+// $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;
import java.io.File;
import java.io.FileInputStream;
+import java.io.IOException;
+import java.math.RoundingMode;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
import java.util.ArrayList;
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.DeleteableMsa;
import org.forester.msa.Msa.MSA_FORMAT;
-import org.forester.msa.MsaCompactor;
+import org.forester.msa.MsaInferrer;
import org.forester.msa.MsaMethods;
+import org.forester.msa_compactor.Chart;
+import org.forester.msa_compactor.MsaCompactor;
+import org.forester.msa_compactor.MsaProperties;
import org.forester.util.CommandLineArguments;
+import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
+
+/*
+java -cp C:\Users\czmasek\SOFTWARE_DEV\ECLIPSE\forester\java\fo
+rester.jar org.forester.application.msa_compactor Bcl-2_e1_20_mafft -t
+*/
+
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 = "0.01";
- final static private String PRG_DATE = "140221";
- final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
+ final private static NumberFormat NF_1 = new DecimalFormat( "0.#" );
+ final private static NumberFormat NF_4 = new DecimalFormat( "0.####" );
+ static {
+ NF_1.setRoundingMode( RoundingMode.HALF_UP );
+ NF_4.setRoundingMode( RoundingMode.HALF_UP );
+ }
+ 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 INFO_ONLY_OPTION = "i";
+ //
+ 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_ENTROPY = "e";
+ final static private String OUTPUT_FORMAT_OPTION = "f";
+ final static private String OUTPUT_REMOVED_SEQS_OPTION = "ro";
+ final static private String MAFFT_OPTIONS = "mo";
+ final static private String PERFORM_PHYLOGENETIC_INFERENCE = "t";
+ //
+ 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 = "0.3";
+ final static private String PRG_DATE = "140508";
+ 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;
boolean realign = false;
+ boolean normalize_for_effective_seq_length = true;
+ String path_to_mafft = null;
+ int step_for_diagnostics = 1;
+ int min_length = -1;
+ double gap_ratio = -1;
+ boolean report_entropy = false;
+ MSA_FORMAT output_format = MSA_FORMAT.FASTA;
+ File removed_seqs_out_base = null;
+ String mafft_options = "--auto";
+ boolean perform_phylogenetic_inference = false;
final List<String> allowed_options = new ArrayList<String>();
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_ENTROPY );
+ allowed_options.add( OUTPUT_FORMAT_OPTION );
+ allowed_options.add( OUTPUT_REMOVED_SEQS_OPTION );
+ allowed_options.add( MAFFT_OPTIONS );
+ allowed_options.add( PERFORM_PHYLOGENETIC_INFERENCE );
+ allowed_options.add( INFO_ONLY_OPTION );
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 );
+ if (cla.isOptionSet( INFO_ONLY_OPTION ) ) {
+ printInfo( in, msa, initial_msa_stats );
+ System.exit( 0 );
+ }
+
+ final boolean chart_only = ( !cla.isOptionSet( LENGTH_OPTION ) )
+ && ( !cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) )
+ && ( !cla.isOptionSet( AV_GAPINESS_OPTION ) && ( !cla.isOptionSet( MIN_LENGTH_OPTION ) ) );
+ if ( !chart_only && ( out == null ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "outfile file missing" );
+ }
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 >= msa.getLength() ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "target length is out of range [longer than MSA (" + msa.getLength()
+ + ")]: " + length );
+ }
+ else if ( length < initial_msa_stats.getMin() ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "target length is out of range [shorter than the shortest sequence ("
+ + initial_msa_stats.getMin() + ") ]: " + length );
+ }
+ }
+ if ( cla.isOptionSet( MIN_LENGTH_OPTION ) ) {
