single line levelsof output for pasting elsewhere

[Girish Venkataraman]

Hello all:

I need to have protein changes separated by a comma in a single line (like R243S, Y220C, ...and so on) to paste into a server for getting scores for each of the mutations. I am copy/pasting from the Results Window, but the output is wrapped with a ">' character for each new line. Is there anyway, I can get -levelsof- to get me a single line of output.

My code:

frame put mischange if mutclass=="missense", into(p53mis)
frame p53mis {
replace mischange = subinstr(mischange, "p.","",.)
levelsof mischange, local(mammoth) sep(,) clean
di "`r(levels)'" _newline
}

My (undesirable) output (whole data, not the dataex portion) which I end up pasting in a text editor cleaning up and then pasting into the webserver for the scores:

A159G,C141R,C176F,C176R,C176S,C238G,C238Y,C242F,C275Y,C277F,C277Y,D259Y,D281E,D2
> 81N,D281V,E258K,E286G,F113V,F134S,F270S,G187S,G244C,G244S,G245C,G245D,G245S,G2
> 66E,G266R,H168R,H179N,H179Q,H179R,H179Y,I195T,I254N,I255T,K120E,K132R,L111P,L1
> 45R,L252P,L265P,L265R,L344P,L344Q,M133K,M237I,M237K,N131I,N239D,P152L,P190R,P2
> 23L,P278A,Q136H,R110L,R158H,R175H,R181H,R196G,R245S,R248G,R248Q,R248W,R249S,R2
> 67W,R273C,R273H,R273P,R273S,R280K,R282G,R290H,S127F,S127T,S215G,S215N,S240G,S2
> 41F,S241Y,T155N,T253A,V143M,V157F,V173G,V173L,V173M,V216L,V216M,V272L,V272M,V2
> 74D,V274L,Y126H,Y163C,Y163N,Y205C,Y220C,Y220H,Y220N,Y234C,Y234N
. di "`r(levels)'" _newline

* Example generated by -dataex-. For more info, type help dataex
clear
input float obs byte mutno str19 mischange str10 mutclass
 1 1 "p.D281V"      "missense"  
 1 2 ""             ""          
 1 3 ""             ""          
 2 1 "p.R196*"      "stop gain" 
 2 2 ""             ""          
 2 3 ""             ""          
 3 1 "p.Y126H"      "missense"  
 3 2 ""             ""          
 3 3 ""             ""          
 4 1 "p.R175H"      "missense"  
 4 2 ""             ""          
 4 3 ""             ""          
 5 1 "p.P190Lfs*57" "frameshift"
 5 2 "p.V272M"      "missense"  
 5 3 ""             ""          
 6 1 "p.F134S"      "missense"  
 6 2 ""             ""          
 6 3 ""             ""          
 7 1 "p.Y220N"      "missense"  
 7 2 ""             ""          
 7 3 ""             ""          
 8 1 "p.N131I"      "missense"  
 8 2 "p.R213*"      "stop gain" 
 8 3 ""             ""          
 9 1 "p.P278A"      "missense"  
 9 2 ""             ""          
 9 3 ""             ""          
10 1 "p.C176F"      "missense"  
10 2 ""             ""          
10 3 ""             ""          
11 1 "p.R342*"      "stop gain" 
11 2 ""             ""          
11 3 ""             ""          
12 1 "p.E258K"      "missense"  
12 2 "p.G112Wfs*12" "frameshift"
12 3 ""             ""          
13 1 "p.Y220C"      "missense"  
13 2 ""             ""          
13 3 ""             ""          
14 1 "p.?"          "splicing"  
14 2 "p.C238Y"      "missense"  
14 3 ""             ""          
15 1 "p.R213Gfs*34" "complex"   
15 2 "p.Y220C"      "missense"  
15 3 ""             ""          
16 1 "p.R248W"      "missense"  
16 2 ""             ""          
16 3 ""             ""          
17 1 "p.C238Lfs*2"  "complex"   
17 2 ""             ""          
17 3 ""             ""          
18 1 "p.R273H"      "missense"  
18 2 "p.K120E"      "missense"  
18 3 ""             ""          
19 1 "p.F113V"      "missense"  
19 2 "p.R213Dfs*34" "frameshift"
19 3 ""             ""          
20 1 "p.Q165*"      "stop gain" 
20 2 ""             ""          
20 3 ""             ""          
21 1 "p.V272M"      "missense"  
21 2 ""             ""          
21 3 ""             ""          
22 1 "p.R175H"      "missense"  
22 2 ""             ""          
22 3 ""             ""          
23 1 "p.H179Q"      "missense"  
23 2 ""             ""          
23 3 ""             ""          
24 1 "p.C277F"      "missense"  
24 2 ""             ""          
24 3 ""             ""          
25 1 "p.G244S"      "missense"  
25 2 ""             ""          
25 3 ""             ""          
26 1 "p.I195T"      "missense"  
26 2 ""             ""          
26 3 ""             ""          
27 1 "p.?"          "splicing"  
27 2 "p.Q144Sfs*26" "frameshift"
27 3 ""             ""          
28 1 "p.R280K"      "missense"  
28 2 ""             ""          
28 3 ""             ""          
29 1 "p.Y234N"      "missense"  
29 2 ""             ""          
29 3 ""             ""          
30 1 "p.N239D"      "missense"  
30 2 ""             ""          
30 3 ""             ""          
31 1 "p.G244C"      "missense"  
31 2 ""             ""          
31 3 ""             ""          
32 1 "p.H168R"      "missense"  
32 2 "p.S215G"      "missense"  
32 3 ""             ""          
33 1 "p.G266E"      "missense"  
33 2 ""             ""          
33 3 ""             ""          
34 1 "p.C242F"      "missense"  
end

[Leonardo Guizzetti]

Thank you for the data example. Here is one technique.

frame put mischange if mutclass=="missense", into(p53mis)
frame p53mis {
  replace mischange = subinstr(mischange, "p.","",.)
  bys mischange : keep if _n==1
  gen want = ""
  replace want = cond(_n==1, mischange, want[_n-1] + "," + mischange)
  keep in l
  keep want
  export delim want using "mischanges.csv", novarnames delim(" ") replace
}

[Girish Venkataraman]

Thank you for the data example. Here is one technique.

frame put mischange if mutclass=="missense", into(p53mis)
frame p53mis {
replace mischange = subinstr(mischange, "p.","",.)
bys mischange : keep if _n==1
gen want = ""
replace want = cond(_n==1, mischange, want[_n-1] + "," + mischange)
keep in l
keep want
export delim want using "mischanges.csv", novarnames delim(" ") replace
}

Took me a while to understand the logic, but it is fascinating how it gets what I wanted, Leonardo Guizzetti