org.dishevelled.bio.tools

Class ExtractFasta

java.lang.Object

org.dishevelled.bio.tools.ExtractFasta

All Implemented Interfaces:

Callable<Integer>

public final class ExtractFasta
extends Object
implements Callable<Integer>

Extract matching DNA or protein sequences in FASTA format.

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
(package private) static String	DESCRIPTION_LINE

Constructor Summary

Constructors

Constructor and Description
ExtractFasta(File inputFastaFile, File outputFastaFile, String name, String description, int lineWidth) Extract matching DNA or protein sequences in FASTA format.
ExtractFasta(File inputFastaFile, File outputFastaFile, String name, String description, String alphabet, int lineWidth) Extract matching DNA or protein sequences in FASTA format.
ExtractFasta(Path inputFastaPath, File outputFastaFile, String name, String description, int lineWidth) Extract matching DNA or protein sequences in FASTA format.
ExtractFasta(Path inputFastaPath, File outputFastaFile, String name, String description, String alphabet, int lineWidth) Extract matching DNA or protein sequences in FASTA format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
(package private) static String	describeSequence(org.biojava.bio.seq.Sequence sequence)
(package private) boolean	isProteinAlphabet()
static void	main(String[] args) Main.
(package private) static void	writeSequence(org.biojava.bio.seq.Sequence sequence, int lineWidth, PrintWriter writer)

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

DESCRIPTION_LINE

static final String DESCRIPTION_LINE

See Also:

Constant Field Values

Constructor Detail

ExtractFasta

public ExtractFasta(File inputFastaFile,
                    File outputFastaFile,
                    String name,
                    String description,
                    int lineWidth)

Extract matching DNA or protein sequences in FASTA format.

Parameters:

inputFastaFile - input FASTA file, if any

outputFastaFile - output FASTA file, if any

name - exact sequence name to match, if any

description - FASTA description line regex pattern to match, if any

lineWidth - line width

ExtractFasta

public ExtractFasta(Path inputFastaPath,
                    File outputFastaFile,
                    String name,
                    String description,
                    int lineWidth)

Extract matching DNA or protein sequences in FASTA format.

Parameters:

inputFastaPath - input FASTA path, if any

outputFastaFile - output FASTA file, if any

name - exact sequence name to match, if any

description - FASTA description line regex pattern to match, if any

lineWidth - line width

Since:

2.1

ExtractFasta

public ExtractFasta(File inputFastaFile,
                    File outputFastaFile,
                    String name,
                    String description,
                    String alphabet,
                    int lineWidth)

Extract matching DNA or protein sequences in FASTA format.

Parameters:

inputFastaFile - input FASTA file, if any

outputFastaFile - output FASTA file, if any

name - exact sequence name to match, if any

description - FASTA description line regex pattern to match, if any

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

lineWidth - line width

Since:

2.0

ExtractFasta

public ExtractFasta(Path inputFastaPath,
                    File outputFastaFile,
                    String name,
                    String description,
                    String alphabet,
                    int lineWidth)

Extract matching DNA or protein sequences in FASTA format.

Parameters:

inputFastaPath - input FASTA path, if any

outputFastaFile - output FASTA file, if any

name - exact sequence name to match, if any

description - FASTA description line regex pattern to match, if any

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

lineWidth - line width

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Specified by:

call in interface Callable<Integer>

Throws:

Exception

isProteinAlphabet

boolean isProteinAlphabet()

describeSequence

static String describeSequence(org.biojava.bio.seq.Sequence sequence)

writeSequence

static void writeSequence(org.biojava.bio.seq.Sequence sequence,
                          int lineWidth,
                          PrintWriter writer)
                   throws IOException

Throws:

IOException

main

public static void main(String[] args)

Main.

Parameters:

args - command line args