25a1ed58b2f9fc2d9ad7fdbe9117f0b2f47253f3
fanhsu
  Tue Nov 9 16:38:23 2010 -0800
Update for RGD Genes, Redmine issue #29.
diff --git src/hg/hgGene/synonym.c src/hg/hgGene/synonym.c
index 1a05c3d..df00f6d 100644
--- src/hg/hgGene/synonym.c
+++ src/hg/hgGene/synonym.c
@@ -1,312 +1,410 @@
 /* Synonym - print out other names for this gene. */
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "hgGene.h"
 #include "spDb.h"
 #include "ccdsGeneMap.h"
 
 static char const rcsid[] = "$Id: synonym.c,v 1.10 2009/01/30 23:30:55 fanhsu Exp $";
 
 static void printOurMrnaUrl(FILE *f, char *accession)
 /* Print URL for Entrez browser on a nucleotide. */
 {
 fprintf(f, "../cgi-bin/hgc?%s&g=mrna&i=%s&c=%s&o=%d&t=%d&l=%d&r=%d&db=%s",
     cartSidUrlString(cart), accession, curGeneChrom, curGeneStart, curGeneEnd, curGeneStart,
     curGeneEnd, database);
 }
 
 static void printOurRefseqUrl(FILE *f, char *accession)
 /* Print URL for Entrez browser on a nucleotide. */
 {
 fprintf(f, "../cgi-bin/hgc?%s&g=refGene&i=%s&c=%s&o=%d&l=%d&r=%d&db=%s",
     cartSidUrlString(cart),  accession, curGeneChrom, curGeneStart, curGeneStart,
     curGeneEnd, database);
 }
 
 static int countAlias(char *id, struct sqlConnection *conn)
 /* Count how many valid gene symbols to be printed */
 {
 char query[256];
 struct sqlResult *sr;
 int cnt = 0;
 char **row;
 safef(query, sizeof(query), "select alias from kgAlias where kgId = '%s' order by alias", id);
 sr = sqlGetResult(conn, query);
 
 row = sqlNextRow(sr);
 while (row != NULL)
     {
     /* skip kgId and the maint gene symbol (curGeneName) */
     if ((!sameWord(id, row[0])) && (!sameWord(row[0], curGeneName))) 
     	{
 	cnt++;
 	}
     row = sqlNextRow(sr);
     }
 sqlFreeResult(&sr);
 return(cnt);
 }
 
 char *aliasString(char *id, struct sqlConnection *conn)
 /* return alias string as it would be printed in html, can free after use */
 {
 char query[256];
 struct sqlResult *sr = NULL;
 char **row;
 int totalCount;
 int cnt = 0;
 
 totalCount = countAlias(id,conn);
 if (totalCount > 0)
     {
     struct dyString *aliasReturn = dyStringNew(0);
     dyStringPrintf(aliasReturn, "<B>Alternate Gene Symbols:</B> ");
     safef(query, sizeof(query), "select alias from kgAlias where kgId = '%s' order by alias", id);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     while (cnt < totalCount)
     	{
         /* skip kgId and the maint gene symbol (curGeneName) */
         if ((!sameWord(id, row[0])) && (!sameWord(row[0], curGeneName))) 
 		{
     		dyStringPrintf(aliasReturn, "%s", row[0]);
 		if (cnt < (totalCount-1)) dyStringPrintf(aliasReturn, ", ");
 		cnt++;
 		}
     	row = sqlNextRow(sr);
     	}
     dyStringPrintf(aliasReturn, "<BR>");   
     sqlFreeResult(&sr);
     return dyStringCannibalize(&aliasReturn);
     }
 return NULL;
 }
 
 static void printAlias(char *id, struct sqlConnection *conn)
 /* Print out description of gene given ID. */
 {
 char *aliases = aliasString(id, conn);
 
 if (aliases)
     {
     hPrintf("%s", aliases);
     freeMem(aliases);
     }
 }
 
 static void printGeneSymbol (char *geneId, char *table, char *idCol, struct sqlConnection *conn)
 /* Print out official Entrez gene symbol from a cross-reference table.*/
 {
 char query[256];
 struct sqlResult *sr = NULL;
 char **row;
 char *geneSymbol;
 
