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.msa.Msa.MSA_FORMAT;
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;
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 = "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 private static NumberFormat NF_1 = new DecimalFormat( "#.0" );
+ static {
+ NF_1.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 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 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 = "p";
+ 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 = "0.02";
- 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";
+ 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 = "0.2";
+ final static private String PRG_DATE = "140428";
+ 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 {
int worst_remove = -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 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";
+ 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( OUTPUT_FORMAT_PHYLIP_OPTION );
allowed_options.add( OUTPUT_REMOVED_SEQS_OPTION );
allowed_options.add( MAFFT_OPTIONS );
+ allowed_options.add( PERFORM_PHYLOGENETIC_INFERENCE );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
msa = DeleteableMsa.createInstance( GeneralMsaParser.parse( is ) );
}
final DescriptiveStatistics initial_msa_stats = MsaMethods.calculateEffectiveLengthStatistics( msa );
- System.out.println( initial_msa_stats.toString() );
+ final boolean chart_only = ( !cla.isOptionSet( LENGTH_OPTION ) )
+ && ( !cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) )
+ && ( !cla.isOptionSet( AV_GAPINESS_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 ) ) {
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 ( 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( STEP_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 )
+ min_length );
}
}
- if ( cla.isOptionSet( MIN_LENGTH_OPTION ) ) {
+ 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 );
output_format = MSA_FORMAT.PHYLIP;
}
if ( cla.isOptionSet( OUTPUT_REMOVED_SEQS_OPTION ) ) {
- String s = cla.getOptionValueAsCleanString( OUTPUT_REMOVED_SEQS_OPTION );
+ final String s = cla.getOptionValueAsCleanString( OUTPUT_REMOVED_SEQS_OPTION );
removed_seqs_out_base = new File( s );
}
if ( realign ) {
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 );
+ 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" );
+ }
+ }
ForesterUtil.printProgramInformation( PRG_NAME,
PRG_DESC,
PRG_VERSION,
E_MAIL,
WWW,
ForesterUtil.getForesterLibraryInformation() );
- //
System.out.println( "Input MSA : " + in );
- if ( out != null ) {
+ System.out.println( " MSA length : " + msa.getLength() );
+ System.out.println( " Number of sequences : " + msa.getNumberOfSequences() );
+ System.out.println( " Median sequence length : " + NF_1.format( initial_msa_stats.median() ) );
+ System.out.println( " Mean sequence length : "
+ + NF_1.format( initial_msa_stats.arithmeticMean() ) );
+ System.out.println( " Max sequence length : " + ( ( int ) initial_msa_stats.getMax() ) );
+ System.out.println( " Min sequence length : " + ( ( int ) initial_msa_stats.getMin() ) );
+ if ( !chart_only ) {
System.out.println( "Output : " + out );
}
else {
if ( worst_remove > 0 ) {
System.out.println( "Number of worst offenders to remove : " + worst_remove );
}
- else if ( av_gap > 0 ) {
+ if ( av_gap > 0 ) {
System.out.println( "Target gap-ratio : " + av_gap );
}
- else if ( length > 0 ) {
+ if ( length > 0 ) {
System.out.println( "Target MSA length : " + length );
}
- else {
- System.out.println( "Chart and diagnostics only : true" );
+ if ( min_length > 1 ) {
+ System.out.println( "Minimal effective sequence length : " + min_length );
}
- if ( out != null || removed_seqs_out_base != null ) {
+ if ( gap_ratio > -1 ) {
+ System.out.println( "Maximum allowed gap ratio per column : " + gap_ratio );
+ }
+ if ( ( out != null ) || ( removed_seqs_out_base != null ) ) {
System.out.println( "Output format : "
+ ( output_format == MSA_FORMAT.FASTA ? "fasta" : "phylip" ) );
}
- System.out.println( "Step for output and re-aligning) : " + step );
+ 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( "Report mean identity (\"MSA quality\") : " + report_aln_mean_identity );
+ System.out.println( "Calculate mean identity : " + report_aln_mean_identity );
if ( !norm ) {
System.out.println( "Normalize : " + norm );
}
- System.out.println( "Realign : " + realign );
+ System.out.println( "Realign with MAFFT : " + realign );
if ( realign ) {
System.out.println( "MAFFT options : " + mafft_options );
}
- if ( min_length > -1 ) {
- System.out.println( "Minimal effective sequence length : " + min_length );
+ 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() );
+ mc.setNorm( norm );
+ mc.setRealign( realign );
+ if ( realign ) {
+ mc.setPathToMafft( path_to_mafft );
+ mc.setMafftOptions( mafft_options );
+ }
+ mc.setStep( step );
+ mc.setStepForDiagnostics( step_for_diagnostics );
+ mc.setReportAlnMeanIdentity( report_aln_mean_identity );
+ mc.setPeformPhylogenticInference( perform_phylogenetic_inference );
+ if ( ( worst_remove > 0 ) || ( av_gap > 0 ) || ( length > 0 ) ) {
+ mc.setOutputFormat( output_format );
+ mc.setOutFileBase( out );
+ if ( removed_seqs_out_base != null ) {
+ mc.setRemovedSeqsOutBase( removed_seqs_out_base );
+ }
}
- if ( gap_ratio > -1 ) {
- System.out.println( "Maximum allowed gap ratio per column : " + gap_ratio );
+ if ( min_length > 1 ) {
+ mc.removeSequencesByMinimalLength( min_length );
+ mc.writeMsa( new File( "removed" ) );
}
- System.out.println();
- //
if ( worst_remove > 0 ) {
- MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out );
+ msa_props = mc.removeWorstOffenders( worst_remove );
}
else if ( av_gap > 0 ) {
- MsaCompactor.reduceGapAverage( msa, av_gap, step, realign, norm, path_to_mafft, out );
+ msa_props = mc.removeViaGapAverage( av_gap );
}
else if ( length > 0 ) {
- // TODO if < shortest seq -> error
- MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out );
+ msa_props = mc.removeViaLength( length );
}
else {
- MsaCompactor.chart( msa, step, realign, norm, path_to_mafft );
+ msa_props = mc.chart( step, realign, norm );
}
+ Chart.display( msa_props, initial_number_of_seqs, report_aln_mean_identity, in.getName() );
+ }
+ 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 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 ) ) {
}
System.out.println( "Usage:" );
System.out.println();
- System.out.println( PRG_NAME + " <options> <msa input file> <output file>" );
+ System.out.println( PRG_NAME + " <options> <msa input file> <output file base>" );
System.out.println();
System.out.println( " options: " );
System.out.println();
+ "=<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_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_ALN_MEAN_IDENTITY
+ + " to calculate mean MSA column identity (\"MSA quality\") (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( " -" + 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( " -" + PERFORM_PHYLOGENETIC_INFERENCE
+ + " to calculate a simple phylogenetic tree (Kimura distances, NJ)" );
System.out.println();
System.out.println();
System.out.println();
git://source.jalview.org / jalview.git / blobdiff