/* doOmimGene2 - This is a one shot program used in the OMIM related subtracks build pipeline */

/* Copyright (C) 2013 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "hCommon.h"
#include "hdb.h"

void usage()
/* Explain usage and exit. */
{
errAbort(
  "doOmimGene2 - This program is part of the OMIM related subtracks build pipeline.\n"
  "usage:\n"
  "   doOmimGene2 db outFileName\n"
  "      db is the database name\n"
  "      outFileName is the filename of the output file\n"
  "example: doOmimGene2 hg19 omimGene2.tab\n");
}

int main(int argc, char *argv[])
{
char *database;
char *outFn;
FILE   *outf;

struct sqlConnection *conn1;
struct sqlConnection *conn2;
struct sqlConnection *conn3;
char query1[256];
char query2[256];
char query3[256];
struct sqlResult *sr1;
struct sqlResult *sr2;
struct sqlResult *sr3;
char **row1;
char **row2;
char **row3;
char *omimId, *geneId;
char *chrom;

if (argc != 3) usage();

database = argv[1];
conn1= hAllocConn(database);
conn2= hAllocConn(database);
conn3= hAllocConn(database);
outFn   = argv[2];
outf    = mustOpen(outFn, "w");

struct hash *idToGene = hashNew(0);
sqlSafef(query1, sizeof query1, "select omimId, geneId from omim2geneNew where geneId <>'-' and entryType='gene' ");
sr1 = sqlMustGetResult(conn1, query1);
while ((row1 = sqlNextRow(sr1)) != NULL)
    {
    /* get all OMIM Genes with Gene ID (Entrez/LocusLink) */
    omimId = row1[0];
    geneId = cloneString(row1[1]);
    hashAdd(idToGene, omimId, geneId);
    }
hFreeConn(&conn1);

struct hashEl *hel, *helList = hashElListHash(idToGene);
for (hel = helList; hel != NULL; hel = hel->next)
    {
    omimId = hel->name;
    geneId = hel->val;

    /* get different chroms from RefSeq for each geneId */
    sqlSafef(query3, sizeof query3, 
    "select distinct r.chrom from refGene r, hgFixed.refLink where mrnaAcc=r.name and locusLinkId = %s order by chrom", geneId);
    sr3 = sqlMustGetResult(conn3, query3);
    row3 = sqlNextRow(sr3);
    while (row3 != NULL)
    	{
    	chrom= row3[0];
    	/* get corresponding RefSeq data, ordered by length of the gene */
    	// added mrnaAcc as the 2nd ordering condition
    	// added txStart as the 3rd ordering condition
    	sqlSafef(query2, sizeof query2, 
    	"select r.chrom, r.txStart, r.txEnd, r.name, r.txEnd-r.txStart, mrnaAcc from refGene r, hgFixed.refLink where mrnaAcc=r.name and locusLinkId = %s and r.chrom = '%s' order by txEnd-txStart desc, mrnaAcc desc, txStart asc", geneId, chrom);
    	sr2 = sqlMustGetResult(conn2, query2);
    	row2 = sqlNextRow(sr2);
    
    	/* take the top logest one */
    	if (row2 != NULL)
    	    {
    	    int j;
    	    for (j=0; j<3; j++)
    	    	{
	    	fprintf(outf, "%s\t", row2[j]);
	    	}
            fprintf(outf, "%s\n", omimId);
	    }
    	sqlFreeResult(&sr2);
        row3 = sqlNextRow(sr3);
	}
    sqlFreeResult(&sr3);
    }

sqlFreeResult(&sr2);

fclose(outf);
hFreeConn(&conn2);
hFreeConn(&conn3);
return(0);
}