X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmsa_compactor.java;h=0a7e386b13025544abc396bef7a78095657a7399;hb=51045a46f54b0cdd39f1e30a06993148e61abde7;hp=5f0140871d6c817dd848d9ddde448244f486b293;hpb=764e1546f1bcc4f6b52be283bdd801372ed2ee54;p=jalview.git diff --git a/forester/java/src/org/forester/application/msa_compactor.java b/forester/java/src/org/forester/application/msa_compactor.java index 5f01408..0a7e386 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -1,3 +1,26 @@ +// $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.application; @@ -8,96 +31,247 @@ import java.util.List; import org.forester.io.parsers.FastaParser; import org.forester.io.parsers.GeneralMsaParser; -import org.forester.msa.Msa; -import org.forester.msa.MsaCompactor; +import org.forester.msa.DeleteableMsa; +import org.forester.msa.Msa.MSA_FORMAT; +import org.forester.msa.MsaInferrer; import org.forester.msa.MsaMethods; +import org.forester.msa_compactor.MsaCompactor; import org.forester.util.CommandLineArguments; +import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterUtil; public class msa_compactor { - final static private String HELP_OPTION_1 = "help"; - final static private String HELP_OPTION_2 = "h"; - final static private String REMOVE_WORST_OFFENDERS_OPTION = "w"; - final static private String AV_GAPINESS_OPTION = "a"; - final static private String STEP_OPTION = "s"; - final static private String LENGTH_OPTION = "l"; - final static private String REALIGN_OPTION = "r"; - final static private String PRG_NAME = "msa_compactor"; - final static private String PRG_DESC = "multiple sequnce aligment compactor"; - final static private String PRG_VERSION = "0.90"; - final static private String PRG_DATE = "2012.07.13"; - final static private String E_MAIL = "phylosoft@gmail.com"; - final static private String WWW = "www.phylosoft.org/forester/"; + final static private String HELP_OPTION_1 = "help"; + final static private String HELP_OPTION_2 = "h"; + final static private String REMOVE_WORST_OFFENDERS_OPTION = "r"; + final static private String AV_GAPINESS_OPTION = "g"; + final static private String STEP_OPTION = "s"; + final static private String LENGTH_OPTION = "l"; + final static private String REALIGN_OPTION = "a"; + // + final static private String STEP_FOR_DIAGNOSTICS_OPTION = "sd"; + final static private String MIN_LENGTH_OPTION = "ml"; + final static private String GAP_RATIO_LENGTH_OPTION = "gr"; + final static private String REPORT_ALN_MEAN_IDENTITY = "q"; + final static private String OUTPUT_FORMAT_PHYLIP_OPTION = "f"; + final static private String OUTPUT_REMOVED_SEQS_OPTION = "ro"; + final static private String MAFFT_OPTIONS = "mo"; + // + final static private String PATH_TO_MAFFT_OPTION = "mafft"; + final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn"; + final static private String PRG_NAME = "msa_compactor"; + final static private String PRG_DESC = "multiple sequence aligment compactor"; + final static private String PRG_VERSION = "0.01"; + final static private String PRG_DATE = "140316"; + final static private String E_MAIL = "czmasek@sanfordburham.org"; + final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; public static void main( final String args[] ) { try { final CommandLineArguments cla = new CommandLineArguments( args ); - if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( cla.getNumberOfNames() != 2 ) ) { + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) + || ( ( cla.getNumberOfNames() < 1 ) || ( cla.getNumberOfNames() > 2 ) ) ) { printHelp(); System.exit( 0 ); } final File in = cla.getFile( 0 ); - final File out = cla.getFile( 1 ); + File out = null; + if ( cla.getNumberOfNames() > 