e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/dnaGene/dnaGene.c src/hg/dnaGene/dnaGene.c
index 7d79622..c8dd2e9 100644
--- src/hg/dnaGene/dnaGene.c
+++ src/hg/dnaGene/dnaGene.c
@@ -1,269 +1,272 @@
 /* dnaGene - collect DNA based RefSeq genes.  To be used by Known Genes track */
 
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "dnaGene - collect DNA based RefSeq genes.  To be used by Known Genes track.\n"
   "usage:\n"
   "   dnaGene xxxx yyyy\n"
   "      xxxx is the genome  database name\n"
   "      yyyy is the protein database name\n"
   "example: dnaGene hg15 proteins0405\n");
 }
 
 char *dbName;
 char *genomeReadOnly;
 char tempDbName[40];
 
 /* check if a locusID points to a KG mRNA */
 boolean checkMrna(char *locusID)
 {
 struct sqlConnection *conn, *conn2;
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 boolean result;
 char cond_str[256];
 
 char *chp;
 char *gbAC;    
 char *gbID;  
 char *knownGeneID;
 
 conn   = hAllocConn();
 conn2  = hAllocConn();
 result = FALSE;
 
 sqlSafef(query2, sizeof query2, "select gbAC from %s.locus2Acc0 where locusID=%s and seqType='m';",
 		tempDbName, locusID);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     gbAC  	= row2[0];
     gbID = strdup(gbAC);
 	
     chp = strstr(gbID, ".");
     if (chp != NULL) *chp = '\0';
 
     sqlSafefFrag(cond_str, sizeof cond_str, "name = '%s';", gbID);
     knownGeneID = sqlGetField(dbName, "knownGene", "name", cond_str);
     if (knownGeneID != NULL)
 	{
 	result=TRUE;
 	break;
 	}
     row2 = sqlNextRow(sr2);
     }
 	
 hFreeConn(&conn);
 hFreeConn(&conn2);
 sqlFreeResult(&sr2);
 return(result);
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2, *conn3, *conn5;
 char query2[256], query3[256], query5[256];
 struct sqlResult *sr2, *sr3, *sr5;
 char **row2, **row3, **row5;
 char cond_str[512];
 
 char *chp;
 FILE *o1, *o2;
 
 boolean hasKGmRNA;
 
 char *proteinDisplayID;
 char *gbAC;    
     
 char *locusID;		/* LocusLink ID */
 char *refAC;		/* Refseq accession.version */
 char *giNCBI2;		/* NCBI gi for the protein record associated with the CDS */
 char *revStatus;	/* review status */
 char *proteinAC2;	/* protein accession.version */
 char *taxID2;		/* tax id */
 
 char *protDbName;
 
 char *refSeq;
 
 char *name, *chrom, *strand, *txStart, *txEnd, *cdsStart, *cdsEnd,
      *exonCount, *exonStarts, *exonEnds;
 
 char *gseq, *hseq, *swissprot;
 int alignmentID=0;
 
 if (argc != 4) usage();
     
 dbName = argv[1];
 protDbName = argv[2];
 genomeReadOnly = argv[3];
 
 sprintf(tempDbName, "%sTemp", dbName);
 
 hSetDb(genomeReadOnly);
 
 conn = hAllocConn();
 conn2= hAllocConn();
 conn3= hAllocConn();
 conn5= hAllocConn();
 
 
 o1 = fopen("dnaGene.tab", "w");
 o2 = fopen("j.dat", "w");
  
 // scan all RefSeq entries
 
 sqlSafef(query2, sizeof query2, "select * from %s.locus2Ref0;", tempDbName);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     locusID 	= row2[0];
     refAC 	= row2[1];
     giNCBI2 	= row2[2];
     revStatus 	= row2[3];
     proteinAC2 	= row2[4];
     taxID2 	= row2[5];
 		
     refSeq = strdup(refAC);
     chp = strstr(refAC, ".");
     if (chp != NULL) *chp = '\0';
 
     proteinDisplayID = NULL;
 
     /* check if the locusID of this RefSeq points to a KG mRNA */
     hasKGmRNA = checkMrna(locusID);	
 
     /* check if this RefSeq has 'g' type sequence(s) referenced */
     sqlSafefFrag(cond_str, sizeof cond_str, "locusID=%s and seqType='g';", locusID);
     gseq = sqlGetField(tempDbName, "locus2Acc0", "gbac", cond_str);
 
