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 REPORT_ENTROPY = "e";
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 = "0.2";
- final static private String PRG_DATE = "140428";
+ 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";
int step_for_diagnostics = 1;
int min_length = -1;
double gap_ratio = -1;
- boolean report_aln_mean_identity = false;
+ 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( 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( REPORT_ENTROPY );
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() );
- if ( ( cla.isOptionSet( LENGTH_OPTION ) || cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) || cla
- .isOptionSet( AV_GAPINESS_OPTION ) ) && ( out == null ) ) {
+ 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 ) ) {
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( REPORT_ENTROPY ) ) {
+ report_entropy = true;
}
if ( cla.isOptionSet( OUTPUT_FORMAT_PHYLIP_OPTION ) ) {
output_format = MSA_FORMAT.PHYLIP;
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.fatalError( PRG_NAME, "illegal or empty MAFFT options: " + mafft_options );
}
}
}
- if ( ( !cla.isOptionSet( LENGTH_OPTION ) && !cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) && !cla
- .isOptionSet( AV_GAPINESS_OPTION ) ) && ( ( out != null ) || ( removed_seqs_out_base != null ) ) ) {
- ForesterUtil.fatalError( PRG_NAME,
- "chart only, no outfile(s) produced (no need to indicate output file(s))" );
+ 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,
+ 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 ( out != null ) {
+ 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 ( 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( "Calculate mean identity : " + report_aln_mean_identity );
+ System.out.println( "Calculate normalized Shannon Entropy : " + report_entropy );
if ( !norm ) {
System.out.println( "Normalize : " + norm );
}
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( "Maximum allowed gap ratio per column : " + gap_ratio );
- }
+ 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;
- if ( worst_remove > 0 ) {
- final MsaCompactor mc = new MsaCompactor( msa );
- mc.setRealign( realign );
+ 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.setCalculateNormalizedShannonEntropy( report_entropy );
+ mc.setPeformPhylogenticInference( perform_phylogenetic_inference );
+ if ( ( worst_remove > 0 ) || ( av_gap > 0 ) || ( length > 0 ) ) {
mc.setOutputFormat( output_format );
- if ( realign ) {
- mc.setPathToMafft( path_to_mafft );
- mc.setMafftOptions( mafft_options );
- }
- mc.setNorm( norm );
- mc.setReportAlnMeanIdentity( report_aln_mean_identity );
mc.setOutFileBase( out );
if ( removed_seqs_out_base != null ) {
mc.setRemovedSeqsOutBase( removed_seqs_out_base );
}
- mc.setStep( step );
- mc.setStepForDiagnostics( step_for_diagnostics );
+ }
+ if ( min_length > 1 ) {
+ mc.removeSequencesByMinimalLength( min_length );
+ mc.writeMsa( new File( "removed" ) );
+ }
+ if ( worst_remove > 0 ) {
msa_props = mc.removeWorstOffenders( worst_remove );
}
else if ( av_gap > 0 ) {
- final MsaCompactor mc = new MsaCompactor( msa );
- mc.setRealign( realign );
- mc.setOutputFormat( output_format );
- if ( realign ) {
- mc.setPathToMafft( path_to_mafft );
- mc.setMafftOptions( mafft_options );
- }
- mc.setNorm( norm );
- mc.setReportAlnMeanIdentity( report_aln_mean_identity );
- mc.setOutFileBase( out );
- if ( removed_seqs_out_base != null ) {
- mc.setRemovedSeqsOutBase( removed_seqs_out_base );
- }
- mc.setStep( step );
- mc.setStepForDiagnostics( step_for_diagnostics );
msa_props = mc.removeViaGapAverage( av_gap );
}
else if ( length > 0 ) {
- final MsaCompactor mc = new MsaCompactor( msa );
- mc.setRealign( realign );
- mc.setOutputFormat( output_format );
- if ( realign ) {
- mc.setPathToMafft( path_to_mafft );
- mc.setMafftOptions( mafft_options );
- }
- mc.setNorm( norm );
- mc.setReportAlnMeanIdentity( report_aln_mean_identity );
- mc.setOutFileBase( out );
- if ( removed_seqs_out_base != null ) {
- mc.setRemovedSeqsOutBase( removed_seqs_out_base );
- }
- mc.setStep( step );
- mc.setStepForDiagnostics( step_for_diagnostics );
msa_props = mc.removeViaLength( length );
}
else {
- //MsaCompactor.chart( msa, step, realign, norm, path_to_mafft );
- final MsaCompactor mc = new MsaCompactor( msa );
- mc.setRealign( realign );
- if ( realign ) {
- mc.setPathToMafft( path_to_mafft );
- mc.setMafftOptions( mafft_options );
- }
- mc.setNorm( norm );
- mc.setReportAlnMeanIdentity( report_aln_mean_identity );
- mc.setOutFileBase( out );
- mc.setStep( step );
- mc.setStepForDiagnostics( step_for_diagnostics );
msa_props = mc.chart( step, realign, norm );
}
- Chart.display( msa_props, initial_number_of_seqs, report_aln_mean_identity, in.toString() );
+ Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
}
catch ( final IllegalArgumentException iae ) {
// iae.printStackTrace(); //TODO remove me
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( " -" + 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 calculate mean MSA column identity (\"MSA quality\") (not recommended for very large alignments)" );
+ System.out.println( " -" + REPORT_ENTROPY
+ + " to calculate normalized Shannon Entropy (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( " -" + 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