangles legitimate IDs that are [A-Z]:[0-9]+. if (singleBaseSpec) { singleBaseSpec = relativeFlag = FALSE; term = sqlEscapeString(originalTerm); relStart = relEnd = 0; } hgFindSpecGetAllSpecs(db, &shortList, &longList); for (hfs = shortList; hfs != NULL; hfs = hfs->next) { if (hgFindUsingSpec(db, hfs, term, hgp, relativeFlag, relStart, relEnd, multiTerm)) { done = TRUE; if (! hgFindSpecSetting(hfs, "semiShortCircuit")) break; } } if (! done) { for (hfs = longList; hfs != NULL; hfs = hfs->next) { hgFindUsingSpec(db, hfs, term, hgp, relativeFlag, relStart, relEnd, multiTerm); } /* Lowe lab additions -- would like to replace these with specs, but * will leave in for now. */ findTigrGenes(db, term, hgp); } hgFindSpecFreeList(&shortList); hgFindSpecFreeList(&longList); if(hgpMatchNames == NULL) hgpMatchNames = newDyString(256); for(hgpItem = hgp; hgpItem != NULL; hgpItem = hgpItem->next) { struct hgPosTable *hpTable = NULL; for(hpTable = hgpItem->tableList; hpTable != NULL; hpTable = hpTable->next) { struct hgPos *pos = NULL; for(pos = hpTable->posList; pos != NULL; pos = pos->next) { dyStringPrintf(hgpMatchNames, "%s,", pos->browserName); } } } if (cart != NULL) cartSetString(cart, "hgFind.matches", hgpMatchNames->string); } slReverse(&hgp->tableList); if (multiTerm) collapseSamePos(hgp); fixSinglePos(hgp); return hgp; } void hgPositionsHelpHtml(char *organism, char *database) /* Display contents of dbDb.htmlPath for database, or print an HTML comment * explaining what's missing. */ { char *htmlPath = hHtmlPath(database); char *htmlString = NULL; size_t htmlStrLength = 0; if (strstrNoCase(organism, "zoo")) webNewSection("About the NISC Comparative Sequencing Program Browser"); else webNewSection("%s Genome Browser – %s assembly" " <A HREF=\"%s?%s=%d&chromInfoPage=\">(sequences)</A>", - trackHubRemoveHubName(organism), - trackHubRemoveHubName(database), + trackHubSkipHubName(organism), + trackHubSkipHubName(database), hgTracksName(), cartSessionVarName(), cartSessionId(cart)); if (htmlPath != NULL && fileExists(htmlPath)) readInGulp(htmlPath, &htmlString, &htmlStrLength); else if ( startsWith("http://" , htmlPath) || startsWith("https://", htmlPath) || startsWith("ftp://" , htmlPath)) { struct lineFile *lf = udcWrapShortLineFile(htmlPath, NULL, 256*1024); htmlString = lineFileReadAll(lf); htmlStrLength = strlen(htmlString); lineFileClose(&lf); } if (htmlStrLength > 0) { puts(htmlString); freeMem(htmlString); freeMem(htmlPath); } else { - printf("<H2>%s</H2>\n", trackHubRemoveHubName(organism)); + printf("<H2>%s</H2>\n", trackHubSkipHubName(organism)); if (htmlPath == NULL || htmlPath[0] == 0) printf("\n<!-- No dbDb.htmlPath for %s -->\n", database); else printf("\n<!-- Couldn't get contents of %s -->\n", htmlPath); } }