1 ) { + out = cla.getFile( 1 ); + } int worst_remove = -1; - double av = -1; + double av_gap = -1; int length = -1; - int step = 1; + int step = -1; boolean realign = false; + boolean norm = true; + String path_to_mafft = null; + int step_for_diagnostics = -1; + int min_length = -1; + double gap_ratio = -1; + boolean report_aln_mean_identity = false; + MSA_FORMAT output_format = MSA_FORMAT.FASTA; + File removed_seqs_out_base = null; + String mafft_options = "--auto"; final List allowed_options = new ArrayList(); allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION ); allowed_options.add( AV_GAPINESS_OPTION ); allowed_options.add( LENGTH_OPTION ); allowed_options.add( REALIGN_OPTION ); + allowed_options.add( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ); allowed_options.add( STEP_OPTION ); + allowed_options.add( PATH_TO_MAFFT_OPTION ); + allowed_options.add( STEP_FOR_DIAGNOSTICS_OPTION ); + allowed_options.add( MIN_LENGTH_OPTION ); + allowed_options.add( GAP_RATIO_LENGTH_OPTION ); + allowed_options.add( REPORT_ALN_MEAN_IDENTITY ); + allowed_options.add( OUTPUT_FORMAT_PHYLIP_OPTION ); + allowed_options.add( OUTPUT_REMOVED_SEQS_OPTION ); + allowed_options.add( MAFFT_OPTIONS ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); } + DeleteableMsa msa = null; + final FileInputStream is = new FileInputStream( in ); + if ( FastaParser.isLikelyFasta( in ) ) { + msa = DeleteableMsa.createInstance( FastaParser.parseMsa( is ) ); + } + else { + msa = DeleteableMsa.createInstance( GeneralMsaParser.parse( is ) ); + } + final DescriptiveStatistics initial_msa_stats = MsaMethods.calculateEffectiveLengthStatistics( msa ); + System.out.println( initial_msa_stats.toString() ); if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) { worst_remove = cla.getOptionValueAsInt( REMOVE_WORST_OFFENDERS_OPTION ); + if ( ( worst_remove < 1 ) || ( worst_remove >= msa.getNumberOfSequences() - 1 ) ) { + ForesterUtil.fatalError( PRG_NAME, "number of worst offender sequences to remove is out of range: " + + worst_remove ); + } } if ( cla.isOptionSet( AV_GAPINESS_OPTION ) ) { - av = cla.getOptionValueAsDouble( AV_GAPINESS_OPTION ); + if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) { + printHelp(); + System.exit( 0 ); + } + av_gap = cla.getOptionValueAsDouble( AV_GAPINESS_OPTION ); + if ( ( av_gap < 0 ) || ( av_gap >= 1 ) ) { + ForesterUtil.fatalError( PRG_NAME, "target gap-ratio is out of range: " + av_gap ); + } } if ( cla.isOptionSet( LENGTH_OPTION ) ) { + if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) || cla.isOptionSet( AV_GAPINESS_OPTION ) ) { + printHelp(); + System.exit( 0 ); + } length = cla.getOptionValueAsInt( LENGTH_OPTION ); + if ( ( length < 2 ) || ( length >= msa.getLength() ) ) { + ForesterUtil.fatalError( PRG_NAME, "target length is out of range: " + length ); + } } if ( cla.isOptionSet( STEP_OPTION ) ) { step = cla.getOptionValueAsInt( STEP_OPTION ); + if ( ( step < 1 ) + || ( ( step > msa.getNumberOfSequences() ) || ( ( worst_remove > 0 ) && ( step > worst_remove ) ) ) ) { + ForesterUtil.fatalError( PRG_NAME, "value for step is out of range: " + step ); + } } if ( cla.isOptionSet( REALIGN_OPTION ) ) { realign = true; } - // else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) { - // step = cla.getOptionValueAsInt( STEP_OPTION ); - // window = cla.getOptionValueAsInt( WINDOW_OPTION ); - // } - // else { - // printHelp(); - // System.exit( 0 ); - // } - Msa msa = null; - final FileInputStream is = new FileInputStream( in ); - if ( FastaParser.isLikelyFasta( in ) ) { - msa = FastaParser.parseMsa( is ); + if ( cla.isOptionSet( PATH_TO_MAFFT_OPTION ) ) { + if ( !realign ) { + ForesterUtil.fatalError( PRG_NAME, "no need to indicate path to MAFFT without realigning" ); + } + path_to_mafft = cla.getOptionValueAsCleanString( PATH_TO_MAFFT_OPTION ); + } + if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) { + norm = false; + } + // + if ( cla.isOptionSet( STEP_FOR_DIAGNOSTICS_OPTION ) ) { + step_for_diagnostics = cla.getOptionValueAsInt( STEP_FOR_DIAGNOSTICS_OPTION ); + if ( ( step_for_diagnostics < 1 ) + || ( ( step_for_diagnostics > msa.getNumberOfSequences() ) || ( ( worst_remove > 0 ) && ( step_for_diagnostics > worst_remove ) ) ) ) { + ForesterUtil.fatalError( PRG_NAME, "value for diagnostic step is out of range: " + + step_for_diagnostics ); + } + } + if ( cla.isOptionSet( MIN_LENGTH_OPTION ) ) { + min_length = cla.getOptionValueAsInt( MIN_LENGTH_OPTION ); + if ( ( min_length < 2 ) || ( min_length > initial_msa_stats.getMax() ) ) { + ForesterUtil.fatalError( PRG_NAME, "value for minimal sequence length is out of range: " + + min_length ); + } + } + if ( cla.isOptionSet( MIN_LENGTH_OPTION ) ) { + gap_ratio = cla.getOptionValueAsDouble( GAP_RATIO_LENGTH_OPTION ); + if ( ( gap_ratio < 0 ) || ( gap_ratio > 1 ) ) { + ForesterUtil.fatalError( PRG_NAME, "gap ratio is out of range: " + gap_ratio ); + } + } + if ( cla.isOptionSet( REPORT_ALN_MEAN_IDENTITY ) ) { + report_aln_mean_identity = true; + } + if ( cla.isOptionSet( OUTPUT_FORMAT_PHYLIP_OPTION ) ) { + output_format = MSA_FORMAT.PHYLIP; + } + if ( cla.isOptionSet( OUTPUT_REMOVED_SEQS_OPTION ) ) { + String s = cla.getOptionValueAsCleanString( OUTPUT_REMOVED_SEQS_OPTION ); + removed_seqs_out_base = new File( s ); + } + if ( realign ) { + if ( ForesterUtil.isEmpty( path_to_mafft ) ) { + path_to_mafft = MsaCompactor.guessPathToMafft(); + } + checkPathToMafft( path_to_mafft ); + if ( cla.isOptionSet( MAFFT_OPTIONS ) ) { + mafft_options = cla.getOptionValueAsCleanString( MAFFT_OPTIONS ); + if ( ForesterUtil.isEmpty( mafft_options ) || mafft_options.length() < 3 ) { + ForesterUtil.fatalError( PRG_NAME, "gap ratio is out of range: " + gap_ratio ); + } + } + } + ForesterUtil.printProgramInformation( PRG_NAME, + PRG_DESC, + PRG_VERSION, + PRG_DATE, + E_MAIL, + WWW, + ForesterUtil.getForesterLibraryInformation() ); + // + System.out.println( "Input MSA: " + in ); + if ( out != null ) { + System.out.println( "Output : " + out ); } else { - msa = GeneralMsaParser.parse( is ); + System.out.println( "Output : n/a" ); + } + if ( removed_seqs_out_base != null ) { + System.out.println( "Write removed sequences to : " + removed_seqs_out_base ); + } + if ( worst_remove > 0 ) { + System.out.println( ": " + worst_remove ); + } + else if ( av_gap > 0 ) { + System.out.println( ": " + av_gap ); + } + else if ( length > 0 ) { + System.out.println( ": " + length ); + } + if ( out != null || removed_seqs_out_base != null ) { + System.out.println( "Output format: " + ( output_format == MSA_FORMAT.FASTA ? "fasta" : "phylip" ) ); } - MsaCompactor mc = null; + System.out.println( "Step for output and re-aligning) : " + step ); + System.out.println( "Step for dia: " + step_for_diagnostics ); + System.out.println( "Step for diagnostics reports: " + report_aln_mean_identity ); + if ( !norm ) { + System.out.println( "Normalize: " + norm ); + } + System.out.println( "Realign: " + realign ); + if ( realign ) { + System.out.println( "MAFFT options: " + mafft_options ); + } + if ( min_length > -1 ) { + System.out.println( "Minimal effective sequence length: " + min_length ); + } + if ( gap_ratio > -1 ) { + System.out.println( ": " + gap_ratio ); + } + // if ( worst_remove > 0 ) { - mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign ); + MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out ); } - else if ( av > 0 ) { - mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50 ); + else if ( av_gap > 0 ) { + MsaCompactor.reduceGapAverage( msa, av_gap, step, realign, norm, path_to_mafft, out ); } else if ( length > 0 ) { - mc = MsaCompactor.reduceLength( msa, length, step, realign ); + // TODO if < shortest seq -> error + MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out ); } - System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) ); - for( final String id : mc.getRemovedSeqIds() ) { - System.out.println( id ); + else { + MsaCompactor.chart( msa, step, realign, norm, path_to_mafft ); } } catch ( final Exception e ) { @@ -106,6 +280,21 @@ public class msa_compactor { } } + private static void checkPathToMafft( final String path_to_mafft ) { + if ( !ForesterUtil.isEmpty( path_to_mafft ) && MsaInferrer.isInstalled( path_to_mafft ) ) { + ForesterUtil.programMessage( PRG_NAME, "using MAFFT at \"" + path_to_mafft + "\"" ); + } + else { + if ( ForesterUtil.isEmpty( path_to_mafft ) ) { + ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable found, use -\"" + PATH_TO_MAFFT_OPTION + + "=\" option" ); + } + else { + ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \"" + path_to_mafft + "\"" ); + } + } + } + private static void printHelp() { ForesterUtil.printProgramInformation( PRG_NAME, PRG_DESC, @@ -114,17 +303,38 @@ public class msa_compactor { E_MAIL, WWW, ForesterUtil.getForesterLibraryInformation() ); + final String path_to_mafft = MsaCompactor.guessPathToMafft(); + String mafft_comment; + if ( !ForesterUtil.isEmpty( path_to_mafft ) ) { + mafft_comment = " (using " + path_to_mafft + ")"; + } + else { + mafft_comment = " (no path to MAFFT found, use -\"" + PATH_TO_MAFFT_OPTION + "=\" option"; + } System.out.println( "Usage:" ); System.out.println(); - System.out.println( PRG_NAME + " " ); + System.out.println( PRG_NAME + " " ); System.out.println(); System.out.println( " options: " ); System.out.println(); - // System.out.println( " -" + FROM_OPTION + "=: from (msa column)" ); - // System.out.println( " -" + TO_OPTION + "=: to (msa column)" ); - // System.out.println( " or" ); - // System.out.println( " -" + WINDOW_OPTION + "=: window size (msa columns)" ); - System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION + "=: step size (msa columns)" ); + System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION + + "= number of worst offender sequences to remove" ); + System.out.println( " -" + LENGTH_OPTION + "= target MSA length" ); + System.out.println( " -" + AV_GAPINESS_OPTION + "= target gap-ratio (0.0-1.0)" ); + System.out.println( " -" + STEP_OPTION + "= step for output and re-aligning (default: 1)" ); + System.out.println( " -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment ); + System.out.println( " -" + MAFFT_OPTIONS + "= options for MAFFT (default: --auto)" ); + System.out.println( " -" + STEP_FOR_DIAGNOSTICS_OPTION + + "= step for diagnostics reports (default: 1)" ); + System.out.println( " -" + MIN_LENGTH_OPTION + + "= minimal effecive sequence length (for deleting of shorter sequences)" ); + System.out.println( " -" + GAP_RATIO_LENGTH_OPTION + + "= maximal allowed gap ratio per column (for deleting of columms) (0.0-1.0)" ); + System.out.println( " -" + REPORT_ALN_MEAN_IDENTITY + + " to report mean identity diagnostic (not recommended for very large alignments)" ); + System.out.println( " -" + OUTPUT_FORMAT_PHYLIP_OPTION + + " to write output alignments in phylip format instead of fasta" ); + System.out.println( " -" + OUTPUT_REMOVED_SEQS_OPTION + "= to output the removed sequences" ); System.out.println(); System.out.println(); System.out.println();