Arachne's alignment pile, more or less. Can accept sequences with alignments (cigars) and generate nice alignment pile plot with indels
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@149 348d0f76-0448-11de-a6fe-93d51630548a
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asivache
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package org.broadinstitute.sting.indels;
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import java.util.List;
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import java.util.ArrayList;
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import net.sf.samtools.*;
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public class SequencePile {
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private List<MSAColumn> mSeqGrid;
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private StringBuffer mRefGrid;
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private int mDepth;
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private List<Boolean> mSeqRC;
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public SequencePile(String ref) {
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mRefGrid = new StringBuffer( ref );
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mSeqGrid = new ArrayList<MSAColumn>();
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for ( int i = 0 ; i < mRefGrid.length(); i++ ) {
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mSeqGrid.add(new MSAColumn());
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}
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mDepth = 0;
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mSeqRC = new ArrayList<Boolean>();
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}
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/** Adds to the pile nucleotide sequence <seq> that aligns at zero-based position <refpos>
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relative to the original reference stretch the pile is built upon; the detailed alignment
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of the sequence to that reference stretch is specified by the <cigar>.
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@param seq nucleotide sequence
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@param isRC true indicates that RC of the <seq> is being aligned
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@param cigar specification of the alignment of the sequence <seq> to the reference
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@param refpos 0-based position of the alignment with respect to the original stretch of the reference
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that was passed to the pile's constructor. Either <pos> or <pos>+sequence_length can be outside of
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the pile's boundaries, the SequencePile class will deal with such situations correctly.
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*/
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public void addAlignedSequence(String seq, boolean isRC, Cigar cigar, int refpos) {
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String alignedSeq = seq ;
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// if ( isRC ) {
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// alignedSeq = ReverseComplement(seq);
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// } else alignedSeq = seq;
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mSeqRC.add(isRC);
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int pos = 0; // actual position on the grid (reference can have insertions)
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for ( int i = 0 ; i < refpos ; i++ ) { // i is the position on the original reference
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// if we got some insertions on the reference prior to refpos, we need to take care of them:
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while( mRefGrid.charAt(pos) == '+' ) {
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mSeqGrid.get(pos).add(' ');
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pos++;
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}
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mSeqGrid.get(pos).add(' '); // fill with ' ' to the left of the read
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pos++;
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}
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// we reached start position of the alignment
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int readpos = 0; // position on the read
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for ( int i = 0 ; i < cigar.numCigarElements() ; i++ ) {
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final CigarElement ce = cigar.getCigarElement(i);
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switch(ce.getOperator()) {
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case I: // read has an insertion
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for ( int j = 0 ; j < ce.getLength() ; j++ ) {
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if ( pos >= mRefGrid.length() ) break;
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if ( pos >= 0 ) {
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if ( mRefGrid.charAt(pos) !='+' ) { // there was no insertion here yet: add it now!
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mRefGrid.insert(pos, '+');
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MSAColumn c = new MSAColumn();
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for ( int k = 0 ; k < mDepth ; k++ ) {
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if ( mSeqGrid.get(pos-1).charAt(k) == ' ') c.add(' ');
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else c.add('*');
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}
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mSeqGrid.add(pos, c);
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}
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try {
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mSeqGrid.get(pos).add(alignedSeq.charAt(readpos));
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} catch (IllegalArgumentException e) {
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throw new IllegalArgumentException(e.getMessage()+": "+seq);
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}
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}
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readpos++;
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pos++;
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}
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break;
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case D: // read has a deletion
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for ( int j = 0 ; j < ce.getLength() ; j++ ) {
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while( pos < mRefGrid.length() && mRefGrid.charAt(pos) == '+' ) { // skip insertions on the ref
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mSeqGrid.get(pos).add('*');
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pos++;
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}
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if ( pos >= mRefGrid.length() ) break;
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mSeqGrid.get(pos).add('-'); // mark deletion
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pos++;
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}
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break;
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case M:
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for ( int j = 0 ; j < ce.getLength() ; j++ ) {
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// if ref has an insertion, but the read does not: skip the insertion and continue with "gapless" alignment
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while( pos < mRefGrid.length() && mRefGrid.charAt(pos) == '+' ) {
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mSeqGrid.get(pos).add('*');
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pos++;
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}
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if ( pos >= mRefGrid.length() ) break;
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try {
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mSeqGrid.get(pos).add(alignedSeq.charAt(readpos));
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} catch (IllegalArgumentException e) {
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throw new IllegalArgumentException(e.getMessage()+": "+seq);
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}
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pos++;
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readpos++;
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}
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break;
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default : throw new IllegalArgumentException("Unknown cigar element");
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}
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}
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for ( int i = pos ; i < mRefGrid.length() ; i++ ) { // i is the position on the modified reference
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mSeqGrid.get(i).add(' '); // fill with ' ' to the left of the read
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}
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mDepth++;
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}
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public String format() {
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StringBuffer b = new StringBuffer();
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b.append(" ");
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b.append(mRefGrid);
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b.append('\n');
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try {
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for ( int i = 0 ; i < mDepth; i++ ) {
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if ( mSeqRC.get(i).booleanValue() ) b.append("<-");
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else b.append("->");
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for ( int j = 0 ; j < mRefGrid.length() ; j++) {
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b.append(mSeqGrid.get(j).charAt(i));
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}
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b.append('\n');
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}
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} catch (Exception e) {}
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return b.toString();
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}
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private String ReverseComplement(String s) {
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StringBuffer b = new StringBuffer();
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char [] data = s.toCharArray();
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for ( int i = data.length - 1 ; i >= 0 ; i-- ) b.append(BaseComplement(data[i]));
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return b.toString();
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}
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private char BaseComplement(char b) {
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switch ( b ) {
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case 'A' : return 'T';
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case 'C': return 'G';
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case 'G': return 'C';
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case 'T': return 'A';
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default: throw new IllegalArgumentException(b + " is not a DNA base");
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}
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}
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public void colorprint() { colorprint(false); }
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public void colorprint(boolean printId) {
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if ( printId ) System.out.print(" ");
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else System.out.print(" ");
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System.out.println(mRefGrid);
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StringBuilder sb = new StringBuilder();
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java.util.Formatter frmt = new java.util.Formatter(sb);
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try {
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for ( int i = 0 ; i < mDepth; i++ ) {
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if ( printId ) {
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sb.delete(0,sb.length());
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frmt.format("%3d:", i);
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System.out.print(frmt.out().toString());
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}
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if ( mSeqRC.get(i).booleanValue() ) System.out.print("<-");
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else System.out.print("->");
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for ( int j = 0 ; j < mRefGrid.length() ; j++) {
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char seqbase = mSeqGrid.get(j).charAt(i);
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char refbase = mRefGrid.charAt(j);
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if ( isBase(refbase) && isBase(seqbase) && refbase != seqbase ) System.out.print("\033[31m"+seqbase+"\033[30m");
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else System.out.print(seqbase);
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}
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System.out.print('\n');
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}
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} catch (Exception e) {}
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}
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private boolean isBase(char b) {
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return ( b=='A' ||b == 'C' || b=='G' || b=='T' || b=='N');
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}
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}
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