static HB_ERRCODE mysqlGoTo( SQLBASEAREAP pArea, HB_ULONG ulRecNo )
{
SDDDATA * pSDDData = ( SDDDATA * ) pArea->pSDDData;
if( ulRecNo == 0 || ulRecNo > pArea->ulRecCount )
{
pArea->pRecord = pArea->pRow[ 0 ];
pArea->bRecordFlags = pArea->pRowFlags[ 0 ];
pArea->fPositioned = HB_FALSE;
}
else
{
pArea->pRecord = pArea->pRow[ ulRecNo ];
pArea->bRecordFlags = pArea->pRowFlags[ ulRecNo ];
if( ! ( pArea->bRecordFlags & SQLDD_FLAG_CACHED ) )
{
mysql_row_seek( pSDDData->pResult, ( MYSQL_ROW_OFFSET ) pArea->pRecord );
pSDDData->pNatRecord = mysql_fetch_row( pSDDData->pResult );
pSDDData->pNatLength = mysql_fetch_lengths( pSDDData->pResult );
}
pArea->fPositioned = HB_TRUE;
}
return HB_SUCCESS;
}
static PyObject* wsql_result_row_seek(wsql_result *self, PyObject *args, PyObject *kwargs)
{
static char *kwlist[] = {"origin", NULL};
int origin=SEEK_CUR;
Py_ssize_t offset;
MYSQL_ROW_OFFSET r;
if (!PyArg_ParseTupleAndKeywords(args, kwargs, "n|i:", kwlist, &offset, &origin))
CHECK_RESULT(self, NULL);
if (self->use)
{
PyErr_SetString(wsql_programming_error, "cannot be used with connection.get_result(use=True)");
return NULL;
}
r = mysql_row_tell(self->result);
switch (origin)
{
case SEEK_CUR:
r += (size_t)offset;
break;
case SEEK_SET:
r = self->result->data->data + (size_t)offset;
break;
default:
PyErr_SetString(wsql_programming_error, "unsupported origin");
return NULL;
};
mysql_row_seek(self->result, r);
Py_RETURN_NONE;
}
int main(int argc,char **argv)
{
MYSQL mysql;
FILE *file;
MYSQL_RES *Gene_Result,*NFI_Result,*ZDR_Result;
MYSQL_ROW *Gene_Row,*NFI_Row,*ZDR_Row;
MYSQL_ROW_OFFSET *NFI_Rollback,*ZDR_Rollback;
gnuplot_ctrl *g;
char Order[32],query[4000],NFI_Table1[100],NFI_Table2[100],ZDR_Table1[100],ZDR_Table2[100],Gene_Table1[100],Gene_Table2[100];
int GenOrd,NfiOrd,ZdrOrd;
long int i,MinDist,MaxDist,GeneCount1,GeneCount2,NfiZdrGenes1,NfiZdrGenes2,GenePos,NfiStart,NfiStop,NfiBst,ZdrStart,ZdrStop,ZdrBst,NFIPos,ZDRPos;
double NfiMin,NfiMax,NfiStp,NfiCut,ZdrMin,ZdrMax,ZdrStp,ZdrCut,GenePerc1,GenePerc2,MinDiff,MaxDiff;
double *NfiScores1,*NfiScores2,*ZdrScores1,*ZdrScores2;
if(argc!=16)
return printf("usage: %s Fasta_File1 Gene_File1 Fasta_File2 Gene_File2 Order MinDist MaxDist NfiMin NfiMax NfiStep ZdrMax ZdrMin ZdrStep OutFile Plot\n",argv[0]);
sprintf(query,argv[1]);
for(i=0;i<100;i++)
switch(query[i])
{
case '.': query[i]='_'; break;
