X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmsa_compactor.java;h=45f66c102d87ec8d5d4186fadaf0f116c7ca29d4;hb=93f740ca4fbd156ba93b07b8e43112f392645c1d;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..45f66c1 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; @@ -9,95 +32,133 @@ 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.MsaMethods; +import org.forester.msa.MsaInferrer; +import org.forester.msa_compactor.MsaCompactor; import org.forester.util.CommandLineArguments; 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 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 = "phylosoft@gmail.com"; + 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; 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 ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); } + Msa msa = null; + final FileInputStream is = new FileInputStream( in ); + if ( FastaParser.isLikelyFasta( in ) ) { + msa = FastaParser.parseMsa( is ); + } + else { + msa = GeneralMsaParser.parse( is ); + } 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 ); } - else { - msa = GeneralMsaParser.parse( is ); + if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) { + norm = false; + } + if ( realign ) { + if ( ForesterUtil.isEmpty( path_to_mafft ) ) { + path_to_mafft = MsaCompactor.guessPathToMafft(); + } + checkPathToMafft( path_to_mafft ); } - MsaCompactor mc = null; 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, realign, norm, path_to_mafft ); } } catch ( final Exception e ) { @@ -106,6 +167,21 @@ 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 +190,26 @@ 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)" ); + System.out.println( " -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment ); System.out.println(); System.out.println(); System.out.println();