forester/java/src/org/forester/application/msa_compactor.java

   1
   2 package org.forester.application;
   3
   4 import java.io.File;
   5 import java.io.FileInputStream;
   6 import java.util.ArrayList;
   7 import java.util.List;
   8
   9 import org.forester.io.parsers.FastaParser;
  10 import org.forester.io.parsers.GeneralMsaParser;
  11 import org.forester.msa.Msa;
  12 import org.forester.msa.MsaInferrer;
  13 import org.forester.msa.Msa.MSA_FORMAT;
  14 import org.forester.msa.MsaMethods;
  15 import org.forester.msa_compactor.MsaCompactor;
  16 import org.forester.util.CommandLineArguments;
  17 import org.forester.util.ForesterUtil;
  18
  19 public class msa_compactor {
  20
  21     final static private String HELP_OPTION_1                          = "help";
  22     final static private String HELP_OPTION_2                          = "h";
  23     final static private String REMOVE_WORST_OFFENDERS_OPTION          = "w";
  24     final static private String AV_GAPINESS_OPTION                     = "a";
  25     final static private String STEP_OPTION                            = "s";
  26     final static private String LENGTH_OPTION                          = "l";
  27     final static private String REALIGN_OPTION                         = "r";
  28     final static private String PATH_TO_MAFFT_OPTION                   = "mafft";
  29     final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
  30     final static private String PRG_NAME                               = "msa_compactor";
  31     final static private String PRG_DESC                               = "multiple sequnce aligment compactor";
  32     final static private String PRG_VERSION                            = "0.01";
  33     final static private String PRG_DATE                               = "140314";
  34     final static private String E_MAIL                                 = "phylosoft@gmail.com";
  35     final static private String WWW                                    = "https://sites.google.com/site/cmzmasek/home/software/forester";
  36
  37     public static void main( final String args[] ) {
  38         try {
  39             final CommandLineArguments cla = new CommandLineArguments( args );
  40             if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( cla.getNumberOfNames() != 2 ) ) {
  41                 printHelp();
  42                 System.exit( 0 );
  43             }
  44             final File in = cla.getFile( 0 );
  45             final File out = cla.getFile( 1 );
  46             int worst_remove = -1;
  47             double av = -1;
  48             int length = -1;
  49             int step = 1;
  50             boolean realign = false;
  51             boolean norm = true;
  52             String path_to_mafft = null;
  53             final List<String> allowed_options = new ArrayList<String>();
  54             allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION );
  55             allowed_options.add( AV_GAPINESS_OPTION );
  56             allowed_options.add( LENGTH_OPTION );
  57             allowed_options.add( REALIGN_OPTION );
  58             allowed_options.add( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION );
  59             allowed_options.add( STEP_OPTION );
  60             allowed_options.add( PATH_TO_MAFFT_OPTION );
  61             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
  62             if ( dissallowed_options.length() > 0 ) {
  63                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
  64             }
  65             if ( cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) {
  66                 worst_remove = cla.getOptionValueAsInt( REMOVE_WORST_OFFENDERS_OPTION );
  67             }
  68             if ( cla.isOptionSet( AV_GAPINESS_OPTION ) ) {
  69                 av = cla.getOptionValueAsDouble( AV_GAPINESS_OPTION );
  70             }
  71             if ( cla.isOptionSet( LENGTH_OPTION ) ) {
  72                 length = cla.getOptionValueAsInt( LENGTH_OPTION );
  73             }
  74             if ( cla.isOptionSet( STEP_OPTION ) ) {
  75                 step = cla.getOptionValueAsInt( STEP_OPTION );
  76             }
  77             if ( cla.isOptionSet( REALIGN_OPTION ) ) {
  78                 realign = true;
  79             }
  80             if ( cla.isOptionSet( PATH_TO_MAFFT_OPTION ) ) {
  81                 if ( !realign ) {
  82                     ForesterUtil.fatalError( PRG_NAME, "no need to indicate path to MAFFT without realigning" );
  83                 }
  84                 path_to_mafft = cla.getOptionValueAsCleanString( PATH_TO_MAFFT_OPTION );
  85             }
  86             if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) {
  87                 norm = false;
  88             }
  89             //            else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) {
  90             //                step = cla.getOptionValueAsInt( STEP_OPTION );
  91             //                window = cla.getOptionValueAsInt( WINDOW_OPTION );
  92             //            }
  93             //            else {
  94             //                printHelp();
  95             //                System.exit( 0 );
  96             //            }
  97
  98             if ( realign ) {
  99                 if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
 100                     path_to_mafft = MsaCompactor.guessPathToMafft();
 101                 }
 102                 checkPathToMafft( path_to_mafft );
 103             }
 104
 105
 106             Msa msa = null;
 107             final FileInputStream is = new FileInputStream( in );
 108             if ( FastaParser.isLikelyFasta( in ) ) {
 109                 msa = FastaParser.parseMsa( is );
 110             }
 111             else {
 112                 msa = GeneralMsaParser.parse( is );
 113             }
 114
 115
 116
 117             MsaCompactor mc = null;
 118             if ( worst_remove > 0 ) {
 119                 mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign, norm, path_to_mafft );
 120             }
 121             else if ( av > 0 ) {
 122                 mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50, path_to_mafft );
 123             }
 124             else if ( length > 0 ) {
 125                 mc = MsaCompactor.reduceLength( msa, length, step, realign, path_to_mafft );
 126             }
 127             System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
 128             for( final String id : mc.getRemovedSeqIds() ) {
 129                 System.out.println( id );
 130             }
 131             mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );
 132         }
 133         catch ( final Exception e ) {
 134             e.printStackTrace();
 135             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
 136         }
 137     }
 138
 139     private static void checkPathToMafft( String path_to_mafft ) {
 140         if ( !ForesterUtil.isEmpty( path_to_mafft ) && MsaInferrer.isInstalled( path_to_mafft ) ) {
 141             ForesterUtil.programMessage( PRG_NAME, "using MAFFT at \"" + path_to_mafft + "\""  );
 142         }
 143         else {
 144             if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
 145                 ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable found, use -\"" + PATH_TO_MAFFT_OPTION + "=<path to MAFFT>\" option" );
 146             }
 147             else {
 148                 ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \""  + path_to_mafft + "\""  );
 149             }
 150         }
 151     }
 152
 153     private static void printHelp() {
 154         ForesterUtil.printProgramInformation( PRG_NAME,
 155                                               PRG_DESC,
 156                                               PRG_VERSION,
 157                                               PRG_DATE,
 158                                               E_MAIL,
 159                                               WWW,
 160                                               ForesterUtil.getForesterLibraryInformation() );
 161         final String path_to_mafft = MsaCompactor.guessPathToMafft();
 162         String mafft_comment;
 163         if ( !ForesterUtil.isEmpty( path_to_mafft ) ) {
 164             mafft_comment = " (" + path_to_mafft + ")";
 165         }
 166         else {
 167             mafft_comment = " (no path to MAFFT found, use -\"" + PATH_TO_MAFFT_OPTION + "=<path to MAFFT>\" option";
 168         }
 169
 170         System.out.println( "Usage:" );
 171         System.out.println();
 172         System.out.println( PRG_NAME + " <options> <msa input file>" );
 173         System.out.println();
 174         System.out.println( " options: " );
 175         System.out.println();
 176         System.out.println( "   -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>  number of sequences to remove" );
 177         System.out.println( "   -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment );
 178         System.out.println();
 179         System.out.println();
 180         System.out.println();
 181     }
 182 }