X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmsa_compactor.java;h=33254a57efd31db447a697e38cdd51c7c06272b0;hb=90e29ddfe15f6c44f3e3ba419a67c3e267e279bd;hp=0f1b961e19ba3c7ccdb1f1aec66fab934a428dc1;hpb=b1a74bd076c917d428002284a53a2c6f390226fb;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 0f1b961..33254a5 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -9,47 +9,51 @@ 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.Msa.MSA_FORMAT; import org.forester.msa.MsaMethods; +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 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 = "2012.07.11"; - 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 = "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 DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn"; + final static private String PRG_NAME = "msa_compactor"; + final static private String PRG_DESC = "multiple sequnce aligment compactor"; + final static private String PRG_VERSION = "0.01"; + final static private String PRG_DATE = "140314"; + 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 ) ) { + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( cla.getNumberOfNames() != 2 ) ) { printHelp(); System.exit( 0 ); } final File in = cla.getFile( 0 ); + final File out = cla.getFile( 1 ); int worst_remove = -1; double av = -1; int length = -1; - final int step = 5; + int step = 1; boolean realign = false; - // int to = 0; - // int window = 0; - // int step = 0; + boolean norm = true; 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 ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); @@ -63,9 +67,15 @@ public class msa_compactor { if ( cla.isOptionSet( LENGTH_OPTION ) ) { length = cla.getOptionValueAsInt( LENGTH_OPTION ); } + if ( cla.isOptionSet( STEP_OPTION ) ) { + step = cla.getOptionValueAsInt( STEP_OPTION ); + } if ( cla.isOptionSet( REALIGN_OPTION ) ) { realign = true; } + if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) { + norm = false; + } // else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) { // step = cla.getOptionValueAsInt( STEP_OPTION ); // window = cla.getOptionValueAsInt( WINDOW_OPTION ); @@ -82,23 +92,21 @@ public class msa_compactor { else { msa = GeneralMsaParser.parse( is ); } - System.out.println( msa.toString() ); - System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).arithmeticMean() ); MsaCompactor mc = null; if ( worst_remove > 0 ) { - mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign ); + mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign, norm ); } else if ( av > 0 ) { - mc = MsaCompactor.reduceGapAverage( msa, av, step, realign ); + mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50 ); } else if ( length > 0 ) { mc = MsaCompactor.reduceLength( msa, length, step, realign ); } - System.out.println( mc.getMsa().toString() ); - System.out.println( MsaMethods.calcBasicGapinessStatistics( mc.getMsa() ).arithmeticMean() ); + System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) ); for( final String id : mc.getRemovedSeqIds() ) { System.out.println( id ); } + mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" ); } catch ( final Exception e ) { e.printStackTrace(); @@ -120,11 +128,8 @@ public class msa_compactor { 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 sequences to remove" ); + System.out.println( " -" + REALIGN_OPTION + " to realign using " ); System.out.println(); System.out.println(); System.out.println();