+ if ( cla.isOptionSet( LENGTH_OPTION ) || cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION )
+ || cla.isOptionSet( AV_GAPINESS_OPTION ) || cla.isOptionSet( STEP_OPTION )
+ || cla.isOptionSet( REALIGN_OPTION ) || cla.isOptionSet( PATH_TO_MAFFT_OPTION )
+ || cla.isOptionSet( STEP_FOR_DIAGNOSTICS_OPTION ) || cla.isOptionSet( REPORT_ENTROPY )
+ || cla.isOptionSet( OUTPUT_REMOVED_SEQS_OPTION )
+ || cla.isOptionSet( PERFORM_PHYLOGENETIC_INFERENCE ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ 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( 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 ) ) {
+ normalize_for_effective_seq_length = 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( GAP_RATIO_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_ENTROPY ) ) {
+ report_entropy = true;
+ }
+ if ( cla.isOptionSet( OUTPUT_FORMAT_OPTION ) ) {
+ final String fs = cla.getOptionValueAsCleanString( OUTPUT_FORMAT_OPTION );
+ if ( fs.equalsIgnoreCase( "p" ) ) {
+ output_format = MSA_FORMAT.PHYLIP;
+ }
+ else if ( fs.equalsIgnoreCase( "f" ) ) {
+ output_format = MSA_FORMAT.FASTA;
+ }
+ else if ( fs.equalsIgnoreCase( "n" ) ) {
+ output_format = MSA_FORMAT.NEXUS;
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "illegal or empty output format option: " + fs );
+ }
+ }
+ if ( cla.isOptionSet( OUTPUT_REMOVED_SEQS_OPTION ) ) {
+ final 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, "illegal or empty MAFFT options: " + mafft_options );
+ }
+ }
+ }
+ else if ( cla.isOptionSet( MAFFT_OPTIONS ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "no need to indicate MAFFT options without realigning" );
+ }
+ if ( cla.isOptionSet( PERFORM_PHYLOGENETIC_INFERENCE ) ) {
+ perform_phylogenetic_inference = true;
+ }
+ if ( chart_only ) {
+ if ( ( out != null ) || ( removed_seqs_out_base != null ) ) {
+ ForesterUtil
+ .fatalError( PRG_NAME,
+ "chart only, no outfile(s) produced, thus no need to indicate output file(s)" );
+ }
+ if ( !realign && cla.isOptionSet( STEP_OPTION ) ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "chart only, no re-aligning, thus no need to use step for output and re-aligning; use -"
+ + STEP_FOR_DIAGNOSTICS_OPTION + " instead" );
+ }
+ }
+ if ( perform_phylogenetic_inference ) {
+ if ( step_for_diagnostics != 1 ) {
+ ForesterUtil.fatalError( PRG_NAME,
+ "step for diagnostics reports needs to be set to 1 for tree calculation" );
+ }
+ }
+ printInfo( in, msa, initial_msa_stats );
+ if ( !chart_only ) {
+ System.out.println( "Output : " + out );
+ }
+
+ if ( removed_seqs_out_base != null ) {
+ System.out.println( "Write removed sequences to : " + removed_seqs_out_base );
}
- MsaCompactor mc = null;
if ( worst_remove > 0 ) {
- mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign );
+ System.out.println( "Number of worst offenders to remove : " + worst_remove );
+ }
+ if ( av_gap > 0 ) {
+ System.out.println( "Target gap-ratio : " + av_gap );
}
- else if ( av > 0 ) {
- mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50 );
+ if ( length > 0 ) {
+ System.out.println( "Target MSA length : " + length );
}
- else if ( length > 0 ) {
- mc = MsaCompactor.reduceLength( msa, length, step, realign );
+ if ( min_length > 1 ) {
+ System.out.println( "Minimal effective sequence length : " + min_length );
}
- System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
- for( final String id : mc.getRemovedSeqIds() ) {
- System.out.println( id );
+ if ( gap_ratio > -1 ) {
+ System.out.println( "Maximum allowed gap ratio per column : " + gap_ratio );
}
- mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );
+ if ( ( out != null ) || ( removed_seqs_out_base != null ) ) {
+ System.out.print( "Output format : " );
+ if ( output_format == MSA_FORMAT.FASTA ) {