 if (sqlTablesExist(conn, table))
     {
     hPrintf("<B>Entrez Gene Official Symbol:</B> ");
     safef(query, sizeof(query), "select geneSymbol from %s where %s = '%s'", table, idCol, geneId);
     sr = sqlGetResult(conn, query);
     if (sr != NULL)
         {
         row = sqlNextRow(sr);
 
         geneSymbol = cloneString(row[0]);
         if (!sameString(geneSymbol, ""))
             hPrintf("%s<BR>", geneSymbol);
         }
     }
 sqlFreeResult(&sr);
 }
 
 static char *getRefSeqAcc(char *id, char *table, char *idCol, struct sqlConnection *conn)
 /* Finds RefSeq accession from a cross-reference table. */
 {
 char query[256];
 struct sqlResult *sr = NULL;
 char **row;
 char *refSeqAcc = NULL;
 
 if (sqlTablesExist(conn, table))
     {
     safef(query, sizeof(query), "select refSeq from %s where %s = '%s'", table, idCol, id);
     sr = sqlGetResult(conn, query);
     if (sr != NULL)
         {
         row = sqlNextRow(sr);
         refSeqAcc = cloneString(row[0]);
         }
     }
 sqlFreeResult(&sr);
 return refSeqAcc;
 }
 
 
 static void printCcds(char *kgId, struct sqlConnection *conn)
 /* Print out CCDS ids most closely matching the kg. */
 {
 struct ccdsGeneMap *ccdsKgs = NULL;
 if (sqlTablesExist(conn, "ccdsKgMap"))
     ccdsKgs = ccdsGeneMapSelectByGene(conn, "ccdsKgMap", kgId, 0.0);
 if (ccdsKgs != NULL)
     {
     struct ccdsGeneMap *ccdsKg;
     hPrintf("<B>CCDS:</B> ");
     /* since kg is not by location (even though we have a
      * curGeneStart/curGeneEnd), we need to use the location in the 
      * ccdsGeneMap */
     for (ccdsKg = ccdsKgs; ccdsKg != NULL; ccdsKg = ccdsKg->next)
         {
         if (ccdsKg != ccdsKgs)
             hPrintf(", ");
         hPrintf("<A href=\"../cgi-bin/hgc?%s&g=ccdsGene&i=%s&c=%s&o=%d&l=%d&r=%d&db=%s\">%s</A>",
                 cartSidUrlString(cart), ccdsKg->ccdsId, ccdsKg->chrom, ccdsKg->chromStart, ccdsKg->chromStart,
                 ccdsKg->chromEnd, database, ccdsKg->ccdsId);
         }
     hPrintf("<BR>\n");   
     }
 }
 
