+// $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 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.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 = "0.01";
- 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 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<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_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 );
}
- mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );
}
catch ( final Exception e ) {
e.printStackTrace();
}
}
+ 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
+ + "=<path to MAFFT>\" option" );
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \"" + path_to_mafft + "\"" );
+ }
+ }
+ }
+
private static void printHelp() {
ForesterUtil.printProgramInformation( PRG_NAME,
PRG_DESC,
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>" );
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( " -" + 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( " -" + STEP_OPTION + "=<integer> step for output and re-aligning (default: 1)" );
+ 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_FOR_DIAGNOSTICS_OPTION
+ + "=<integer> step for diagnostics reports (default: 1)" );
+ 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( " -" + 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 + "=<file> to output the removed sequences" );
System.out.println();
System.out.println();
System.out.println();
git://source.jalview.org / jalview.git / blobdiff