User:Lindenb/Notebook/UMR915/20101011

20101008        Top        20101012       

Charpak

Re-Implementing LINKAGE.

Belgium

TODO: for chr1XXX

• list SNP with mutation
• SIFT
• polyphen
• remove individual 4
• add annotations, etc...

Generatic SIFT input for indi2

Used jrunscript for extracting data

   importPackage(java.io);
   importPackage(java.util.zip);
   var f=new File("*.csv.gz");
   var input=new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(f))));
   var line;
   while((line=input.readLine())!=null)
     {
     if(!line.startsWith("\"chXXXXX mapping")) continue;
     
     line=line.replaceAll("\"","").replace(" mapping","").replace(".","");
     var tokens=line.split("[;]");
     if(tokens[3].indexOf("SNP")==-1) continue;
     var bases=tokens[7].split("/");
     for(var i=0;i< bases.length;++i)
       {
       println("XXXXXX,"+tokens[1]+",1,"+tokens[5]+"/"+bases[i]);
       }
     }
   
   input.close();

run

   /usr/local/package/glassfishv3/jdk/bin/jrunscript -f ~/jeter20101011a.js  > ~/result.txt

split input

 split -C 900k result.txt sift_

and polyphen

 importPackage(java.io);
 importPackage(java.util.zip);
 var f=new File("XXXXXX.csv.gz");
 var input=new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(f))));
 var line;
 while((line=input.readLine())!=null)
   {
   if(!line.startsWith("\"chrXXXXXXXXXXXXXXXXXXXXXXXXXX mapping")) continue;
   
   line=line.replaceAll("\"","").replace(" mapping","").replace(".","");
   var tokens=line.split("[;]");
   if(tokens[3].indexOf("SNP")==-1) continue;
   var bases=tokens[7].split("/");
   print("chrXXXXXXXXXXXXXX:"+tokens[1]+"\t"+tokens[7]);
   if(tokens[7].indexOf(tokens[5])==-1) print("/"+tokens[5]);
   println("");
   }
 
 input.close();