Originally Posted by kswapnadevi (Post 4150773)

THANKS IN ADVANCE.

Originally Posted by catkin (Post 4150893)

I'd like to help but you haven't asked a question!

It might help if you

1. posted the input data files (or a few lines, if they are big)
2. the directory+file tree
3. how what happens when you run your script (copy and paste from the terminal into the post is good) and explain how it differe from what you want.

This would give a clear understanding of what you are doing and what you question is.

Originally Posted by catkin (Post 4150893)

I'd like to help but you haven't asked a question!

It might help if you

1. posted the input data files (or a few lines, if they are big)
2. the directory+file tree
3. how what happens when you run your script (copy and paste from the terminal into the post is good) and explain how it differe from what you want.

This would give a clear understanding of what you are doing and what you question is.

Originally Posted by catkin (Post 4151618)

-------------------------------------------------------------------------
My Java Code:
import java.io.*;
import java.util.*;

public class RNA
{
public static final String inputFile1 = "t1out";
public static final String inputFile2 = "t2out";


private Hashtable rangeTable = new Hashtable();
private ArrayList multiloopList = new ArrayList();
private ArrayList hairPinList = new ArrayList();
private int STARTRANGE = -1;
private int DEFAULTSTARTRANGE = 40;

private static final boolean DEBUG = false;


public RNA()
{
}

public RNA(int STARTRANGE)
{

this.STARTRANGE = STARTRANGE;
if(STARTRANGE == -1) this.STARTRANGE = DEFAULTSTARTRANGE;
}


private void init() throws IOException
{
FileReader fileReaderObj = new FileReader(inputFile2);
BufferedReader bufferReaderObj = new BufferedReader(fileReaderObj);

String line = null;
line = bufferReaderObj.readLine();
String saveLine = null;
boolean advanced = false;
while(line != null)
{
advanced = false;

if (line.trim().startsWith("-"))
{

saveLine = line.trim();
String multiloop = new String();
if(DEBUG) System.out.println(saveLine);

while (((line = bufferReaderObj.readLine()) != null) && !line.trim().startsWith("Hairpin loop:"))
{
if (line.trim().equals("Multi-loop:"))
{
multiloop = bufferReaderObj.readLine();
multiloopList = new ArrayList();
multiloopList.add("Multi-loop:");
multiloopList.add(multiloop);
if(DEBUG) System.out.println("multiloop--->"+multiloop);

}
}

if(line.trim().equals("Hairpin loop:"))
{
multiloopList.add("Hairpin loop:");
while (((line = bufferReaderObj.readLine()) != null) && !line.trim().startsWith("-"))
{
advanced = true;
if(line.trim().length() > 0)multiloopList.add(line);
if(DEBUG) System.out.println("Hairpin loop--->"+line);


}
if(DEBUG) System.out.println("Hairpin loop size--->"+multiloopList.size());

}



}
rangeTable.put(saveLine,multiloopList);
if(!advanced )
{
line = bufferReaderObj.readLine();
//System.out.println("advance-->"+line);

}
}

}


public void compare() throws IOException
{
FileReader fileReaderObj = new FileReader(inputFile1);
BufferedReader bufferReaderObj = new BufferedReader(fileReaderObj);
boolean advanced = false;
String line = null;
line = bufferReaderObj.readLine();

while(line != null)
{
advanced = false;
System.out.println(line);
if(line.trim().startsWith("-"))
{
List list = (ArrayList)rangeTable.get(line.trim());
while(((line = bufferReaderObj.readLine()) != null) && !line.trim().startsWith("-"))
{

String []result = line.trim().split("-");
int left = Integer.parseInt(result[0].trim());
int right = Integer.parseInt(result[1].trim());
if(left > STARTRANGE && (right - left) > 20)
{
String multiLoopRange = (String)list.get(1);
String []result1 = multiLoopRange.trim().split("-");
int multiLoopLeft = Integer.parseInt(result1[0].trim());
int multiLoopRight = Integer.parseInt(result1[1].trim());

if(left > multiLoopLeft)
{
for(int i = 3; i < list.size(); i++)
{

String hairPinValue = (String)list.get(i);
String []hairPinresult = hairPinValue.trim().split("-");
int hairPinleft = Integer.parseInt(hairPinresult[0].trim());
int hairPinRight = Integer.parseInt(hairPinresult[1].trim());

if(left < hairPinleft && right > hairPinRight)
{

int microRNAleft = left + 21;

if (microRNAleft <= hairPinleft)
{
System.out.println("MIRNA--"+ left +":"+microRNAleft);
}
int microRNAright = hairPinRight + 1 + 21;

if(microRNAright <= right)
{
System.out.println("MIRNA--"+ (hairPinRight+1)+":"+microRNAright);

}

}
}

}


}
advanced = true;
}
}

if(!advanced) line = bufferReaderObj.readLine();
}
}

public static void main(String []r) throws Exception
{
System.out.println("Enter the Starting Micro RNA range to be computed...");
BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
String sInputRange = in.readLine();
int inputRange = -1;
try
{

inputRange = Integer.parseInt(sInputRange);
}
catch(Exception e)
{
System.out.println("Invalid input...computing with DEFAULT Micro RNA Range 40.");
inputRange = -1;
}
RNA rna = new RNA(inputRange);
rna.init();
rna.compare();

}

}

CAPITAL LETTERS usually denote heavy emphasis or shouting on bulletin boards, thus your "PLS. KINDLY HELP ME WHICH IS VERY ESSENTAIL FOR ME. THANKING YOU" could be taken as demanding -- which is more likely to put people off answering than encourage them.

It also helps us understand if you use code tags (that's a link to instructions or you may prefer to use "Advanced Edit" which has a # button to insert code tags.

Another very useful (and easy) technique for explaining what you are doing is to copy and paste from a terminal emulator, into code tags to show us what you have done. Your
would have been clearer as
Let's start with a clear definition of the requirement before misunderstanding and so wasting time on a solution to some other requirement.

As I understand it the directory+file hierarchy relative to the mfold directory is (this is output from the tree command):
Mmm ... maybe this does what you want (not tested). It exits if any of the programs set a non-zero return code, conventionally used to indicate failure. That may not be what you want but it usually is.

Originally Posted by kswapnadevi (Post 4153082)

When I run the script I am getting the following errors. The shell processing the input in 'dir1' and generating two output files t1out and t2out. It is not processing for inputs in 'dir2'. For each folder output i.e., t1out and t2out Java program has to be executed and it has to redirect the output to a folder. That is also not working. I am herewith submitting my java program also. . When I am executing single data set 't1out' and 't2out'(using the following code) Java program is running successuflly and giving output.Pls help me. I am in confusion