Read a fasta file | Java

Question

[ozdavidd]

Hey, I'm in my final project for finding hidden repeats in DNA sequence. I have to read a fasta file and get only the sequence without the genome's name, which starts with '>' and save it into a string.

Wish you guys could help me

Thanks

[Pierre Lindenbaum]

what have you tried ?

[ozdavidd]

I know how to read a regular file, but I dont know what should indicate me to start reading the nucleotides. The question is - when the gonome name ended? So I cant really write something

[ozdavidd]

Thank you very much.

Answer 1

[Pierre Lindenbaum]

a solution:

Answer 2

[vmicrobio]

Hi ozdavidd,

you may try this :

private void readFastaFile(File fastaFile) {
    InputStream flux;
    String line;
    try {
        flux = new FileInputStream(fastaFile);
        InputStreamReader lecture = new InputStreamReader(flux);
        BufferedReader buff = new BufferedReader(lecture);
        int lineNb = 0;
        StringBuilder sb = new StringBuilder();
        while ((line = buff.readLine()) != null){
            if (lineNb == 0) {
                this.header = line;
            }
            else {
                sb.append(line);
            }
            lineNb++;
        }
        this.sequence = sb.toString();
        buff.close();
    }
    catch(Exception e) {
        e.printStackTrace();
    }
}

[ozdavidd]

Thanks for comment. what sould I put in

this.header = line;

[vmicrobio]

you can create a class FastaSequence containing the code above, add a 'getHeader' and 'getSequence' and then return only the sequence for your use

[ozdavidd]

What in this code indicates u for the start of the nucleotides?

Answer 3

[Hugo]

You may have a look at SEDA (http://www.sing-group.org/seda/), which also provides a Java API for easily manipulation of FASTA sequences (https://github.com/sing-group/seda).