Parse Text File Line by Line, Skipping Certain Lines

I have a file that looks like this (but is much bigger):

>some text
ABC
DEF
GHI
>some more text
JKL
MNO
PQR

I have been playing around with it in Java for some time and have been able to build arrays with the lines, etc. The lines with '>' are usually one line but sometimes could be 2, 3 or more lines. The lines tha开发者_高级运维t don't begin with '>' are the same length in characters but there may be 10, 20 or 30 or more of these lines. I am at the point now where I want to create an string array, where each string in the array contains a string of the lines that don't begin with '>' like so:

array element 1 = ABCDEFGHI
array element 2 = JKLMONPQR

I feel like I am close but need a small kick in the butt to get me going. I'm sure this is easy for a pro, but I am still new to Java.

Specific problem is related to other posts I made on this board. It's a FASTA file:

>3BHS_BOVIN (P14893) 3 beta-hydroxysteroid
AGWSCLVTGGGGFLGQRIICLLVEEKDLQEIRVLDKVFRPEVREEFSKLQSKIKLTLLEG
DILDEQCLKGACQGTSVVIHTASVIDVRNAVPRETIMNVNVKGTQLLLEACVQASVPVFI
>41_BOVIN (Q9N179) Protein 4.1 
MHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAK
EIKKQVRGVPWNFTFNVKFYPPDPAQLTEDITRYYLCLQLRQDIVSGRLPCSFATLALLG
SYTIQSELGDYDPELHGADYVSDFKLAPNQTKELEEKVMELHKSYRSMTPAQADLEFLEN
>5NTD_BOVIN (Q05927) 5'-nucleotidase 
MNPGAARTPALRILPLGALLWPAARPWELTILHTNDVHSRLEQTSEDSSKCVNASRCVGG
VARLATKVHQIRRAEPHVLLLDAGDQYQGTIWFTVYKGTEVAHFMNALGYESMALGNHEF
DNGVEGLIDPLLKEVNFPILSANIKAKGPLASKISGLYSPYKILTVGDEVVGIVGYTSKE
TPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEVDKLIAQKVKGVDVVV

I ultimately need the sequences in their own array element so that I can manipulate them later.

Assuming you can iterate over the lines:

List<String> array = new ArrayList<String>();
StringBuilder buf = new StringBuilder();
for (String line : lines) {
  if (line.startsWith(">")) {
    if (buf.length() > 0) {
      array.add(buf.toString());
      buf.setLength(0);
    }
  } else {
    buf.append(line);
  }
}
if (buf.length() > 0) { // Add the final text element(s).
  array.add(buf.toString());
}

Try this. I didn't bother with proper variable names. Also it works assuming first line has a >. It's probably not optimised either but should give you an idea of how this is possible.

import java.io.BufferedReader;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;


public class Parse {
    public static void main(String[] args) throws IOException {
        String lala = ">some text\r\n" + 
                "ABC\r\n" + 
                "DEF\r\n" + 
                "GHI\r\n" + 
                ">some more text\r\n" + 
                "JKL\r\n" + 
                "MNO\r\n" + 
                "PQR";

        ArrayList<String> lines = new ArrayList<String>();

        BufferedReader in = new BufferedReader( new StringReader( lala ) );

        String line;
        while( ( line = in.readLine() ) != null ) {
            lines.add( line );
        }

        ArrayList<String> parsed = new ArrayList<String>();

        for( String s : lines ) {
            if( s.contains(">") ) {
                parsed.add("");
            } else {
                String current = parsed.get( parsed.size() - 1 );
                parsed.set( parsed.size() - 1, current + s );
            }
        }

        for( String s : parsed ) {
            System.out.println( s );
        }
    }

}

The above will output:

ABCDEFGHI
JKLMNOPQR

Another interesting way you could do it is at the 'in.readLine()' loop you can check for the > and if it exists add a < at the end of that string before pushing it onto 'lines'. You can then use a regex to grab the other lines back out later.

Something like this?

Array<String> lines    
 //Open the file for reading
    try {    
       BufferedReader br = new BufferedReader(new FileReader(<FileNameGoesHere>));
       while ((thisLine = br.readLine()) != null) { // while loop begins here
         if(thisLine.charAt(0) != '>') {
           lines.add(thisLine);
         }
       } // end while 
     } // end try
     catch (IOException e) {
       System.err.println("Error: " + e);
     }

skipping the lines starting with > is easy;

while((line=istream.readLine())!=null){
    if(line.charAt(0)=='>')continue;

    //do normal concat to buffers
}

if you want to go to the next buffer on lines starting with > is a bit more involved

while((line=istream.readLine())!=null){
    if(line.charAt(0)=='>'){
         //create new buffer and append the current one to the list (check first if current one is not empty)
         continue;
    }

    //do normal concat to buffer
}