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package driver;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Collections;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Shared;
import stream.ConcurrentReadInputStream;
import stream.Read;
import structures.ListNum;
/**
* @author Brian Bushnell
* @date Jul 29, 2014
*
*/
public class EstherFilter {
public static void main(String[] args){
String query=args[0];
String ref=args[1];
float cutoff=Float.parseFloat(args[2]);
boolean outputFasta=false;
if(args.length>3 && args[3].equalsIgnoreCase("fasta")){
outputFasta=true;
}
String command="blastall -p blastn -i "+query+" -d "+ref+" -e 0.00001 -m 8";
ReadWrite.FORCE_KILL=true;
// InputStream is=ReadWrite.getInputStreamFromProcess("stdin", command, false);
// InputStream is=ReadWrite.getInputStreamFromProcess("", command, false);
InputStream is=ReadWrite.getInputStreamFromProcess("foo", command, false, false, true);
InputStreamReader isr=new InputStreamReader(is);
BufferedReader b=new BufferedReader(isr, 32768);
// System.out.println("Before");
if(outputFasta){
// System.out.println("A");
processToFasta(b, cutoff, query);
}else{
// System.out.println("B");
processToNames(b, cutoff);
}
// System.out.println("Finished");
// ReadWrite.finishReading(is, "stdin", true, b, isr);
// ReadWrite.finishReading(is, "", true, b, isr);
ReadWrite.finishReading(is, "foo", true, b, isr);
}
public static void processToFasta(BufferedReader b, float cutoff, String query){
String s=null;
ArrayList<String> names=new ArrayList<String>();
// System.out.println("Reading line 0");
try {
s=b.readLine();
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
// System.out.println("Starting");
String prev="";
while(s!=null){
String[] split=s.split("\t");
float value=0;
try {
value=Float.parseFloat(split[11].trim());
} catch (NumberFormatException e) {
e.printStackTrace();
// System.err.println("Bad line:\n"+s);
}
if(value>=cutoff){
if(!prev.equals(split[0])){
prev=split[0];
names.add(split[0]);
}
}
// System.out.println("Reading line");
try {
s=b.readLine();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
outputFasta(query, names);
}
public static void processToNames(BufferedReader b, float cutoff){
String s=null;
// System.out.println("Reading line 0");
try {
s=b.readLine();
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
// System.out.println("Starting");
String prev="";
while(s!=null){
String[] split=s.split("\t");
float value=0;
try {
value=Float.parseFloat(split[11].trim());
} catch (NumberFormatException e) {
e.printStackTrace();
// System.err.println("Bad line:\n"+s);
}
if(value>=cutoff){
System.out.println(split[0]);
}
// System.out.println("Reading line");
try {
s=b.readLine();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
public static void outputFasta(String fname, ArrayList<String> names){
Shared.sort(names);
FileFormat ff=FileFormat.testInput(fname, FileFormat.FASTA, null, false, true);
ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1L, false, ff, null);
cris.start(); //4567
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
/* Iterate through read lists from the input stream */
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
for(Read r : reads){
if(Collections.binarySearch(names, r.id)>=0){
System.out.println(r.toFasta(70));
}
}
/* Dispose of the old list and fetch a new one */
cris.returnList(ln);
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
/* Cleanup */
cris.returnList(ln);
}
}
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