case '/': sprintf(query,&query[i+1],100);
i=0;
}
sprintf(NFI_Table1,"NFI_DNA.%s_nfihunt_classeq",query);
sprintf(ZDR_Table1,"Z_DNA.%s_zhunt_classeq",query);
sprintf(query,argv[2]);
for(i=0;i<100;i++)
switch(query[i])
{
case '.': query[i]='_'; break;
case '/': sprintf(query,&query[i+1]);
i=0;
}
sprintf(Gene_Table1,"Genomes.%s",query);
sprintf(query,argv[3]);
for(i=0;i<100;i++)
switch(query[i])
{
case '.': query[i]='_'; break;
case '/': sprintf(query,&query[i+1],100);
i=0;
}
sprintf(NFI_Table2,"NFI_DNA.%s_nfihunt_classeq",query);
sprintf(ZDR_Table2,"Z_DNA.%s_zhunt_classeq",query);
sprintf(query,argv[4]);
for(i=0;i<100;i++)
switch(query[i])
{
case '.': query[i]='_'; break;
case '/': sprintf(query,&query[i+1],100);
i=0;
}
sprintf(Gene_Table2,"Genomes.%s",query);
sprintf(Order,argv[5]);
MinDist=atoi(argv[6]);
MaxDist=atoi(argv[7]);
NfiMin=atof(argv[8]);
NfiMax=atof(argv[9]);
NfiStp=atof(argv[10]);
ZdrMax=atof(argv[11]);
ZdrMin=atof(argv[12]);
ZdrStp=atof(argv[13]);
if(argc==15||strcmp(argv[15],"-r"))
{
if(!(strstr(Order,"T")&&strstr(Order,"N")&&strstr(Order,"Z")&&strlen(Order)==3))
return printf("Improper Order format '%s'\n",Order);
GenOrd=strstr(Order,"T")-Order;
NfiOrd=strstr(Order,"N")-Order;
ZdrOrd=strstr(Order,"Z")-Order;
mysql_apps_logon(&mysql);
fprintf(stderr,"Populating internal table 1\n");
sprintf(query,"select start_site,strand,gene_num,gene_name from %s order by start_site",Gene_Table1);
printf(mysql_query(&mysql,query)?strcat(strcat(query,"\n"),strcat(mysql_error(&mysql),"\n\n")):"");
Gene_Result=mysql_store_result(&mysql);
GeneCount1=mysql_num_rows(Gene_Result);
sprintf(query,"select position,nfiscore from %s where nfiscore>=%f order by position",NFI_Table1,NfiMin);
printf(mysql_query(&mysql,query)?strcat(strcat(query,"\n"),strcat(mysql_error(&mysql),"\n\n")):"");
NFI_Result=mysql_store_result(&mysql);
sprintf(query,"select position,deltalinking from %s where deltalinking<=%f order by position",ZDR_Table1,ZdrMax);
printf(mysql_query(&mysql,query)?strcat(strcat(query,"\n"),strcat(mysql_error(&mysql),"\n\n")):"");
ZDR_Result=mysql_store_result(&mysql);
NfiScores1=(double*)malloc(GeneCount1*sizeof(double));
ZdrScores1=(double*)malloc(GeneCount1*sizeof(double));
NFI_Rollback=mysql_row_tell(NFI_Result);
ZDR_Rollback=mysql_row_tell(ZDR_Result);
for(i=0;i<GeneCount1;i++)
{
Gene_Row=mysql_fetch_row(Gene_Result);
