src/hg/utils/rgdGeneXref2/rgdGeneXref2.c 1.1

Index: src/hg/utils/rgdGeneXref2/rgdGeneXref2.c
===================================================================
RCS file: src/hg/utils/rgdGeneXref2/rgdGeneXref2.c
diff -N src/hg/utils/rgdGeneXref2/rgdGeneXref2.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/utils/rgdGeneXref2/rgdGeneXref2.c	5 Feb 2010 22:33:20 -0000	1.1
@@ -0,0 +1,115 @@
+/* rgdGeneXref2 - from all mRNAs in a genome (e.g. rn3) referenced by SWISS-PROT 
+          generate a list of proteins and a list of protein/mRNA pairs */
+#include "common.h"
+#include "hCommon.h"
+#include "hdb.h"
+
+void usage()
+/* Explain usage and exit. */
+{
+errAbort(
+  "rgdGeneXref2 - parse out Dbxref field of the raw RGD Gene GFF file to generate data for the rgdGeneXref22 table\n"
+  "       generate a list of proteins and a list of protein/mRNA pairs.\n"
+  "usage:\n"
+  "   rgdGeneXref2 databas outfile\n"
+  "      database is the genome database\n"
+  "      outfile  is the output file name\n"
+  "example: rgdGeneXref2 rn4 rgdGeneXref2.tab\n");
+}
+
+int main(int argc, char *argv[])
+{
+struct sqlConnection *conn;
+ 
+char query[512];
+struct sqlResult *sr;
+char **row;
+
+char *dataBase;
+char *chp;
+char *chp9;
+char *feature, *xrefStr;
+char *Dbxref;
+char *DbxrefEnd = NULL;
+char *rgdGeneId;
+char *rest = NULL;
+FILE *outf;
+char *outfileName;
+boolean more;
+
+if (argc != 3) usage();
+dataBase    = argv[1];
+outfileName = argv[2];
+
+outf = mustOpen(outfileName, "w");
+
+conn= hAllocConn(dataBase);
+	
+sprintf(query,"select feature, rgdId from rgdGeneRaw0 where feature = 'gene'");
+sr = sqlMustGetResult(conn, query);
+row = sqlNextRow(sr);
+while (row != NULL)
+    {
+    feature 	= row[0];
+    xrefStr     = row[1];
+
+    Dbxref = row[1];
+    chp9 = strstr(xrefStr, ";");
+    if (chp9 != NULL) 
+    	{
+	*chp9 = '\0';
+	DbxrefEnd = chp9;
+	}
+
+    chp = Dbxref;
+
+    /* get start of "RGD:" */
+    chp = strstr(chp, ",");
+    chp ++;
+    rgdGeneId = chp;
+    
+    /* check if there are other references beside the RGD: entry */
+    more = FALSE;
+    chp = strstr(rgdGeneId, ",");
+    if (chp != NULL) 
+    	{
+	more = TRUE;
+	*chp = '\0';
+        chp++;
+	rest = chp;
+	}
+
+    if (more)
+    	{
+	chp9 = strstr(rest, ",");
+	while (chp9 != NULL)
+	    {
+	    *chp9 = '\0';
+	    fprintf(outf, "%s\t%s\n", rgdGeneId, chp); fflush(stdout);
+	    if (DbxrefEnd == chp9)
+	    	{
+		/* if end is reached, break */
+		break;
+		}
+	    else
+	    	{
+		/* keep looking for next entry */
+		chp9++;
+		chp = chp9;
+		chp9 = strstr(chp, ",");
+		}
+	    }
+	
+	/* print last entry */
+	fprintf(outf, "%s\t%s\n", rgdGeneId, chp); fflush(stdout);
+	}
+    
+    row = sqlNextRow(sr);
+    }
+sqlFreeResult(&sr);
+hFreeConn(&conn);
+fclose(outf);
+
+return(0);
+}
+