+ System.out.println( "fasta" );
+ }
+ else if ( output_format == MSA_FORMAT.PHYLIP ) {
+ System.out.println( "phylip" );
+ }
+ else if ( output_format == MSA_FORMAT.NEXUS ) {
+ System.out.println( "nexus" );
+ }
+ }
+ if ( min_length == -1 ) {
+ if ( chart_only && !realign ) {
+ System.out.println( "Step for output and re-aligning : n/a" );
+ }
+ else {
+ if ( chart_only ) {
+ System.out.println( "Step for re-aligning : " + step );
+ }
+ else {
+ System.out.println( "Step for output and re-aligning : " + step );
+ }
+ }
+ System.out.println( "Step for diagnostics reports : " + step_for_diagnostics );
+ System.out.println( "Calculate normalized Shannon Entropy : " + report_entropy );
+ if ( normalize_for_effective_seq_length ) {
+ System.out.println( "Normalize : with individual, effective sequence lenghts" );
+ }
+ else {
+ System.out.println( "Normalize : with MSA length" );
+ }
+ System.out.println( "Realign with MAFFT : " + realign );
+ if ( realign ) {
+ System.out.println( "MAFFT options : " + mafft_options );
+ }
+ System.out.println( "Simple tree (Kimura distances, NJ) : " + perform_phylogenetic_inference );
+ }
+ System.out.println();
+ final int initial_number_of_seqs = msa.getNumberOfSequences();
+ List<MsaProperties> msa_props = null;
+ final MsaCompactor mc = new MsaCompactor( msa );
+ mc.setInfileName( in.getName() );
+ if ( ( worst_remove > 0 ) || ( av_gap > 0 ) || ( length > 0 ) || ( min_length != -1 ) ) {
+ mc.setOutputFormat( output_format );
+ mc.setOutFileBase( out );
+ }
+ if ( min_length != -1 ) {
+ mc.removeSequencesByMinimalLength( min_length );
+ }
+ else {
+ mc.setPeformPhylogenticInference( perform_phylogenetic_inference );
+ if ( removed_seqs_out_base != null ) {
+ mc.setRemovedSeqsOutBase( removed_seqs_out_base );
+ }
+ mc.setNorm( normalize_for_effective_seq_length );
+ mc.setRealign( realign );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ mc.setMafftOptions( mafft_options );
+ }
+ mc.setStep( step );
+ mc.setStepForDiagnostics( step_for_diagnostics );
+ mc.setCalculateNormalizedShannonEntropy( report_entropy );
+ if ( worst_remove > 0 ) {
+ msa_props = mc.removeWorstOffenders( worst_remove );
+ }
+ else if ( av_gap > 0 ) {
+ msa_props = mc.removeViaGapAverage( av_gap );
+ }
+ else if ( length > 0 ) {
+ msa_props = mc.removeViaLength( length );
+ }
+ else {
+ msa_props = mc.chart( step, realign, normalize_for_effective_seq_length );
+ }
+ Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
+ System.out.println();
+ System.out.println( "Final MSA properties" );
+ printMsaInfo( msa, MsaMethods.calculateEffectiveLengthStatistics( msa ));
+ }
+ }
+ catch ( final IllegalArgumentException iae ) {
+ // iae.printStackTrace(); //TODO remove me
+ ForesterUtil.fatalError( PRG_NAME, iae.getMessage() );
+ }
+ catch ( final IOException ioe ) {
+ // ioe.printStackTrace(); //TODO remove me
+ ForesterUtil.fatalError( PRG_NAME, ioe.getMessage() );
}
catch ( final Exception e ) {
- e.printStackTrace();
- ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ ForesterUtil.unexpectedFatalError( PRG_NAME, e );
+ }
+ }
+
+ private static void printInfo( final File in, DeleteableMsa msa, final DescriptiveStatistics initial_msa_stats ) {
+ ForesterUtil.printProgramInformation( PRG_NAME,
+ PRG_DESC,
+ PRG_VERSION,
+ PRG_DATE,
+ E_MAIL,
+ WWW,
+ ForesterUtil.getForesterLibraryInformation() );
+ System.out.println( "Input MSA : " + in );
+ printMsaInfo( msa, initial_msa_stats );
+ }
+
+ private static void printMsaInfo( DeleteableMsa msa, final DescriptiveStatistics msa_stats ) {
+ System.out.println( "MSA length : " + msa.getLength() );
+ System.out.println( "Number of sequences : " + msa.getNumberOfSequences() );
