User:Lindenb/Notebook/UMR915/20101011: Difference between revisions
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(New page: {{PLNB|20101008|20101012}} ==Charpak== Re-Implementing LINKAGE. ==Belgium== TODO: for chr1XXX * list SNP with mutation * SIFT * polyphen * remove individual 4 * add annotations, etc...) |
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* remove individual 4 | * remove individual 4 | ||
* add annotations, etc... | * 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_ |
Revision as of 06:00, 11 October 2010
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_