--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2014 Christian M. Zmasek
+// Copyright (C) 2014 Sanford-Burnham Medical Research Institute
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+
+package org.forester.msa_compactor;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.Writer;
+import java.math.RoundingMode;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.forester.evoinference.distance.NeighborJoiningF;
+import org.forester.evoinference.distance.PairwiseDistanceCalculator;
+import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
+import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
+import org.forester.evoinference.tools.BootstrapResampler;
+import org.forester.msa.DeleteableMsa;
+import org.forester.msa.Mafft;
+import org.forester.msa.Msa;
+import org.forester.msa.Msa.MSA_FORMAT;
+import org.forester.msa.MsaInferrer;
+import org.forester.msa.MsaMethods;
+import org.forester.msa.ResampleableMsa;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.sequence.Sequence;
+import org.forester.tools.ConfidenceAssessor;
+import org.forester.util.ForesterUtil;
+
+public class MsaCompactor2 {
+
+ final private static NumberFormat NF_3 = new DecimalFormat( "#.###" );
+ final private static NumberFormat NF_4 = new DecimalFormat( "#.####" );
+ // private final String _maffts_opts = "--retree 1";
+ private final String _maffts_opts = "--auto";
+ private DeleteableMsa _msa;
+ private File _out_file_base;
+ private String _path_to_mafft;
+ private final SortedSet<String> _removed_seq_ids;
+ static {
+ NF_4.setRoundingMode( RoundingMode.HALF_UP );
+ NF_3.setRoundingMode( RoundingMode.HALF_UP );
+ }
+
+ private MsaCompactor2( final DeleteableMsa msa ) {
+ _msa = msa;
+ _removed_seq_ids = new TreeSet<String>();
+ }
+
+ final public Msa getMsa() {
+ return _msa;
+ }
+
+ final public SortedSet<String> getRemovedSeqIds() {
+ return _removed_seq_ids;
+ }
+
+ final public void setOutFileBase( final File out_file_base ) {
+ _out_file_base = out_file_base;
+ }
+
+ final public String writeMsa( final File outfile, final MSA_FORMAT format, final String suffix ) throws IOException {
+ final Double gr = MsaMethods.calcGapRatio( _msa );
+ final String s = outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_"
+ + ForesterUtil.roundToInt( gr * 100 );
+ writeMsa( s + suffix, format );
+ return s;
+ }
+
+ final int calcNonGapResidues( final Sequence seq ) {
+ int ng = 0;
+ for( int i = 0; i < seq.getLength(); ++i ) {
+ if ( !seq.isGapAt( i ) ) {
+ ++ng;
+ }
+ }
+ return ng;
+ }
+
+ Phylogeny pi( final String matrix ) {
+ final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, true, matrix );
+ final int seed = 15;
+ final int n = 100;
+ final ResampleableMsa resampleable_msa = new ResampleableMsa( _msa );
+ final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa.getLength(),
+ n,
+ seed );
+ final Phylogeny[] eval_phys = new Phylogeny[ n ];
+ for( int i = 0; i < n; ++i ) {
+ resampleable_msa.resample( resampled_column_positions[ i ] );
+ eval_phys[ i ] = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, resampleable_msa, false, null );
+ }
+ ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
+ PhylogenyMethods.extractFastaInformation( master_phy );
+ return master_phy;
+ }
+
+ private final GapContribution[] calcGapContribtions( final boolean normalize_for_effective_seq_length ) {
+ final double gappiness[] = calcGappiness();
+ final GapContribution stats[] = new GapContribution[ _msa.getNumberOfSequences() ];
+ for( int row = 0; row < _msa.getNumberOfSequences(); ++row ) {
+ stats[ row ] = new GapContribution( _msa.getIdentifier( row ) );
+ for( int col = 0; col < _msa.getLength(); ++col ) {
+ if ( !_msa.isGapAt( row, col ) ) {
