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Initial Analysis toolkit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4 348d0f76-0448-11de-a6fe-93d51630548a
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depristo committed Feb 26, 2009
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242 changes: 242 additions & 0 deletions lib/edu/mit/broad/arachne/Alignment.java
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/*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2008 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever.
* Neither the Broad Institute nor MIT can be responsible for its use, misuse,
* or functionality.
*/
package edu.mit.broad.arachne;


/**
* This class represents an arachne LookAlign alignment (or other related data structures).
*/
public class Alignment {

private static final char TAB = '\t';

private int mASequenceId;
private int mASequenceLength;
private int mAStart;
private int mAEnd;
private int mBSequenceId;
private int mBSequenceLength;
private int mBStart;
private int mBEnd;
private char mOrientation;
private int[] mAlignmentBlocks;


public Alignment() {
}

public int getASequenceId() {
return mASequenceId;
}

public void setASequenceId(int value) {
mASequenceId = value;
}

public int getASequenceLength() {
return mASequenceLength;
}

public void setASequenceLength(int value) {
mASequenceLength = value;
}

public int getAStart() {
return mAStart;
}

public void setAStart(int value) {
mAStart = value;
}

public int getAEnd() {
return mAEnd;
}

public void setAEnd(int value) {
mAEnd = value;
}

public int getBSequenceId() {
return mBSequenceId;
}

public void setBSequenceId(int value) {
mBSequenceId = value;
}

public int getBSequenceLength() {
return mBSequenceLength;
}

public void setBSequenceLength(int value) {
mBSequenceLength = value;
}

public int getBStart() {
return mBStart;
}

public void setBStart(int value) {
mBStart = value;
}

public int getBEnd() {
return mBEnd;
}

public void setBEnd(int value) {
mBEnd = value;
}

public char getOrientation() {
return mOrientation;
}

public void setOrientation(char value) {
mOrientation = value;
}

public int[] getAlignmentBlocks() {
return mAlignmentBlocks;
}

public void setAlignmentBlocks(int[] value) {
mAlignmentBlocks = value;
}

public static Alignment parse(String text) {

if (text == null) {
return null;
}

String[] fields = text.trim().split("\t");
if (fields.length == 0) {
return null;
}

if (!fields[0].equals("QUERY")) {
throw new IllegalArgumentException("Invalid alignment: " + text);
}
if (fields.length < 14) {
throw new IllegalArgumentException("Invalid alignment: " + text);
}

int seqAId = parseIntField(fields[1]);
int seqAStart = parseIntField(fields[2]);
int seqAEnd = parseIntField(fields[3]);
int seqALength = parseIntField(fields[4]);
int orientation = parseIntField(fields[5]);
int seqBId = parseIntField(fields[6]);
int seqBStart = parseIntField(fields[7]);
int seqBEnd = parseIntField(fields[8]);
int seqBLength = parseIntField(fields[9]);
int blockCount = parseIntField(fields[10]);

if (seqAStart < 0 || seqAEnd <= 0 || seqALength <= 0 ||
seqAStart >= seqALength || seqAEnd > seqALength || seqAStart >= seqAEnd) {
throw new IllegalArgumentException("Invalid alignment: " + text);
}
if (seqBStart < 0 || seqBEnd <= 0 || seqBLength <= 0 ||
seqBStart >= seqBLength || seqBEnd > seqBLength || seqBStart >= seqBEnd) {
throw new IllegalArgumentException("Invalid alignment: " + text);
}
if (orientation < 0 || orientation > 1) {
throw new IllegalArgumentException("Invalid alignment: " + text);
}
if (fields.length != (11 + 3*blockCount)) {
throw new IllegalArgumentException("Invalid alignment: " + text);
}

int[] alignmentBlocks = new int[3*blockCount];
for (int i = 0; i < 3*blockCount; i++) {
alignmentBlocks[i] = parseIntField(fields[11 + i]);
}

Alignment alignment = new Alignment();
alignment.setASequenceId(seqAId);
alignment.setASequenceLength(seqALength);
alignment.setAStart(seqAStart+1);
alignment.setAEnd(seqAEnd);
alignment.setBSequenceId(seqBId);
alignment.setBSequenceLength(seqBLength);
alignment.setBStart(seqBStart+1);
alignment.setBEnd(seqBEnd);
alignment.setOrientation((orientation == 0) ? '+' : '-');
alignment.setAlignmentBlocks(alignmentBlocks);
return alignment;
}

private static int parseIntField(String text) {
try {
return Integer.parseInt(text);
} catch (NumberFormatException exc) {
throw new IllegalArgumentException("Illegal alignment field: " + text);
}
}