+ System.out.println( "Median sequence length : " + NF_1.format( msa_stats.median() ) );
+ System.out.println( "Mean sequence length : "
+ + NF_1.format( msa_stats.arithmeticMean() ) );
+ System.out.println( "Max sequence length : " + ( ( int ) msa_stats.getMax() ) );
+ System.out.println( "Min sequence length : " + ( ( int ) msa_stats.getMin() ) );
+ System.out.println( "Gap ratio : "
+ + NF_4.format( MsaMethods.calcGapRatio( msa ) ) );
+ System.out.println( "Mean gap count per sequence : "
+ + NF_1.format( MsaMethods.calcNumberOfGapsStats( msa ).arithmeticMean() ) );
+ System.out.println( "Normalized Shannon Entropy (entn7) : "
+ + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 7, msa ) ) );
+ System.out.println( "Normalized Shannon Entropy (entn21) : "
+ + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) );
+ }
+
+ private static void checkPathToMafft( final String path_to_mafft ) {
+ if ( !ForesterUtil.isEmpty( path_to_mafft ) && MsaInferrer.isInstalled( path_to_mafft ) ) {
+ }
+ else {
+ if ( ForesterUtil.isEmpty( path_to_mafft ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable found, use -\"" + PATH_TO_MAFFT_OPTION
+ + "=<path to MAFFT>\" option" );
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \"" + path_to_mafft + "\"" );
+ }
}
}
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 + "=<path to MAFFT>\" option";
+ }
System.out.println( "Usage:" );
System.out.println();
- System.out.println( PRG_NAME + " <options> <msa input file>" );
+ System.out.println( PRG_NAME + " [options] <msa input file> [output file base]" );
System.out.println();
System.out.println( " options: " );
System.out.println();
- System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION + "=<integer>: step size (msa columns)" );
+ System.out.println( " -" + INFO_ONLY_OPTION
+ + " to only display same basic information about the MSA" );
+ System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION
+ + "=<integer> number of worst offender sequences to remove" );
+ System.out.println( " -" + LENGTH_OPTION + "=<integer> target MSA length" );
+ System.out.println( " -" + AV_GAPINESS_OPTION + "=<decimal> target gap-ratio (0.0-1.0)" );
+ System.out.println( " -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment );
+ System.out.println( " -" + MAFFT_OPTIONS + "=<string> options for MAFFT (default: --auto)" );
+ System.out.println( " -" + STEP_OPTION + "=<integer> step for output and re-aligning (default: 1)" );
+ System.out.println( " -" + STEP_FOR_DIAGNOSTICS_OPTION
+ + "=<integer> step for diagnostics reports (default: 1)" );
+ System.out.println( " -" + REPORT_ENTROPY
+ + " to calculate normalized Shannon Entropy (not recommended for very large alignments)" );
+ System.out.println( " -" + OUTPUT_FORMAT_OPTION
+ + "=<f|p|n> format for output alignments: f for fasta (default), p for phylip, or n for nexus" );
+ System.out.println( " -" + OUTPUT_REMOVED_SEQS_OPTION + "=<file> to output the removed sequences" );
+ System.out.println( " -" + MIN_LENGTH_OPTION
+ + "=<integer> minimal effecive sequence length (for deleting of shorter sequences)" );
+ System.out.println( " -" + GAP_RATIO_LENGTH_OPTION
+ + "=<decimal> maximal allowed gap ratio per column (for deleting of columms) (0.0-1.0)" );
+ System.out.println( " -" + PERFORM_PHYLOGENETIC_INFERENCE
+ + " to calculate a simple phylogenetic tree (Kimura distances, NJ)" );
+ System.out.println( " -" + DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION
+ + " to normalize gap-contributions with MSA length, instead of individual effective sequence lenghts" );
+
System.out.println();
System.out.println();
System.out.println();
git://source.jalview.org / jalview.git / blobdiff