+ stats[ row ].addToValue( gappiness[ col ] );
+ }
+ }
+ if ( normalize_for_effective_seq_length ) {
+ stats[ row ].divideValue( calcNonGapResidues( _msa.getSequence( row ) ) );
+ }
+ else {
+ stats[ row ].divideValue( _msa.getLength() );
+ }
+ }
+ return stats;
+ }
+
+ final private GapContribution[] calcGapContribtionsStats( final boolean norm ) {
+ final GapContribution stats[] = calcGapContribtions( norm );
+ Arrays.sort( stats );
+ return stats;
+ }
+
+ private final double[] calcGappiness() {
+ final int l = _msa.getLength();
+ final double gappiness[] = new double[ l ];
+ final int seqs = _msa.getNumberOfSequences();
+ for( int i = 0; i < l; ++i ) {
+ gappiness[ i ] = ( double ) MsaMethods.calcGapSumPerColumn( _msa, i ) / seqs;
+ }
+ return gappiness;
+ }
+
+ final private List<MsaProperties> chart( final int step,
+ final boolean realign,
+ final boolean norm,
+ final boolean verbose ) throws IOException, InterruptedException {
+ final GapContribution stats[] = calcGapContribtionsStats( norm );
+ final List<String> to_remove_ids = new ArrayList<String>();
+ final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
+ for( final GapContribution gap_gontribution : stats ) {
+ to_remove_ids.add( gap_gontribution.getId() );
+ }
+ if ( verbose ) {
+ printTableHeader();
+ }
+ int i = 0;
+ final int s = _msa.getNumberOfSequences();
+ final int x = ForesterUtil.roundToInt( s / 20.0 );
+ while ( _msa.getNumberOfSequences() > x ) {
+ final String id = to_remove_ids.get( i );
+ //~_msa = MsaMethods.removeSequence( _msa, id );
+ _msa.deleteRow( id );
+ if ( ( s < 500 ) || ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) ) {
+ removeGapColumns();
+ if ( realign && ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) ) {
+ realignWithMafft();
+ msa_props.add( new MsaProperties( _msa ) );
+ if ( verbose ) {
+ printMsaStats( id );
+ }
+ if ( verbose ) {
+ System.out.print( "(realigned)" );
+ }
+ }
+ else {
+ msa_props.add( new MsaProperties( _msa ) );
+ if ( verbose ) {
+ printMsaStats( id );
+ }
+ }
+ if ( verbose ) {
+ System.out.println();
+ }
+ }
+ ++i;
+ }
+ return msa_props;
+ }
+
+ private Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method,
+ final Msa msa,
+ final boolean write_matrix,
+ final String matrix_name ) {
+ BasicSymmetricalDistanceMatrix m = null;
+ switch ( pwd_distance_method ) {
+ case KIMURA_DISTANCE:
+ m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
+ break;
+ case POISSON_DISTANCE:
+ m = PairwiseDistanceCalculator.calcPoissonDistances( msa );
+ break;
+ case FRACTIONAL_DISSIMILARITY:
+ m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
+ break;
+ default:
+ throw new IllegalArgumentException( "invalid pwd method" );
+ }
+ if ( write_matrix ) {
+ try {
+ m.write( ForesterUtil.createBufferedWriter( matrix_name ) );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ }
+ final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
+ final Phylogeny phy = nj.execute( m );
+ return phy;
+ }
+
+ private StringBuilder msaStatsAsSB() {
+ final StringBuilder sb = new StringBuilder();
+ sb.append( _msa.getNumberOfSequences() );
+ sb.append( "\t" );
+ sb.append( _msa.getLength() );
+ sb.append( "\t" );
+ sb.append( NF_4.format( MsaMethods.calcGapRatio( _msa ) ) );
+ sb.append( "\t" );
+ sb.append( NF_4.format( MsaMethods.calculateIdentityRatio( 0, _msa.getLength() - 1, _msa ).arithmeticMean() ) );
+ return sb;
+ }
+
+ private final void printMsaStats( final String id ) {
+ System.out.print( ForesterUtil.pad( id, 20, ' ', false ) );
+ System.out.print( "\t" );
+ final StringBuilder sb = msaStatsAsSB();
+ System.out.print( sb );
+ System.out.print( "\t" );
+ }
+
+ final private void printMsaStatsWriteOutfileAndRealign( final boolean realign,
