+++ /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 MsaCompactor {
-
- 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 MsaCompactor( 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 MsaCompactor 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 MsaCompactor mc = new MsaCompactor( 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 MsaCompactor 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 MsaCompactor mc = new MsaCompactor( 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 MsaCompactor 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 MsaCompactor mc = new MsaCompactor( msa );
- if ( realign ) {
- mc.setPathToMafft( path_to_mafft );
- }
- mc.setOutFileBase( out );
- mc.removeViaLength( length, step, realign, norm, true );
- return mc;
- }
-
- public final static MsaCompactor 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 MsaCompactor mc = new MsaCompactor( 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