97c67666efd79c8d87918466629ee1781138797c braney Thu Jun 25 17:39:35 2020 -0700 ongoing work on gencodeV35 diff --git src/hg/near/hgNear/knownGene.c src/hg/near/hgNear/knownGene.c index d3075ce..32b5f11 100644 --- src/hg/near/hgNear/knownGene.c +++ src/hg/near/hgNear/knownGene.c @@ -1,355 +1,355 @@ /* colKnownGene - columns having to do with knownGene and closely tables. */ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "obscure.h" #include "dystring.h" #include "jksql.h" #include "cheapcgi.h" #include "cart.h" #include "hdb.h" #include "hCommon.h" #include "hgNear.h" #include "kgAlias.h" #include "findKGAlias.h" static char *posFromRow3(char **row) /* Convert chrom/start/end row to position. */ { char buf[128]; char *chrom; int start,end; chrom = row[0]; start = sqlUnsigned(row[1]); end = sqlUnsigned(row[2]); safef(buf, sizeof(buf), "%s:%d-%d", chrom, start+1, end); return cloneString(buf); } static char *genePredPosFromTable(char *table, struct genePos *gp, struct sqlConnection *conn) /* Get genePred position from table. Well, actually just get it from gp. */ { if (gp->chrom != NULL) { char pos[256]; safef(pos, sizeof(pos), "%s:%d-%d", gp->chrom, gp->start+1, gp->end); return cloneString(pos); } else { char query[256]; struct sqlResult *sr; char *pos = NULL; char **row; sqlSafef(query, sizeof(query), "select chrom,txStart,txEnd from %s where name = '%s'", table, gp->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) pos = posFromRow3(row); sqlFreeResult(&sr); return pos; } } static char *genePredPosVal(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Get genome position of genePred type table. */ { return genePredPosFromTable(col->table, gp, conn); } static void genePredPosPrint(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Print genome position with hyperlink to browser. */ { char *pos = col->cellVal(col, gp, conn); char *chrom; int start, end; hPrintf("<TD>"); if (pos == NULL) hPrintf("n/a"); else { char numBuf[32]; hgParseChromRange(database, pos, &chrom, &start, &end); sprintLongWithCommas(numBuf, (start+end+1)/2); hPrintf("<A HREF=\"%s?db=%s&position=%s&%s&%s=full\">", hgTracksName(), database, pos, cartSidUrlString(cart), genomeSetting("geneTable")); hPrintf("%s %s</A>", chrom, numBuf); freeMem(pos); } hPrintf("</TD>"); } static void genePredPosFilterControls(struct column *col, struct sqlConnection *conn) /* Print out controls for advanced filter. */ { hPrintf("chromosome: "); advFilterRemakeTextVar(col, "chr", 8); hPrintf(" start: "); advFilterRemakeTextVar(col, "start", 8); hPrintf(" end: "); advFilterRemakeTextVar(col, "end", 8); } static struct genePos *genePredPosAdvFilter(struct column *col, struct sqlConnection *conn, struct genePos *list) /* Do advanced filter on position. */ { char *chrom = advFilterVal(col, "chr"); char *startString = advFilterVal(col, "start"); char *endString = advFilterVal(col, "end"); if (chrom != NULL) { struct genePos *newList = NULL, *gp, *next; for (gp = list; gp != NULL; gp = next) { next = gp->next; if (sameWord(chrom, gp->chrom)) { slAddHead(&newList, gp); } } slReverse(&newList); list = newList; } if (startString != NULL) { int start = atoi(startString)-1; struct genePos *newList = NULL, *gp, *next; for (gp = list; gp != NULL; gp = next) { next = gp->next; if (gp->end > start) { slAddHead(&newList, gp); } } slReverse(&newList); list = newList; } if (endString != NULL) { int end = atoi(endString); struct genePos *newList = NULL, *gp, *next; for (gp = list; gp != NULL; gp = next) { next = gp->next; if (gp->start < end) { slAddHead(&newList, gp); } } slReverse(&newList); list = newList; } return list; } static void genePredPosMethods(struct column *col, char *table) /* Put in methods for genePred based positions. */ { col->table = table; col->exists = simpleTableExists; col->cellVal = genePredPosVal; col->cellPrint = genePredPosPrint; col->filterControls = genePredPosFilterControls; col->advFilter = genePredPosAdvFilter; } static char *knownPosCellVal(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Get genome position of knownPos table. Ok to have col NULL. */ { char *pos = genePredPosFromTable("knownGene", gp, conn); if (pos == NULL) { /* As a backup plan, try to find accession in all_mrna table. */ char query[256]; struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "select tName, tStart, tEnd from %s where qName = '%s'", "all_mrna", gp->name); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) pos = posFromRow3(row); sqlFreeResult(&sr); } return pos; } static struct genePos *genePosFromQuery(struct sqlConnection *conn, char *query, boolean oneOnly) /* Get all positions from a query that returns 5 columns. */ { struct sqlResult *sr; char **row; struct genePos *gpList = NULL, *gp; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(gp); genePosFillFrom5(gp, row); slAddHead(&gpList, gp); if (oneOnly) break; } sqlFreeResult(&sr); return gpList; } struct genePos *knownPosAll(struct sqlConnection *conn) /* Get all positions in knownGene table. */ { char query[1024]; // just for side-effect of adding NOSQLINJ prefix if (showOnlyCanonical()) sqlSafef(query, sizeof query, "%-s", genomeSetting("allGeneQuery")); else sqlSafef(query, sizeof query, "%-s", genomeSetting("allTranscriptQuery")); return genePosFromQuery(conn, query, FALSE); } struct genePos *knownPosOne(struct sqlConnection *conn, char *name) /* Get all positions of named gene. */ { char query[1024]; sqlSafef(query, sizeof(query), genomeSetting("oneGeneQuery"), name); return genePosFromQuery(conn, query, FALSE); } struct genePos *knownPosFirst(struct sqlConnection *conn) /* Get first gene in known gene table. */ { char query[1024]; // just for side-effect of adding NOSQLINJ prefix sqlSafef(query, sizeof query, "%-s", genomeSetting("allGeneQuery")); struct genePos *gp = genePosFromQuery(conn, query, TRUE); return gp; } void setupColumnKnownPos(struct column *col, char *parameters) /* Set up column that links to genome browser based on known gene * position. */ { genePredPosMethods(col, genomeSetting("geneTable")); col->cellVal = knownPosCellVal; } static void linkToDetailsCellPrint(struct column *col, struct genePos *gp, struct sqlConnection *conn) /* Print a link to known genes details page. */ { char *s = col->cellVal(col, gp, conn); fillInKnownPos(gp, conn); hPrintf("<TD>"); hPrintf("<A HREF=\"../cgi-bin/hgGene?%s&%s=%s&%s=%s&%s=%s&%s=%d&%s=%d\">", cartSidUrlString(cart), "db", database, "hgg_gene", gp->name, "hgg_chrom", gp->chrom, "hgg_start", gp->start, "hgg_end", gp->end); if (s == NULL) { hPrintf("n/a"); } else { hPrintEncodedNonBreak(s); freeMem(s); } hPrintf("</A></TD>"); } void fillInKnownPos(struct genePos *gp, struct sqlConnection *conn) /* If gp->chrom is not filled in go look it up. */ { if (gp->chrom == NULL) { char *pos = knownPosCellVal(NULL, gp, conn); char *chrom; hgParseChromRange(database, pos, &chrom, &gp->start, &gp->end); gp->chrom = cloneString(chrom); } } struct searchResult *knownGeneSearchResult(struct sqlConnection *conn, char *kgID, char *alias) /* Return a searchResult for a known gene. */ { struct searchResult *sr; struct dyString *dy = dyStringNew(1024); char query[256]; char name[64]; char *description = NULL; /* Allocate and fill in with geneID. */ AllocVar(sr); sr->gp.name = cloneString(kgID); /* Get gene symbol into short label if possible. */ sqlSafef(query, sizeof(query), "select geneSymbol from kgXref where kgID = '%s'", kgID); if (sqlQuickQuery(conn, query, name, sizeof(name))) sr->shortLabel = cloneString(name); else sr->shortLabel = cloneString(kgID); /* Add alias to long label if need be */ if (alias != NULL && !sameWord(name, alias)) dyStringPrintf(dy, "(aka %s) ", alias); /* Add description to long label. */ sqlSafef(query, sizeof(query), "select description from kgXref where kgID = '%s'", kgID); description = sqlQuickString(conn, query); if (description != NULL) dyStringAppend(dy, description); sr->longLabel = cloneString(dy->string); /* Cleanup and go home. */ dyStringFree(&dy); return sr; } static struct searchResult *knownNameSimpleSearch(struct column *col, struct sqlConnection *conn, char *search) /* Look for matches to known genes. */ { struct kgAlias *ka, *kaList; struct searchResult *srList = NULL, *sr; -kaList = findKGAlias(database, search, "F"); +kaList = findKGAlias(sqlGetDatabase(conn), search, "F"); for (ka = kaList; ka != NULL; ka = ka->next) { sr = knownGeneSearchResult(conn, ka->kgID, ka->alias); slAddHead(&srList, sr); } return srList; } void setupColumnKnownDetails(struct column *col, char *parameters) /* Set up a column that links to details page for known genes. */ { setupColumnLookup(col, parameters); col->cellPrint = linkToDetailsCellPrint; } void setupColumnKnownName(struct column *col, char *parameters) /* Set up a column that looks up name to display, and selects on a click. */ { setupColumnLookup(col, parameters); col->cellPrint = cellSelfLinkPrint; col->simpleSearch = knownNameSimpleSearch; }