+ final boolean verbose,
+ final String id ) throws IOException, InterruptedException {
+ if ( realign ) {
+ realignWithMafft();
+ }
+ if ( verbose ) {
+ printMsaStats( id );
+ }
+ final String s = writeOutfile();
+ if ( verbose ) {
+ System.out.print( "-> " + s + ( realign ? "\t(realigned)" : "" ) );
+ }
+ }
+
+ final private void realignWithMafft() throws IOException, InterruptedException {
+ // final MsaInferrer mafft = Mafft
+ // .createInstance( "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft" );
+ final MsaInferrer mafft = Mafft.createInstance( _path_to_mafft );
+ final List<String> opts = new ArrayList<String>();
+ for( final String o : _maffts_opts.split( "\\s" ) ) {
+ opts.add( o );
+ }
+ _msa = DeleteableMsa.createInstance( mafft.infer( _msa.asSequenceList(), opts ) );
+ }
+
+ final private void removeGapColumns() {
+ _msa.deleteGapOnlyColumns();
+ }
+
+ final private void removeViaGapAverage( final double mean_gapiness,
+ final int step,
+ final boolean realign,
+ final boolean norm,
+ final boolean verbose ) throws IOException, InterruptedException {
+ final GapContribution stats[] = calcGapContribtionsStats( norm );
+ final List<String> to_remove_ids = new ArrayList<String>();
+ for( final GapContribution gap_gontribution : stats ) {
+ to_remove_ids.add( gap_gontribution.getId() );
+ }
+ if ( verbose ) {
+ printTableHeader();
+ }
+ int i = 0;
+ while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) {
+ final String id = to_remove_ids.get( i );
+ //`_msa = MsaMethods.removeSequence( _msa, id );
+ _msa.deleteRow( id );
+ removeGapColumns();
+ if ( ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) )
+ || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) {
+ printMsaStatsWriteOutfileAndRealign( realign, verbose, id );
+ }
+ else if ( verbose ) {
+ printMsaStats( id );
+ }
+ if ( verbose ) {
+ System.out.println();
+ }
+ ++i;
+ }
+ }
+
+ final private void removeViaLength( final int length,
+ final int step,
+ final boolean realign,
+ final boolean norm,
+ final boolean verbose ) throws IOException, InterruptedException {
+ final GapContribution stats[] = calcGapContribtionsStats( norm );
+ final List<String> to_remove_ids = new ArrayList<String>();
+ for( final GapContribution gap_gontribution : stats ) {
+ to_remove_ids.add( gap_gontribution.getId() );
+ }
+ if ( verbose ) {
+ printTableHeader();
+ }
+ int i = 0;
+ while ( _msa.getLength() > length ) {
+ final String id = to_remove_ids.get( i );
+ //~_msa = MsaMethods.removeSequence( _msa, id );
+ _msa.deleteRow( id );
+ removeGapColumns();
+ if ( ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) || ( _msa.getLength() <= length ) ) {
+ printMsaStatsWriteOutfileAndRealign( realign, verbose, id );
+ }
+ else if ( verbose ) {
+ printMsaStats( id );
+ }
+ if ( verbose ) {
+ System.out.println();
+ }
+ ++i;
+ }
+ }
+
+ final private void removeWorstOffenders( final int to_remove,
+ final int step,
+ final boolean realign,
+ final boolean norm,
+ final boolean verbose ) throws IOException, InterruptedException {
+ final GapContribution stats[] = calcGapContribtionsStats( norm );
+ final List<String> to_remove_ids = new ArrayList<String>();
+ for( int j = 0; j < to_remove; ++j ) {
+ to_remove_ids.add( stats[ j ].getId() );
+ _removed_seq_ids.add( stats[ j ].getId() );
+ }
+ if ( verbose ) {
+ printTableHeader();
+ }
+ for( int i = 0; i < to_remove_ids.size(); ++i ) {
+ final String id = to_remove_ids.get( i );
+ //~ _msa = MsaMethods.removeSequence( _msa, id );
+ _msa.deleteRow( id );
+ removeGapColumns();
+ if ( ( ( step > 0 ) && ( ( ( i + 1 ) % step ) == 0 ) ) || ( i == ( to_remove_ids.size() - 1 ) ) ) {
+ printMsaStatsWriteOutfileAndRealign( realign, verbose, id );
+ }
+ else if ( verbose ) {