if(atoi(Gene_Row[0])-GenePos<=2000)
{
mysql_row_seek(NFI_Result,NFI_Rollback);
mysql_row_seek(ZDR_Result,ZDR_Rollback);
}
GenePos=atoi(Gene_Row[0]);
sprintf(query,Gene_Row[1]);
switch(query[0])
{
case '+': GenOrd=abs(GenOrd);
NfiOrd=abs(NfiOrd);
ZdrOrd=abs(ZdrOrd);
break;
case '-': GenOrd=-abs(GenOrd);
NfiOrd=-abs(NfiOrd);
ZdrOrd=-abs(ZdrOrd);
break;
default: return fprintf(stderr,"Invalid Gene Strand '%s\n'",Gene_Row[1]);
}
NfiStart=GenOrd<NfiOrd?(GenePos+1):(GenePos-1000);
NfiStop=GenOrd<NfiOrd?(GenePos+1000):(GenePos-1);
NfiBst=GenePos+100000;
NfiScores1[i]=-100;
while(NFI_Row=mysql_fetch_row(NFI_Result),NFIPos=NFI_Row?atoi(NFI_Row[0]):NfiStop+1,NFIPos<=NfiStop)
if(NFIPos>=NfiStart&&NfiScores1[i]<=atoi(NFI_Row[1]))
{
if(NfiScores1[i]<atoi(NFI_Row[1])||abs(atoi(NFI_Row[0])-GenePos)<abs(NfiBst-GenePos))
{
NfiBst=atoi(NFI_Row[0]);
NfiScores1[i]=atoi(NFI_Row[1]);
}
}
ZdrStart=NfiOrd<ZdrOrd?(NfiBst+MinDist):(NfiBst-MaxDist);
ZdrStop=NfiOrd<ZdrOrd?(NfiBst+MaxDist):(NfiBst-MinDist);
ZdrStart=(GenOrd<ZdrOrd&&GenePos>ZdrStart)?GenePos:ZdrStart;
ZdrStart=(GenOrd>ZdrOrd&&GenePos<ZdrStart)?GenePos:ZdrStart;
ZdrStop=(GenOrd<ZdrOrd&&GenePos>ZdrStop)?GenePos:ZdrStop;
ZdrStop=(GenOrd>ZdrOrd&&GenePos<ZdrStop)?GenePos:ZdrStop;
ZdrBst=GenePos+100000;
ZdrScores1[i]=100;
while(ZDR_Row=mysql_fetch_row(ZDR_Result),ZDRPos=ZDR_Row?atoi(ZDR_Row[0]):ZdrStop+1,ZDRPos<=ZdrStop)
if(ZDRPos>=ZdrStart&&ZdrScores1[i]>=atoi(ZDR_Row[1]))
{
if(ZdrScores1[i]>atoi(ZDR_Row[1])||abs(atoi(ZDR_Row[0])-NfiBst)<abs(ZdrBst-NfiBst))
{
ZdrBst=atoi(ZDR_Row[0]);
ZdrScores1[i]=atof(ZDR_Row[1]);
}
}
printf("%3s %d %-16s %4d %4.0f %4d %4.2f %4d\n",Gene_Row[2],GenePos,Gene_Row[3],NfiBst-GenePos,NfiScores1[i],ZdrBst-GenePos,ZdrScores1[i],NfiBst-ZdrBst);
}
mysql_free_result(Gene_Result);
mysql_free_result(NFI_Result);
mysql_free_result(ZDR_Result);
fprintf(stderr,"Populating internal table 2\n");
sprintf(query,"select start_site,strand from %s order by start_site",Gene_Table2);
printf(mysql_query(&mysql,query)?strcat(strcat(query,"\n"),strcat(mysql_error(&mysql),"\n\n")):"");
Gene_Result=mysql_store_result(&mysql);
GeneCount2=mysql_num_rows(Gene_Result);
sprintf(query,"select position,nfiscore from %s where nfiscore>=%f order by position",NFI_Table2,NfiMin);
printf(mysql_query(&mysql,query)?strcat(strcat(query,"\n"),strcat(mysql_error(&mysql),"\n\n")):"");
NFI_Result=mysql_store_result(&mysql);