public String arachneFormat() {
StringBuilder builder = new StringBuilder();
builder.append("QUERY");
builder.append(TAB);
builder.append(mASequenceId);
builder.append(TAB);
builder.append(mAStart-1); // zero based
builder.append(TAB);
builder.append(mAEnd);
builder.append(TAB);
builder.append(mASequenceLength);
builder.append(TAB);
builder.append(mOrientation == '+' ? 0 : 1);
builder.append(TAB);
builder.append(mBSequenceId);
builder.append(TAB);
builder.append(mBStart-1); // zero based
builder.append(TAB);
builder.append(mBEnd);
builder.append(TAB);
builder.append(mBSequenceLength);
builder.append(TAB);
builder.append(mAlignmentBlocks.length / 3);
for (int i = 0; i < mAlignmentBlocks.length; i++) {
builder.append(TAB);
builder.append(mAlignmentBlocks[i]);
}
return builder.toString();
}

public String format() {
StringBuilder builder = new StringBuilder();
builder.append("Alignment");
builder.append(' ');
builder.append(mASequenceId);
builder.append(' ');
builder.append(mAStart);
builder.append(' ');
builder.append(mAEnd);
builder.append(' ');
builder.append(mOrientation);
builder.append(' ');
builder.append(mBSequenceId);
builder.append(' ');
builder.append(mBStart);
builder.append(' ');
builder.append(mBEnd);
builder.append(' ');
builder.append(mAlignmentBlocks.length / 3);
for (int i = 0; i < mAlignmentBlocks.length; i++) {
builder.append(' ');
builder.append(mAlignmentBlocks[i]);
}
return builder.toString();
}
}
132 changes: 132 additions & 0 deletions lib/edu/mit/broad/arachne/Fastb2Fasta.java
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/*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2008 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever.
* Neither the Broad Institute nor MIT can be responsible for its use, misuse,
* or functionality.
*/
package edu.mit.broad.arachne;

import java.io.*;

/**
* Utility to convert fastb to fasta files.
* More importantly, can be used to extract a subset of the reads.
*/
public class Fastb2Fasta {

private boolean mVerbose = false;
private boolean mDebug = false;
private String mInputPath = null;
private String mIdListFilePath = null;


public static void main(String[] args)
throws Exception {
new Fastb2Fasta().run(args);
}

private void usage() {
System.out.println("Usage: Fastb2Fasta ... <fastb-file>");
System.out.println(" -idlist <file-of-read-ids>");
System.out.println(" -verbose");
System.out.println(" -debug");
}

private boolean parseArguments(String[] args) {

int argpos = 0;
int argsleft = 0;

while (argpos < args.length) {
argsleft = args.length - argpos;
String arg = args[argpos];
if (arg.equals("-idlist") && argsleft > 1) {
argpos++;
mIdListFilePath = args[argpos++];
} else if (arg.equals("-verbose")) {
argpos++;
mVerbose = true;
} else if (arg.equals("-debug")) {
argpos++;
mDebug = true;
} else if (arg.startsWith("-")) {
usage();
return false;
} else {
break;
}
}

argsleft = args.length - argpos;
if (argsleft != 1) {
usage();
return false;
}

mInputPath = args[argpos];
return true;
}

private void run(String[] args)
throws Exception {

if (!parseArguments(args)) {
System.exit(1);
}

FastbReader fastbReader = new FastbReader(new File(mInputPath));
try {
if (mIdListFilePath != null) {
LineNumberReader reader = new LineNumberReader(new FileReader(mIdListFilePath));
while (true) {
String line = reader.readLine();
if (line == null) {
reader.close();
break;
}
Integer id = parseReadId(line);
if (id == null) {
continue;
}
if (id < 0 || id >= fastbReader.getSequenceCount()) {
System.out.println("ERROR: Illegal sequence id: " + id);
System.exit(1);
}
String sequence = fastbReader.readSequence(id);
System.out.println(">" + id);
System.out.println(sequence);
}
} else {
int id = 0;
while (fastbReader.hasNext()) {
String sequence = fastbReader.next();
System.out.println(">" + id);
System.out.println(sequence);
id++;
}
}
} finally {
fastbReader.close();
}
}

private Integer parseReadId(String line) {
String text = line.trim();
if (text.length() == 0 || text.charAt(0) == '#') {
return null;
}
String token = text.split("\\s+")[0];
Integer id = null;
try {
id = new Integer(token);
} catch (NumberFormatException exc) {
System.out.println("ERROR: Invalid sequence id: " + token);
System.exit(1);
}
return id;
}
}
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