+ printMsaStats( id );
+ }
+ if ( verbose ) {
+ System.out.println();
+ }
+ }
+ }
+
+ private void setPathToMafft( final String path_to_mafft ) {
+ _path_to_mafft = path_to_mafft;
+ }
+
+ final private void writeMsa( final String outfile, final MSA_FORMAT format ) throws IOException {
+ final Writer w = ForesterUtil.createBufferedWriter( outfile );
+ _msa.write( w, format );
+ w.close();
+ }
+
+ private String writeOutfile() throws IOException {
+ final String s = writeMsa( _out_file_base, MSA_FORMAT.PHYLIP, ".aln" );
+ //writeMsa( _out_file_base, MSA_FORMAT.FASTA, ".fasta" );
+ return s;
+ }
+
+ public final static MsaCompactor2 chart( final DeleteableMsa msa,
+ final int step,
+ final boolean realign,
+ final boolean norm,
+ final String path_to_mafft ) throws IOException, InterruptedException {
+ final int initial_number_of_seqs = msa.getNumberOfSequences();
+ final MsaCompactor2 mc = new MsaCompactor2( msa );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ }
+ final List<MsaProperties> msa_props = mc.chart( step, realign, norm, true );
+ Chart.display( msa_props, initial_number_of_seqs );
+ return mc;
+ }
+
+ // Returns null if not path found.
+ final public static String guessPathToMafft() {
+ String path;
+ if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) >= 0 ) {
+ path = "C:\\Program Files\\mafft-win\\mafft.bat";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ }
+ path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ path = "/usr/local/bin/mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ path = "/usr/bin/mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ path = "/bin/mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ path = "mafft";
+ if ( MsaInferrer.isInstalled( path ) ) {
+ return path;
+ }
+ return null;
+ }
+
+ public final static MsaCompactor2 reduceGapAverage( final DeleteableMsa msa,
+ final double max_gap_average,
+ final int step,
+ final boolean realign,
+ final boolean norm,
+ final String path_to_mafft,
+ final File out ) throws IOException, InterruptedException {
+ final MsaCompactor2 mc = new MsaCompactor2( msa );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ }
+ mc.setOutFileBase( out );
+ mc.removeViaGapAverage( max_gap_average, step, realign, norm, true );
+ return mc;
+ }
+
+ public final static MsaCompactor2 reduceLength( final DeleteableMsa msa,
+ final int length,
+ final int step,
+ final boolean realign,
+ final boolean norm,
+ final String path_to_mafft,
+ final File out ) throws IOException, InterruptedException {
+ final MsaCompactor2 mc = new MsaCompactor2( msa );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ }
+ mc.setOutFileBase( out );
+ mc.removeViaLength( length, step, realign, norm, true );
+ return mc;
+ }
+
+ public final static MsaCompactor2 removeWorstOffenders( final DeleteableMsa msa,
+ final int worst_offenders_to_remove,
+ final int step,
+ final boolean realign,
+ final boolean norm,
+ final String path_to_mafft,
+ final File out ) throws IOException, InterruptedException {
+ final MsaCompactor2 mc = new MsaCompactor2( msa );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ }
+ mc.setOutFileBase( out );
+ mc.removeWorstOffenders( worst_offenders_to_remove, step, realign, norm, true );
+ return mc;
+ }
+
+ private final static void printTableHeader() {
+ System.out.print( ForesterUtil.pad( "Id", 20, ' ', false ) );
+ System.out.print( "\t" );
+ System.out.print( "Seqs" );
+ System.out.print( "\t" );
+ System.out.print( "Length" );
+ System.out.print( "\t" );
+ System.out.print( "Gaps" );
+ System.out.print( "\t" );
+ System.out.print( "MSA qual" );
+ System.out.print( "\t" );
+ System.out.println();
+ }
+}
git://source.jalview.org / jalview.git / commitdiff