org.dishevelled.bio.tools

Class FastaToText

java.lang.Object

org.dishevelled.bio.tools.FastaToText

All Implemented Interfaces:

Callable<Integer>

public final class FastaToText
extends Object
implements Callable<Integer>

Convert DNA or protein sequences in FASTA format to tab-separated values (tsv) text format.

Since:

2.2

Author:

Michael Heuer

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static String	DEFAULT_ALPHABET

Constructor Summary

Constructors

Constructor and Description
FastaToText(Path fastaPath, File textFile, String alphabet) Convert DNA or protein sequences in FASTA format to tab-separated values (tsv) text format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
(package private) boolean	isProteinAlphabet()
static void	main(String[] args) Main.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_ALPHABET

static final String DEFAULT_ALPHABET

See Also:

Constant Field Values

Constructor Detail

FastaToText

public FastaToText(Path fastaPath,
                   File textFile,
                   String alphabet)

Convert DNA or protein sequences in FASTA format to tab-separated values (tsv) text format.

Parameters:

fastaPath - input FASTA path, if any

textFile - output text file, if any

alphabet - input FASTA file alphabet { dna, protein }, if any

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

isProteinAlphabet

boolean isProteinAlphabet()

main

public static void main(String[] args)

Main.

Parameters:

args - command line args