org.dishevelled.bio.tools

Class TextToFasta

java.lang.Object

org.dishevelled.bio.tools.TextToFasta

All Implemented Interfaces:

Callable<Integer>

public final class TextToFasta
extends Object
implements Callable<Integer>

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

Since:

2.2

Author:

Michael Heuer

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor and Description
TextToFasta(Path textPath, File fastaFile, String alphabet, int lineWidth) Convert DNA or protein sequences in tab-separated values (tsv) text format to FASTA format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
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

DEFAULT_LINE_WIDTH

static final int DEFAULT_LINE_WIDTH

See Also:

Constant Field Values

Constructor Detail

TextToFasta

public TextToFasta(Path textPath,
                   File fastaFile,
                   String alphabet,
                   int lineWidth)

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

Parameters:

textPath - input text path, if any

fastaFile - output FASTA file, if any

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

lineWidth - output line width

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args