public BlastResult performTBlastn(File pssm, File db) {
Runtime rt = Runtime.getRuntime();
BlastResult result = null;
try {
String db_path = db.getAbsolutePath();
// db_path = db_path.substring(0, db_path.lastIndexOf('.')-1);
String commandline =
tblastn_exec_path
+ " -in_pssm "
+ pssm.getAbsolutePath()
+ " -db "
+ db_path
+ " -outfmt 6";
Process pr = rt.exec(commandline);
BufferedReader in = new BufferedReader(new InputStreamReader(pr.getInputStream()));
String line = null;
double minEvalue = 0.01;
while ((line = in.readLine()) != null) {
BlastResult r = new BlastResult();
r.parse(line);
if (r.getEvalue() < minEvalue) {
result = r;
minEvalue = r.getEvalue();
}
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return result;
}