sprintf(query,"select position,deltalinking from %s where deltalinking<=%f order by position",ZDR_Table2,ZdrMax);
printf(mysql_query(&mysql,query)?strcat(strcat(query,"\n"),strcat(mysql_error(&mysql),"\n\n")):"");
ZDR_Result=mysql_store_result(&mysql);
NfiScores2=(double*)malloc(GeneCount2*sizeof(double));
ZdrScores2=(double*)malloc(GeneCount2*sizeof(double));
NFI_Rollback=mysql_row_tell(NFI_Result);
ZDR_Rollback=mysql_row_tell(ZDR_Result);
for(i=0;i<GeneCount2;i++)
{
Gene_Row=mysql_fetch_row(Gene_Result);
if(atoi(Gene_Row[0])-GenePos<=2000)
{
mysql_row_seek(NFI_Result,NFI_Rollback);
mysql_row_seek(ZDR_Result,ZDR_Rollback);
}
GenePos=atoi(Gene_Row[0]);
sprintf(query,Gene_Row[1]);
switch(query[0])
{
case '+': GenOrd=abs(GenOrd);
NfiOrd=abs(NfiOrd);
ZdrOrd=abs(ZdrOrd);
break;
case '-': GenOrd=-abs(GenOrd);
NfiOrd=-abs(NfiOrd);
ZdrOrd=-abs(ZdrOrd);
break;
default: return fprintf(stderr,"Invalid Gene Strand '%s\n'",Gene_Row[1]);
}
NfiStart=GenOrd<NfiOrd?(GenePos+1):(GenePos-1000);
NfiStop=GenOrd<NfiOrd?(GenePos+1000):(GenePos-1);
NfiBst=GenePos+100000;
NfiScores2[i]=-100;
while(NFI_Row=mysql_fetch_row(NFI_Result),NFIPos=NFI_Row?atoi(NFI_Row[0]):NfiStop+1,NFIPos<=NfiStop)
if(NFIPos>=NfiStart&&NfiScores2[i]<=atoi(NFI_Row[1]))
{
if(NfiScores2[i]<atoi(NFI_Row[1])||abs(atoi(NFI_Row[0])-GenePos)<abs(NfiBst-GenePos))
{
NfiBst=atoi(NFI_Row[0]);
NfiScores2[i]=atoi(NFI_Row[1]);
}
}
ZdrStart=NfiOrd<ZdrOrd?(NfiBst+MinDist):(NfiBst-MaxDist);
ZdrStop=NfiOrd<ZdrOrd?(NfiBst+MaxDist):(NfiBst-MinDist);
ZdrStart=(GenOrd<ZdrOrd&&GenePos>ZdrStart)?GenePos:ZdrStart;
ZdrStart=(GenOrd>ZdrOrd&&GenePos<ZdrStart)?GenePos:ZdrStart;
ZdrStop=(GenOrd<ZdrOrd&&GenePos>ZdrStop)?GenePos:ZdrStop;
ZdrStop=(GenOrd>ZdrOrd&&GenePos<ZdrStop)?GenePos:ZdrStop;
ZdrBst=GenePos+100000;
ZdrScores2[i]=100;
while(ZDR_Row=mysql_fetch_row(ZDR_Result),ZDRPos=ZDR_Row?atoi(ZDR_Row[0]):ZdrStop+1,ZDRPos<=ZdrStop)
if(ZDRPos>=ZdrStart&&ZdrScores2[i]>=atoi(ZDR_Row[1]))
{
if(ZdrScores2[i]>atoi(ZDR_Row[1])||abs(atoi(ZDR_Row[0])-NfiBst)<abs(ZdrBst-NfiBst))
{
ZdrBst=atoi(ZDR_Row[0]);
ZdrScores2[i]=atof(ZDR_Row[1]);
}
}
}
mysql_free_result(Gene_Result);
mysql_free_result(NFI_Result);
mysql_free_result(ZDR_Result);
mysql_close(&mysql);
FILE *OutFile=fopen(argv[14],"w");
if(!OutFile)
return printf("Could not write to file '%s'\n",argv[14]);
fprintf(stderr,"Generating results\n");
MinDiff=100;