     /* process only 'g' type record which does not have corresponding KG entry */
     if ((!hasKGmRNA) && (gseq != NULL))
 	{
 	sqlSafefFrag(cond_str, sizeof cond_str, "name='%s'", refAC);
 	hseq = sqlGetField(genomeReadOnly, "refGene", "name", cond_str);
 	if (hseq != NULL)
 	    {
 	    sqlSafefFrag(cond_str, sizeof cond_str, "refseq='%s';", refAC);
 	    swissprot = sqlGetField(protDbName, "hugo", "swissprot", cond_str);
 	    if (swissprot != NULL) 
 		{
 		if (strlen(swissprot) >0)	
 		    {
 		    // HUGO has an entry with swissprot ID, get display ID
 		    sqlSafefFrag(cond_str, sizeof cond_str, "accession='%s';", swissprot);
 		    proteinDisplayID = sqlGetField(protDbName, 
 						   "spXref2", "displayID", cond_str);
 		    if (proteinDisplayID == NULL) 
 			{
 			fprintf(stderr, "%s: a HUGO.swissprot, ", swissprot);
 					fprintf(stderr, "but not a SP Primary AC.\n");
 			fflush(stdout);
 			}
 		    }
 		else
 		    {
 		    //printf("HGNC has a non-NULL but empty swissprot field ");
 		    //printf("for %s\n", refAC);fflush(stdout);
 		    }
 		}
 
 	    // not finding it in HUGO does not mean not a valid one for sure
 	    if (proteinDisplayID == NULL)
 		{
 		// get gbAC and check if spXref2 actually has it
 		sqlSafef(query3, sizeof query3, "select gbAC from %s.locus2Acc0 where locusID=%s;", 
 				tempDbName, locusID);
         	sr3 = sqlMustGetResult(conn3, query3);
         	row3 = sqlNextRow(sr3);
         	
 		while (row3 != NULL)
                     {
                     gbAC = row3[0];
 		    chp = strstr(gbAC, ".");
 		    if (chp != NULL) *chp = '\0';
 		    sqlSafefFrag(cond_str, sizeof cond_str, "extAC='%s'", gbAC);
 		    proteinDisplayID = sqlGetField(protDbName, 
 						   "spXref2", "displayID", cond_str);
 		    if (proteinDisplayID == NULL) 
 			{
 			//printf("%s %s is in refGene, but has no SWISS-PROT.\n", 
 			//	locusID, refAC);
 			//fflush(stdout);
 			}
 		    else
 			{
 			//printf("%s %s got 2nd chance.\n", refAC, gbAC);fflush(stdout);
 			break;	
 			}		
         	    row3 = sqlNextRow(sr3);
 		    }
 		sqlFreeResult(&sr3);
 		}
 
 	    if (proteinDisplayID != NULL)
 		{
 		// generate KG entry
 					
                 sqlSafef(query5, sizeof query5, "select * from %s.refGene where name='%s';", genomeReadOnly, refAC);
 		sr5 = sqlMustGetResult(conn5, query5);
     		row5 = sqlNextRow(sr5);
     		while (row5 != NULL)
 	    	    {
  	    	    name 	= row5[0];
 	    	    chrom 	= row5[1];
 	    	    strand	= row5[2];
  	    	    txStart 	= row5[3];
 	    	    txEnd   	= row5[4];
 	    	    cdsStart	= row5[5]; 
 	    	    cdsEnd	= row5[6];
 	    	    exonCount   = row5[7]; 
 	    	    exonStarts  = row5[8]; 
 	    	    exonEnds    = row5[9];	
 
 		    fprintf(o1, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\tdna%d\n",
  	    			name,
 		    		chrom,
 		    		strand,
  	    			txStart,
 	    			txEnd,
 	 	   		cdsStart,
 	    			cdsEnd,
 		    		exonCount,
 		    		exonStarts,
 	    			exonEnds,
 				
 				proteinDisplayID,
 				alignmentID);
 		    alignmentID++;
 		
 		    fprintf(o2, "%s\t%c\t%s\n", name, 'g', proteinAC2);
 		    row5 = sqlNextRow(sr5);
 		    }
 		sqlFreeResult(&sr5);
 		}
 	    }
 	}
     row2 = sqlNextRow(sr2);
     }
 		
 fclose(o1);
 fclose(o2);
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 hFreeConn(&conn5);
 system("sort j.dat|uniq >dnaLink.tab");
 system("rm j.dat");
 return(0);
 }