+char *addComma(char *inStr)
+{
+char *chp;
+chp = inStr;
+
+while (*chp != '\0')
+    {
+    if (*chp == '|')
+       *chp = ',';
+    chp++;
+    }
+return inStr;
+}
+
+static void rgdGene2SynonymPrint(struct section *section,
+        struct sqlConnection *conn, char *rgdGeneId)
+{
+char *geneSym = NULL, *geneName = NULL;
+char query[256], **row;
+struct sqlResult *sr;
+if (rgdGeneId != NULL)
+    {
+    safef(query, sizeof(query), 
+	    "select old_symbol, old_name from genes_rat where gene_rgd_id = '%s'", 
+	    rgdGeneId+4L);
+    sr = sqlGetResult(conn, query);
+    if ((row = sqlNextRow(sr)) != NULL)
+	{
+	if (row[0][0] != 0 && !sameString(row[0], "n/a"))
+	    {
+	    geneSym = cloneString(row[0]);
+	    hPrintf("<B>Symbol:</B> %s ", addComma(row[0]));
+	    //hPrintf("<BR>\n");
+	    }
+	if (row[1][0] != 0 && !sameString(row[0], "n/a"))
+	    {
+	    geneName = cloneString(row[1]);
+	    hPrintf("<BR><B>Name:</B> %s ", addComma(geneName));
+	    hPrintf("<BR>\n");
+	    }
+	}
+    sqlFreeResult(&sr);
+
+    safef(query, sizeof(query), 
+	    "select value from rgdGene2ToRefSeq where name= '%s'", rgdGeneId);
+    sr = sqlGetResult(conn, query);
+    if ((row = sqlNextRow(sr)) != NULL)
+	{
+        hPrintf("<B>RefSeq Accession: </B> <A HREF=\"");
+	printOurRefseqUrl(stdout, row[0]);
+	hPrintf("\">%s</A><BR>\n", row[0]);
+	}
+    sqlFreeResult(&sr);
+    
+    safef(query, sizeof(query), 
+	    "select value from rgdGene2ToUniProt where name= '%s'", rgdGeneId);
+    sr = sqlGetResult(conn, query);
+    if ((row = sqlNextRow(sr)) != NULL)
+    	{
+	char *spId, *spDisplayId, *oldDisplayId;
+	spId = row[0];
+	hPrintf("<B>Protein: </B>");
+        hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
+	    "TARGET=_blank>%s</A>\n",
+	    spId, spId);
+    
+        /* show SWISS-PROT display ID if it is different than the accession ID */
+        /* but, if display name is like: Q03399 | Q03399_HUMAN, then don't show display name */
+        spDisplayId = spAnyAccToId(spConn, spId);
+        if (spDisplayId == NULL) 
+    	    {
+	    errAbort("<br>The corresponding protein %s of this gene is not found in our current UniProtKB DB.", spId);
+	    }   
+	
+        if (strstr(spDisplayId, spId) == NULL)
+	    {
+	    hPrintf(" (aka %s", spDisplayId);
+	    /* show once if the new and old displayId are the same */
+ 	    oldDisplayId = oldSpDisplayId(spDisplayId);
+	    if (oldDisplayId != NULL)
+ 	    	{
+            	if (!sameWord(spDisplayId, oldDisplayId)
+                    && !sameWord(spId, oldDisplayId))
+	    	    {
+	    	    hPrintf(" or %s", oldDisplayId);
+	    	    }  
+	        }	
+	    hPrintf(")<BR>\n");
+	    }  
+   	}
+    sqlFreeResult(&sr);
+    }
+}
 static void synonymPrint(struct section *section, 
 	struct sqlConnection *conn, char *id)
 /* Print out SwissProt comments - looking up typeId/commentVal. */
 {
 char *protAcc = getSwissProtAcc(conn, spConn, id);
 char *spDisplayId;
 char *refSeqAcc = "";
 char *mrnaAcc = "";
 char *oldDisplayId;
 char condStr[255];
 char *kgProteinID;
 char *parAcc; /* parent accession of a variant splice protein */
 char *chp;
 
+if (isRgdGene(conn))
+    {
+    rgdGene2SynonymPrint(section,conn, id);
+    return;
+    }
 if (sqlTablesExist(conn, "kgAlias"))
     printAlias(id, conn);
 if (sameWord(genome, "Zebrafish"))
     {
     char *xrefTable = "ensXRefZfish";
     char *geneIdCol = "ensGeneId";
     /* get Gene Symbol and RefSeq accession from Zebrafish-specific */
     /* cross-reference table */
     printGeneSymbol(id, xrefTable, geneIdCol, conn);
     refSeqAcc = getRefSeqAcc(id, xrefTable, geneIdCol, conn);
     hPrintf("<B>ENSEMBL ID:</B> %s", id);
     }
 else
     {
     char query[256];
     char *toRefTable = genomeOptionalSetting("knownToRef");
     if (toRefTable != NULL && sqlTableExists(conn, toRefTable))
         {
 	safef(query, sizeof(query), "select value from %s where name='%s'", toRefTable,
 		id);
 	refSeqAcc = emptyForNull(sqlQuickString(conn, query));
 	}
     if (sqlTableExists(conn, "kgXref"))
 	{
 	safef(query, sizeof(query), "select mRNA from kgXref where kgID='%s'", id);
 	mrnaAcc = emptyForNull(sqlQuickString(conn, query));
 	}
     if (sameWord(genome, "C. elegans"))
 	hPrintf("<B>WormBase ID:</B> %s<BR>", id);
     else
 	hPrintf("<B>UCSC ID:</B> %s<BR>", id);
     }
     