MaxDiff=0;
for(ZdrCut=ZdrMax;ZdrCut>=ZdrMin;ZdrCut-=ZdrStp)
{
for(NfiCut=NfiMin;NfiCut<=NfiMax;NfiCut+=NfiStp)
{
NfiZdrGenes1=0;
for(i=0;i<GeneCount1;i++)
if(NfiScores1[i]>=NfiCut&&ZdrScores1[i]<=ZdrCut)
NfiZdrGenes1++;
NfiZdrGenes2=0;
for(i=0;i<GeneCount2;i++)
if(NfiScores2[i]>=NfiCut&&ZdrScores2[i]<=ZdrCut)
NfiZdrGenes2++;
GenePerc1=(100.0*NfiZdrGenes1)/GeneCount1;
GenePerc2=(100.0*NfiZdrGenes2)/GeneCount2;
fprintf(OutFile,"%f %f %f %f %f\n",NfiCut,ZdrCut,GenePerc1-GenePerc2,GenePerc1,GenePerc2);
fflush(OutFile);
MinDiff=MinDiff>GenePerc1-GenePerc2?GenePerc1-GenePerc2:MinDiff;
MaxDiff=MaxDiff<GenePerc1-GenePerc2?GenePerc1-GenePerc2:MaxDiff;
}
}
fclose(OutFile);
}
if(argc>15)
{
sprintf(NFI_Table1,NFI_Table1+8);
NFI_Table1[strlen(NFI_Table1)-8]='\0';
sprintf(NFI_Table2,NFI_Table2+8);
NFI_Table2[strlen(NFI_Table2)-8]='\0';
g=gnuplot_init();
sprintf(query,"set title \"%% Difference Between %s and %s of TSS w/(NFI + Z-DNA-12bps)\\n",NFI_Table1,NFI_Table2);
for(i=0;i<argc;i++)
{
strcat(query,argv[i]);
strcat(query," ");
}
strcat(query,"\"");
gnuplot_cmd(g,query);
sprintf(query,"set dgrid3d %.0f,%.0f,8",(ZdrMax-ZdrMin)/ZdrStp,(NfiMax-NfiMin)/NfiStp);
gnuplot_cmd(g,query);
sprintf(query,"set xrange [%f:%f]",NfiMin,NfiMax);
sprintf(query,"set yrange [%f:%f]",ZdrMin,ZdrMax);
gnuplot_cmd(g,query);
if(!strcmp(argv[15],"-r"))
{
sprintf(query,"set zrange [*:*]");
gnuplot_cmd(g,query);
sprintf(query,"set cntrparam levels incremental -10,1,10");
gnuplot_cmd(g,query);
}
else
{
sprintf(query,"set zrange [%f:%f]",MinDiff,MaxDiff);
gnuplot_cmd(g,query);
sprintf(query,"set cntrparam levels incremental %.0f,%d,%.0f",MinDiff,1+(int)((MaxDiff-MinDiff)/10),MaxDiff);
gnuplot_cmd(g,query);
}
sprintf(query,"call 'Format/%s.format'",argv[0]);
gnuplot_cmd(g,query);
sprintf(query,"sp '%s' u 1:2:3 notitle",argv[14]);
//sprintf(query,"sp '%s' w l lw 2",argv[14]);
gnuplot_cmd(g,query);
printf("Hit Enter to continue\n");
getchar();
}
return 0;
}
MYSQL_ROW seekandgetrow(value dbresval, int n) {
/* mysql_row_seek seems to take time O(1), mysql_data_seek takes O(n) */
mysql_row_seek(DBresult_val(dbresval),
DBresultindex_val(dbresval)[n]);
return mysql_fetch_row(DBresult_val(dbresval));
}
/* row_seek(offset) */
static VALUE row_seek(VALUE obj, VALUE offset)
{
check_free(obj);
return INT2NUM((int)mysql_row_seek(GetMysqlRes(obj), (MYSQL_ROWS*)NUM2INT(offset)));
}
