133 lines
4.0 KiB
Java
133 lines
4.0 KiB
Java
/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2008 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever.
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* Neither the Broad Institute nor MIT can be responsible for its use, misuse,
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* or functionality.
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*/
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package edu.mit.broad.arachne;
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import java.io.*;
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/**
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* Utility to convert fastb to fasta files.
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* More importantly, can be used to extract a subset of the reads.
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*/
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public class Fastb2Fasta {
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private boolean mVerbose = false;
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private boolean mDebug = false;
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private String mInputPath = null;
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private String mIdListFilePath = null;
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public static void main(String[] args)
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throws Exception {
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new Fastb2Fasta().run(args);
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}
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private void usage() {
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System.out.println("Usage: Fastb2Fasta ... <fastb-file>");
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System.out.println(" -idlist <file-of-read-ids>");
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System.out.println(" -verbose");
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System.out.println(" -debug");
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}
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private boolean parseArguments(String[] args) {
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int argpos = 0;
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int argsleft = 0;
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while (argpos < args.length) {
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argsleft = args.length - argpos;
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String arg = args[argpos];
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if (arg.equals("-idlist") && argsleft > 1) {
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argpos++;
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mIdListFilePath = args[argpos++];
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} else if (arg.equals("-verbose")) {
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argpos++;
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mVerbose = true;
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} else if (arg.equals("-debug")) {
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argpos++;
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mDebug = true;
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} else if (arg.startsWith("-")) {
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usage();
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return false;
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} else {
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break;
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}
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}
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argsleft = args.length - argpos;
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if (argsleft != 1) {
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usage();
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return false;
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}
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mInputPath = args[argpos];
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return true;
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}
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private void run(String[] args)
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throws Exception {
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if (!parseArguments(args)) {
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System.exit(1);
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}
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FastbReader fastbReader = new FastbReader(new File(mInputPath));
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try {
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if (mIdListFilePath != null) {
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LineNumberReader reader = new LineNumberReader(new FileReader(mIdListFilePath));
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while (true) {
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String line = reader.readLine();
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if (line == null) {
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reader.close();
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break;
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}
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Integer id = parseReadId(line);
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if (id == null) {
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continue;
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}
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if (id < 0 || id >= fastbReader.getSequenceCount()) {
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System.out.println("ERROR: Illegal sequence id: " + id);
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System.exit(1);
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}
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String sequence = fastbReader.readSequence(id);
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System.out.println(">" + id);
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System.out.println(sequence);
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}
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} else {
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int id = 0;
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while (fastbReader.hasNext()) {
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String sequence = fastbReader.next();
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System.out.println(">" + id);
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System.out.println(sequence);
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id++;
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}
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}
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} finally {
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fastbReader.close();
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}
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}
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private Integer parseReadId(String line) {
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String text = line.trim();
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if (text.length() == 0 || text.charAt(0) == '#') {
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return null;
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}
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String token = text.split("\\s+")[0];
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Integer id = null;
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try {
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id = new Integer(token);
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} catch (NumberFormatException exc) {
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System.out.println("ERROR: Invalid sequence id: " + token);
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System.exit(1);
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}
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return id;
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}
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}
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