src/hg/protein/spToProteins/spToProteins.c 1.6

Index: src/hg/protein/spToProteins/spToProteins.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/protein/spToProteins/spToProteins.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/protein/spToProteins/spToProteins.c	3 Sep 2008 19:21:02 -0000	1.5
+++ src/hg/protein/spToProteins/spToProteins.c	23 Sep 2009 18:42:25 -0000	1.6
@@ -1,150 +1,150 @@
 /* spToProteins- Create tab delimited data file for proteinsxxxx database */
 /* CURRENTLY UNUSED because it's horribly slow perhaps.... */
 
 #include "common.h"
 #include "hCommon.h"
 #include "hdb.h"
 #include "spDb.h"
 #include "options.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "spToProteins- Create tab delimited data files from spxxxx database for proteinsxxxx database.\n"
   "usage:\n"
   "   spToProteins xxxx\n"
   "      xxxx is the release date of SWISS-PROT data\n"
   "Example: spToProteins 100503\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn, *conn2, *conn3;
 char query[256], query2[256];
 struct sqlResult *sr, *sr2;
 char **row, **row2;
 char cond_str[255];
 char proteinDatabaseName[255];
 char proteinsDB[255];
 char *isCurated;
 char *desc;
 char *hugoSymbol, *hugoDesc;
 char empty_str[1] = {""};
 FILE *o1, *o2, *o3;
 char *proteinDataDate;
 int  bioDatabase, bioentryId;
 char *displayId;
 char *accession;
 char *extAC;
 char *extDb;
 int taxon;
 struct slName *taxonList, *name;
 
 optionHash(&argc, argv);
 if (argc != 2) usage();
 
 proteinDataDate = argv[1];
 safef(proteinDatabaseName, sizeof(proteinDatabaseName), "sp%s", proteinDataDate);
 safef(proteinsDB, sizeof(proteinsDB), "proteins%s", proteinDataDate);
 
 o1 = mustOpen("temp_spXref2.dat", "w");
 o2 = mustOpen("spXref3.tab", "w");
 o3 = mustOpen("temp_spOrganism.dat", "w");
 
 conn  = hAllocConn(hDefaultDb());
 conn2 = hAllocConn(hDefaultDb());
 conn3 = sqlConnect(proteinDatabaseName);
 
 bioentryId = 0;
 
 safef(query2, sizeof(query2), "select count(*) from %s.info", proteinDatabaseName);
 int totalIds = sqlQuickNum(conn2, query2);
 safef(query2, sizeof(query2), "select acc, isCurated from %s.info;", proteinDatabaseName);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     if (bioentryId%1000 == 0)
         verbose(1, "Processed %d of %d %5.2f%%\n", bioentryId, totalIds, 100.0*bioentryId/totalIds);
     bioentryId++;
         
     accession		= row2[0];   
     isCurated           = row2[1];
     verbose(3, "%d %s %s\n", bioentryId, accession, isCurated);
   
     if (*isCurated == '1')
 	{
 	bioDatabase = 1;
 	}
     else
 	{
 	if (strlen(accession) > 7) 
 	    {
 	    bioDatabase = 3;
 	    }
 	else
 	    {
 	    bioDatabase = 2;
 	    }
 	}
     safef(cond_str, sizeof(cond_str), "acc='%s'", accession);
     displayId = sqlGetField(proteinDatabaseName, "displayId", "val", cond_str);
 
     // !!! the divsion field probably should be eliminated later
     // use the simple 1 taxon returned value function for the time being, 
     // could expand into multiple by calling spBinomialNames later 
     taxon = spTaxon(conn3, accession);
 
     taxonList = spTaxons(conn3, accession);
     for (name = taxonList; name != NULL; name = name->next)
 	{
 	fprintf(o3, "%s\t%s\n", displayId, name->name);
 	}
 
     safef(cond_str, sizeof(cond_str), "acc='%s'", accession);
     desc = sqlGetField(proteinDatabaseName, "description", "val", cond_str);
     safef(cond_str, sizeof(cond_str), "uniProt='%s'", accession);
     hugoSymbol = sqlGetField(proteinsDB, "hgnc", "symbol", cond_str);
     hugoDesc = sqlGetField(proteinsDB, "hgnc", "name", cond_str);
     if (hugoSymbol==NULL) hugoSymbol = empty_str;
     if (hugoDesc==NULL)   hugoDesc   = empty_str;
 
     fprintf(o2, "%s\t%s\t%d\t%d\t%d\t%s\t%s\t%s\n", accession, displayId, 
 	   taxon, bioentryId, bioDatabase, desc, hugoSymbol, hugoDesc);
     
     safef(query, sizeof(query),
 	    "select extAcc1, extDb.val from sp%s.extDb, sp%s.extDbRef where extDbRef.acc='%s' %s",
 	    proteinDataDate, proteinDataDate, accession, "and extDb.id = extDbRef.extDb;"); 
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     while (row != NULL)
     	{
     	extAC = row[0];
 	extDb = row[1];
 
         fprintf(o1, "%s\t%s\t%d\t%s\t%s\t%d\t%d\n", accession, displayId, taxon, 
 		extDb, extAC, bioentryId, bioDatabase);
   
 	row = sqlNextRow(sr);
 	}
     sqlFreeResult(&sr);
     row2 = sqlNextRow(sr2);
     }
 
 fclose(o1);
 fclose(o2);
 fclose(o3);
 
 sqlFreeResult(&sr2);
 hFreeConn(&conn);
 hFreeConn(&conn2);
 sqlDisconnect(&conn3);
 
-system("cat temp_spXref2.dat | sort |uniq > spXref2.tab");
-system("rm temp_spXref2.dat");
-system("cat temp_spOrganism.dat | sort |uniq > spOrganism.tab");
-system("rm temp_spOrganism.dat");
+mustSystem("cat temp_spXref2.dat | sort |uniq > spXref2.tab");
+mustSystem("rm temp_spXref2.dat");
+mustSystem("cat temp_spOrganism.dat | sort |uniq > spOrganism.tab");
+mustSystem("rm temp_spOrganism.dat");
 return(0);
 }