Date:         Tue, 29 Jul 2008 13:27:12 -0400
Reply-To:     msz03@albany.edu
Sender:       "SAS(r) Discussion" <SAS-L@LISTSERV.UGA.EDU>
From:         Mike Zdeb <msz03@ALBANY.EDU>
Subject:      Re: data mining
Content-Type: text/plain;charset=iso-8859-1

hi ... I was able to get the results you posted (plus I faked another sequence so I had two
observations) ...

seq  motif  rept  stpos endpos  len
seq1-1 ag   2      1     4      45
seq1-2 cg   2      12   15      45
seq1-3 ct   8      16   31      45
seq1-4 ga   2      37   40      45
seq1-6 tcga 2      31   38      45

with this ... but, I also got a SEQ1-5 that was not on your list ...

seq1-5    ctct      4       16      31  45

(***** we all await the 5-lines of code SQL method *****)


data sequence;
infile datalines missover;
input seq : $4. h : $100.;
datalines;
seq1 agagattcgatcgcgctctctctctctctctcgatcgagatcgat
seq2 agagtctctcga
;
run;

data x;
set sequence;
ll = length(h);
s = 0;
* start at position 1 in sequence, look for motifs length 2 to 5;
do j=2 to 5;
do i=1 to length(h)-4;
   motif = substr(h,i,j);
   start = i;
   rpt = 1;
   do while (trim(motif) eq trim(substr(h,i+j,j)));
      rpt + 1;
          i + j;
   end;
   if rpt ge 2 then do;
     end = start + (j*rpt) - 1;
     s + 1;
         seqq = catx('-',seq,s);
     output;
   end;
end;
end;
keep seqq motif rpt start end ll;
run;

proc print data=x;
var seqq motif rpt start end ll;
run;


--
Mike Zdeb
U@Albany School of Public Health
One University Place
Rensselaer, New York 12144-3456
P/518-402-6479 F/630-604-1475