src/hg/protein/pfamXref/pfamXref.c 1.10

Index: src/hg/protein/pfamXref/pfamXref.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/pfamXref/pfamXref.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 1000000 -r1.9 -r1.10
--- src/hg/protein/pfamXref/pfamXref.c	23 Sep 2009 18:42:25 -0000	1.9
+++ src/hg/protein/pfamXref/pfamXref.c	25 Sep 2009 08:52:45 -0000	1.10
@@ -1,159 +1,168 @@
 /* pfamXref read and parse the Pfam-A data file to generate 
    the .tab files to enable xref between Pfam and SWISS-PROT entries */
 
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "pfamXref - create pfam xref .tab file "
   "usage:\n"
   "   pfamXref pn pfamInput pfamOutput pfamXref\n"
   "            pn is protein database name\n"
   "            pfamInput  is input  file name of Pfam data.\n"
   "            pfamOutput is output file name of output file of Pfam AC and description.\n"
   "            pfamXref   is output file name of xref file of Pfam AC and SWISS-PROT ID and KG ID.\n"
   "Example: pfamXref rn3 proteins07030 /cluster/store5/proteins/pfam/071803/Pfam-A.full pfamA.tab pfamAXref.tab\n");
 }
 
 char line[2000];
 int main(int argc, char *argv[])
 {
 FILE *inf;
 FILE *o1, *o2;
 
 char cond_str[256];
 char *proteinDB;
 char *proteinFileName;
 char *answer;
 char *outputFileName, *outputFileName2;
 char *desc;
 char *chp1, *chp=NULL;
 char *pfamID, *pfamAC;
 char *swissAC, *swissDisplayID;
 char emptyString[10] = {""};
 int done, gsDone, gsFound, idFound;
 char *chp2 = NULL;
 
 if (argc != 5) usage();
    
 proteinDB	 = cloneString(argv[1]);
 proteinFileName  = cloneString(argv[2]);
 outputFileName   = cloneString(argv[3]);
 outputFileName2  = cloneString(argv[4]);
 
 o1 = mustOpen(outputFileName, "w");
 o2 = mustOpen("jj.dat", "w");
     
+/* Build up hash for quick access to displayIds. */
+struct hash *displayIdHash = hashNew(20);
+struct sqlConnection *conn = sqlConnect(proteinDB);
+struct sqlResult *sr = sqlGetResult(conn, "select accession,displayID from spXref3");
+char **row;
+while ((row = sqlNextRow(sr)) != NULL)
+    hashAdd(displayIdHash, row[0], cloneString(row[1]));
+sqlFreeResult(&sr);
+sqlDisconnect(&conn);
+    
 if ((inf = mustOpen(proteinFileName, "r")) == NULL)
     {		
     fprintf(stderr, "Can't open file %s.\n", proteinFileName);
     exit(8);
     }
 	
 done = 0;
 while (!done)
     {
     /* get to the beginning of a Pfam record */
     idFound = 0;
     while (fgets(line, sizeof(line), inf) != NULL)
     	{
     	chp = strstr(line, "GF ID");
     	if (chp != NULL)
 		{
 		idFound = 1;
 		break;
 		}
 	}
     if (!idFound) break;
     
     chp = chp + 8;
     *(chp + strlen(chp) - 1) = '\0'; /* remove LF */
     pfamID = strdup(chp);
     
     /* Get Pfam AC */
 
     mustGetLine(inf, line, sizeof(line));
     chp = strstr(line, "GF AC   ");
     chp = chp + 8;
     *(chp + strlen(chp) - 1) = '\0'; // remove LF
     chp1 = strstr(chp, ".");
     if (chp1 != NULL) *chp1 = '\0';
     pfamAC = strdup(chp);
     
     /* Get Pfam description.  Please note, Pfam-B does not have this field.*/
     mustGetLine(inf, line, sizeof(line));
     chp = strstr(line, "GF DE   ");
     chp = chp + 8;
     *(chp + strlen(chp) - 1) = '\0'; // remove LF
     desc = chp;
 
     fprintf(o1, "%s\t%s\t%s\n", pfamAC, pfamID, desc);
 
     /* work on "#=GS ... AC ... " lines to get SWISS-PROT accession number */
 
     gsDone  = 0;
     gsFound = 0;
     while (!gsDone)
 	{
 	mustGetLine(inf, line, sizeof(line));
     	chp = strstr(line, "#=GS ");
     	if (chp != NULL)
 	    {
 	    chp = strstr(chp, " AC ");
 	    if (chp != NULL)
 		{
 		gsFound = 1;
 	    	chp = chp + 4;
 		chp2 = strstr(chp, ".");
     	    	*(chp + strlen(chp) - 1) = '\0'; // remove LF
 		if (chp2 != NULL) *chp2='\0';
     		swissAC = chp;
 
 		// get display ID from AC		
-		sprintf(cond_str, "accession = '%s'", swissAC);
-    		answer = sqlGetField(proteinDB, "spXref3", "displayID", cond_str);
+		answer = hashFindVal(displayIdHash, swissAC);
 		if (answer != NULL)
 		    {
 		    swissDisplayID = answer;
 		    }
 		else
 		    {
 		    // ACs missing from spXref3 might be found from spSecondardy table
 		    sprintf(cond_str, "accession2 = '%s'", swissAC);
     		    answer = sqlGetField(proteinDB, "spSecondaryID", "displayID", cond_str);
 		    if (answer != NULL)
 		    	{
 		    	swissDisplayID = answer;
 		    	}
 		    else
 			{
 		    	printf("%s not found in %s.spXref3\n", swissAC, proteinDB);fflush(stdout);
 		    	swissDisplayID = emptyString;
 			}
 		    }
 	    	fprintf(o2, "%s\t%s\t%s\n", pfamAC, swissAC, swissDisplayID);
 		}
 	    }
     	else
 	    {
 	    if (gsFound)
 		{
 		gsDone = 1;
 		}
 	    }
 	} 
     }
 carefulClose(&o1);
 carefulClose(&o2);
 
 sprintf(cond_str, "cat jj.dat | sort | uniq >%s",outputFileName2);
 mustSystem(cond_str);
 mustSystem("rm jj.dat");
 
 return(0);
 }