int findspans ( int start, int end, char *seq, char *seqname )
{
int i ;
int sc = 0 ;
int lsc = 0 ;
int imn = -1 ; /* else sequences which start with pattern reported badly */
int imx = 0 ;
int mx = 0 ;
int ncpg, ngpc, ngc ;
i = start ;
while ( i < end )
{
lsc = sc ;
sc = ( end-1-i && seq[i]=='C' && seq[i+1]=='G' ) ? sc += CPGSCORE : --sc ;
sc = sc < 0 ? 0 : sc ;
/* printf("%d \t %d \t%d \t %d \t%d \t%d\n", i, sc, lsc, imn, imx, mx) ; */
if ( sc == 0 && lsc ) /* should threshold here */
{
/* imn+1 is the start of the match.
imx+1 is the end of the match, given pattern-length=2.
fetchdb using reported co-ordinates will return a sequence
which both starts and ends with a complete pattern.
Further +1 adjusts so that start of sequence = 1
*/
getstats ( imn+1, imx+2, seq, seqname, &ncpg, &ngpc, &ngc ) ;
printf("%s\t %d\t %d\t %d\t CpG: %d\t %.1f\t %.1f\n", seqname, imn+2, imx+2, mx, ncpg, ngc*100.0/(imx+1-imn), 1.0*ncpg/ngpc) ;
/* printf("%s \t %d\t %d\t %d \n", seqname, imn+2, imx+2, mx ) ;
*/
/* Recursive call searches from one position after the end of the
last match to the current position */
findspans( imx+2, i, seq, seqname ) ;
sc = lsc = imn = imx = mx = 0 ;
}
imx = sc > mx ? i : imx ;
mx = sc > mx ? sc : mx ;
imn = sc == 0 ? i : imn ;
++i ;
}
if ( sc != 0 ) /* should threshold here */
{
/* printf("%d \t %d \t%d \t %d \t%d \t%d\n", i, sc, lsc, imn, imx, mx) ; */
getstats ( imn+1, imx+2, seq, seqname, &ncpg, &ngpc, &ngc ) ;
printf("%s\t %d\t %d\t %d\t CpG: %d\t %.1f\t %.2f\n", seqname, imn+2, imx+2, mx, ncpg, ngc*100.0/(imx+1-imn), 1.0*ncpg/ngpc) ;
/* printf("%s \t %d\t %d\t %d \n", seqname, imn+2, imx+2, mx ) ;
*/
findspans( imx+2, end, seq, seqname ) ;
}
}
/*------------------------------------------------------*/
void main (int argc, char **argv)
{
char *seq, *seqname, *desc ;
int conv[] = { 0, 1, 2, 3, 4 } ;
int length ;
int i ;
static FILE *fil ;
char c, *cp ;
extern char* malloc() ;
/*------------------------------------------------------*/
switch ( argc )
{
default: if (argc != 2)
usage () ;
}
if (!(seqname = malloc (MAXNAMELEN+1)))
{ fprintf (stderr, "Couldn't malloc %d bytes", MAXNAMELEN) ;
exit (-1) ;
}
if (!(seq = malloc (MALLOCBLOCK+1)))
{ fprintf (stderr, "Couldn't malloc %d bytes", MALLOCBLOCK) ;
exit (-1) ;
}
if (!(fil = fopen ( argv[1], "r" )))
usage ();
while ( readSequence(fil, dna2textConv, &seq, &seqname, &desc, &length) )
/* once through per sequence */
{
i = 0 ;
while ( seqname[i] != ' ' && seqname[i] != '\0' && i < 256 )
++i ;
seqname[i] = '\0' ;
findspans ( 0, length, seq, seqname ) ;
}
exit (0);
}
void findspans ( int start, int end, char *seq, char *seqname )
{
int i ;
int sc = 0 ;
int lsc = 0 ;
int imn = -1 ; /* else sequences which start with pattern reported badly */
int imx = 0 ;
int mx = 0 ;
int winlen = 0;
float expect, obsToExp;
int ncpg, ngpc, ngc, ng, nc;
i = start ;
while ( i < end )
{
lsc = sc ;
sc += ( end-1-i && seq[i]=='C' && seq[i+1]=='G' ) ? CPGSCORE : -1 ;
sc = sc < 0 ? 0 : sc ;
/* printf("%d \t %d \t%d \t %d \t%d \t%d\n", i, sc, lsc, imn, imx, mx) ; */
if ( sc == 0 && lsc ) /* should threshold here */
{
/* imn+1 is the start of the match.
imx+1 is the end of the match, given pattern-length=2.
fetchdb using reported co-ordinates will return a sequence
which both starts and ends with a complete pattern.
Further +1 adjusts so that start of sequence = 1
*/
getstats ( imn+1, imx+2, seq, seqname, &ncpg, &ngpc, &ng, &nc ) ;
ngc = ng + nc;
if (((imx+2)-(imn+2))>199 && (ngc*100.0/(imx+1-imn))>50.0 ) {
/* old gos estimate printf("%s\t %d\t %d\t %d\t CpG: %d\t %.1f\t %.1f\n", seqname, imn+2, imx+2, mx, ncpg, ngc*100.0/(imx+1-imn), 1.0*ncpg/ngpc) ; */
winlen=imx+1-imn;
/* ASH 3/23/04: expected val from Gardiner-Garden & Frommer '87: */
expect = (float)(nc * ng) / (float)winlen;
obsToExp = (float)ncpg / expect;
if ( obsToExp > 0.60 )
printf("%s\t %d\t %d\t %d\t CpG: %d\t %.1f\t %.2f\t %.2f\n",
seqname, imn+2, imx+2, mx, ncpg, ngc*100.0/(imx+1-imn),
1.0*ncpg/ngpc, obsToExp) ;
}
/* printf("%s \t %d\t %d\t %d \n", seqname, imn+2, imx+2, mx ) ;
*/
/* Recursive call searches from one position after the end of the
last match to the current position */
findspans( imx+2, i, seq, seqname ) ;
sc = lsc = imn = imx = mx = 0 ;
}
imx = sc > mx ? i : imx ;
mx = sc > mx ? sc : mx ;
imn = sc == 0 ? i : imn ;
++i ;
}
if ( sc != 0 ) /* should threshold here */
{
/* printf("%d \t %d \t%d \t %d \t%d \t%d\n", i, sc, lsc, imn, imx, mx) ; */
/* ASH 3/23/04: Make this test & output consistent w/above. */
getstats ( imn+1, imx+2, seq, seqname, &ncpg, &ngpc, &ng, &nc ) ;
ngc = nc + ng;
if (((imx+2)-(imn+2))>199 && (ngc*100.0/(imx+1-imn))>50.0 ) {
winlen=imx+1-imn;
expect = (float)(nc * ng) / (float)winlen;
obsToExp = (float)ncpg / expect;
if ( obsToExp > 0.60 )
printf("%s\t %d\t %d\t %d\t CpG: %d\t %.1f\t %.2f\t %.2f\n",
seqname, imn+2, imx+2, mx, ncpg, ngc*100.0/(imx+1-imn),
1.0*ncpg/ngpc, obsToExp) ;
}
/* printf("%s \t %d\t %d\t %d \n", seqname, imn+2, imx+2, mx ) ;
*/
findspans( imx+2, end, seq, seqname ) ;
}
}
