X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmsa_compactor.java;h=329af42c5984108a61a59dbbfbc0e03bfa8525ac;hb=7a194f3da2c3a659ecc67bff021d9f64c845e923;hp=7f652691f54e67a0b7a7c38656044a9123f84944;hpb=504b2b133e9814ac9ee966dc04a1408c455c6a2f;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 7f65269..329af42 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -48,9 +48,11 @@ import org.forester.util.ForesterUtil; public class msa_compactor { - final private static NumberFormat NF_1 = new DecimalFormat( "#.0" ); + 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"; @@ -63,17 +65,18 @@ public class msa_compactor { 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 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 = "0.2"; - 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"; @@ -100,10 +103,11 @@ public class msa_compactor { 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 allowed_options = new ArrayList(); allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION ); allowed_options.add( AV_GAPINESS_OPTION ); @@ -115,10 +119,11 @@ public class msa_compactor { 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( 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 ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); @@ -134,13 +139,13 @@ public class msa_compactor { final DescriptiveStatistics initial_msa_stats = MsaMethods.calculateEffectiveLengthStatistics( msa ); final boolean chart_only = ( !cla.isOptionSet( LENGTH_OPTION ) ) && ( !cla.isOptionSet( REMOVE_WORST_OFFENDERS_OPTION ) ) - && ( !cla.isOptionSet( AV_GAPINESS_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 ) ) { + 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 ); } @@ -172,6 +177,22 @@ public class msa_compactor { + 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 ) @@ -199,24 +220,29 @@ public class msa_compactor { + 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( 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_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( 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 ); @@ -237,6 +263,9 @@ public class msa_compactor { 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 @@ -249,6 +278,12 @@ public class msa_compactor { + 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, @@ -264,6 +299,10 @@ public class msa_compactor { + 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() ) ); + System.out.println( " Gap ratio : " + + NF_4.format( MsaMethods.calcGapRatio( msa ) ) ); + System.out.println( " Normalized Shannon Entropy (entn21): " + + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) ); if ( !chart_only ) { System.out.println( "Output : " + out ); } @@ -289,66 +328,80 @@ public class msa_compactor { 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" ) ); - } - if ( chart_only && !realign ) { - System.out.println( "Step for output and re-aligning : n/a" ); + 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" ); + } } - else { - if ( chart_only ) { - System.out.println( "Step for re-aligning : " + step ); + if ( min_length == -1 ) { + if ( chart_only && !realign ) { + System.out.println( "Step for output and re-aligning : n/a" ); } else { - System.out.println( "Step for output and re-aligning : " + step ); + 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 ); - if ( !norm ) { - System.out.println( "Normalize : " + norm ); - } - System.out.println( "Realign with MAFFT : " + realign ); - if ( realign ) { - System.out.println( "MAFFT options : " + mafft_options ); + System.out.println( "Step for diagnostics reports : " + step_for_diagnostics ); + System.out.println( "Calculate normalized Shannon Entropy : " + report_entropy ); + if ( !norm ) { + System.out.println( "Normalize : " + norm ); + } + 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 msa_props = null; final MsaCompactor mc = new MsaCompactor( msa ); - 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 ); - if ( ( worst_remove > 0 ) || ( av_gap > 0 ) || ( length > 0 ) ) { + mc.setInfileName( in.getName() ); + if ( ( worst_remove > 0 ) || ( av_gap > 0 ) || ( length > 0 ) || ( min_length != -1 ) ) { mc.setOutputFormat( output_format ); mc.setOutFileBase( out ); - if ( removed_seqs_out_base != null ) { - mc.setRemovedSeqsOutBase( removed_seqs_out_base ); - } } - if ( min_length > 1 ) { + 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 ) { - msa_props = mc.removeViaGapAverage( av_gap ); - } - else if ( length > 0 ) { - msa_props = mc.removeViaLength( length ); } else { - msa_props = mc.chart( step, realign, norm ); + mc.setPeformPhylogenticInference( perform_phylogenetic_inference ); + if ( removed_seqs_out_base != null ) { + mc.setRemovedSeqsOutBase( removed_seqs_out_base ); + } + 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 ); + 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, norm ); + } + Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() ); } - Chart.display( msa_props, initial_number_of_seqs, report_aln_mean_identity, in.toString() ); } catch ( final IllegalArgumentException iae ) { // iae.printStackTrace(); //TODO remove me @@ -408,17 +461,17 @@ public class msa_compactor { System.out.println( " -" + STEP_OPTION + "= step for output and re-aligning (default: 1)" ); System.out.println( " -" + STEP_FOR_DIAGNOSTICS_OPTION + "= 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( " -" + REPORT_ENTROPY + + " to calculate normalized Shannon Entropy (not recommended for very large alignments)" ); + System.out.println( " -" + OUTPUT_FORMAT_OPTION + + "= format for output alignments: f for fasta (default), p for phylip, or n for nexus" ); System.out.println( " -" + OUTPUT_REMOVED_SEQS_OPTION + "= to output the removed sequences" ); System.out.println( " -" + MIN_LENGTH_OPTION + "= minimal effecive sequence length (for deleting of shorter sequences)" ); System.out.println( " -" + GAP_RATIO_LENGTH_OPTION + "= 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();