Scripts/Codonweight.run

macro =;

if ( !argnumber ) errmsg

This macro differentially weights codon positions. Rerun with 5 arguments specifying:

     1st - first pos weight
     2nd - second pos weight
     3rd - third pos weight
     4th - starting char num 
     5th - ending char num

Of course it assumes that starting char num is pos 1 And checks if you want to downweight

end if (%5 > nchar) errmsg

End of partition exceeds character numbers. Everything starts from 0 not from 1

end if (%4 == 1) errmsg

Everything starts from 0 not from 1

end if (%4 >= %5) errmsg

Did you want me to count backwards? That makes no sense at all!

end

var: i j group1[(nchar/3+1)] group2[(nchar/3+1)] group3[(nchar/3+1)] gp1 gp2 gp3 maxwt;

if (getresponse [Would you like to reset all character weights to the maximum you have entered? If you answer Y all prior weights are gone.]==1)

if (%1 > 'maxwt') set maxwt %1; end if (%2 > 'maxwt') set maxwt %2; end if (%3 > 'maxwt') set maxwt %3; end ccode /'maxwt' .; end;

set gp1 0; set gp2 0; set gp3 0;

set j %4 ; loop  %4 %5 if (#1 == 'j') set group1['gp1'] #1; set gp1++; end if (#1 == ('j'+1)) set group2['gp2'] #1; set gp2 ++ ; end if (#1 == ('j'+2)) set group3['gp3'] #1;

     		set gp3 ++ ;
     		set j +=3;

end

     stop	;	

set gp1--;
set gp2--;
set gp3--;

loop 0 'gp1' set i 'group1[#1]'; ccode /%1 'i'; stop;

loop 0 'gp2' set i 'group2[#1]'; ccode /%2 'i'; stop;

loop 0 'gp3' set i 'group3[#1]'; ccode /%3 'i'; stop;

ccode; quote If your intent was to downweight third positions in this partition

     do consider upweighting the characters NOT in the partition.;

macro-; proc/;