User:Lindenb/Notebook/UMR915/20101130

Thesis Stéphanie Chatel

Belgium
Working on belgium data.

script jrunscript sift
more jeter20101011a.js

importPackage(java.io); importPackage(java.util.zip); var f=new File("/GENOTYPAGE/data/project/belgium/20101007/XXXXXXXXXXXXXXXXXXXXXXX.csv.gz"); var input=new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(f)))); var line; while((line=input.readLine)!=null) { if(!(line.startsWith("\"chr"))) 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) {   if(bases[i].equals(tokens[5])) continue; println(tokens[0].replace("chr","")+","+tokens[1]+",1,"+tokens[5]+"/"+bases[i]); } }

input.close;

f= new File("/GENOTYPAGE/data/project/belgium/XXXXXXXXXXXXXXXX/454AllDiffs.txt.gz"); input=new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(f)))); while((line=input.readLine)!=null) { if(!(line.startsWith(">chr"))) continue;

var tokens=line.split("[\t]"); if(!tokens[1].equals(tokens[2])) continue; if(tokens[3].equals("-") || tokens[4].length!=1) continue; println(tokens[0].replace(">chr","")+","+tokens[1]+",1,"+tokens[3]+"/"+tokens[4]); }

input.close;

polyphen
importPackage(java.io); importPackage(java.util.zip); var f=new File("/GENOTYPAGE/data/project/belgium/20101007/XXXXXXXXXXXXXXXXXXXXXX.csv.gz"); var input=new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(f)))); var line; while((line=input.readLine)!=null) { if(!(line.startsWith("\"chr"))) 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) {   if(bases[i].equals(tokens[5])) continue; println(tokens[0]+":"+tokens[1]+"\t"+tokens[5]+"/"+bases[i]); } }

input.close;

f= new File("/GENOTYPAGE/data/project/belgium/XXXXXX/454AllDiffs.txt.gz"); input=new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(f)))); while((line=input.readLine)!=null) { if(!(line.startsWith(">chr"))) continue;

var tokens=line.split("[\t]"); if(!tokens[1].equals(tokens[2])) continue; if(tokens[3].equals("-") || tokens[4].length!=1) continue; println(tokens[0].replace(">","")+":"+tokens[1]+"\t"+tokens[3]+"/"+tokens[4]); }

input.close;