 if (refSeqAcc[0] != 0)
     {
     hPrintf("<B>RefSeq Accession: </B> <A HREF=\"");
     printOurRefseqUrl(stdout, refSeqAcc);
     hPrintf("\">%s</A><BR>\n", refSeqAcc);
     }
 else if (mrnaAcc[0] != 0)
     {
     safef(condStr, sizeof(condStr), "acc = '%s'", mrnaAcc);
     if (sqlGetField(database, "gbCdnaInfo", "acc", condStr) != NULL)
         {
     	hPrintf("<B>Representative RNA: </B> <A HREF=\"");
     	printOurMrnaUrl(stdout, mrnaAcc);
     	hPrintf("\">%s</A><BR>\n", mrnaAcc);
     	}
     else
     /* do not show URL link if it is not found in gbCdnaInfo */
     	{
     	hPrintf("<B>Representative RNA: %s </B>", mrnaAcc);
     	}
     }
 if (protAcc != NULL)
     {
     kgProteinID = cloneString("");
     if (hTableExists(sqlGetDatabase(conn), "knownGene")
         && (isNotEmpty(cartOptionalString(cart, hggChrom)) &&
 	      differentWord(cartOptionalString(cart, hggChrom),"none")))
     	{
     	safef(condStr, sizeof(condStr), "name = '%s' and chrom = '%s' and txStart=%s and txEnd=%s", 
 	        id, cartOptionalString(cart, hggChrom), 
     	        cartOptionalString(cart, hggStart), 
 		cartOptionalString(cart, hggEnd));
     	kgProteinID = sqlGetField(database, "knownGene", "proteinID", condStr);
     	}
 
     hPrintf("<B>Protein: ");
     if (strstr(kgProteinID, "-") != NULL)
         {
 	parAcc = cloneString(kgProteinID);
 	chp = strstr(parAcc, "-");
 	*chp = '\0';
 	
         /* show variant splice protein and the UniProt link here */
 	hPrintf("<A HREF=\"http://www.uniprot.org/uniprot%s\" "
 	    "TARGET=_blank>%s</A></B>, splice isoform of ",
 	    kgProteinID, kgProteinID);
         hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
 	    "TARGET=_blank>%s</A></B>\n",
 	    parAcc, parAcc);
 	}
     else
         {
         hPrintf("<A HREF=\"http://www.uniprot.org/uniprot/%s\" "
 	    "TARGET=_blank>%s</A></B>\n",
 	    protAcc, protAcc);
 	}
     /* show SWISS-PROT display ID if it is different than the accession ID */
     /* but, if display name is like: Q03399 | Q03399_HUMAN, then don't show display name */
     spDisplayId = spAnyAccToId(spConn, protAcc);
     if (spDisplayId == NULL) 
     	{
 	errAbort("<br>%s seems to no longer be a valid protein ID in our latest UniProtKB DB.", protAcc);
 	}
 	
     if (strstr(spDisplayId, protAcc) == NULL)
 	{
 	hPrintf(" (aka %s", spDisplayId);
 	/* show once if the new and old displayId are the same */
  	oldDisplayId = oldSpDisplayId(spDisplayId);
 	if (oldDisplayId != NULL)
  	    {
             if (!sameWord(spDisplayId, oldDisplayId)
                 && !sameWord(protAcc, oldDisplayId))
 	    	{
 	    	hPrintf(" or %s", oldDisplayId);
 	    	}
 	    }
 	hPrintf(")<BR>\n");
 	}
     }
 printCcds(id, conn);
 
 }
 
 struct section *synonymSection(struct sqlConnection *conn,
 	struct hash *sectionRa)
 /* Create synonym (aka Other Names) section. */
 {
 struct section *section = sectionNew(sectionRa, "synonym");
 section->print = synonymPrint;
 return section;
 }