X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmsa_compactor.java;h=15c2d4c7e164cd1284fb9c41309bfd89d64a06bb;hb=02bf2b081aed88622e3279e816f0aeb45cba546e;hp=4c500285c15e1cb0d74d69256c35a0cd5da21a64;hpb=db8b10baefc3e1b5fee9b8192657ecc97ca5b86d;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 4c50028..15c2d4c 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -26,34 +26,66 @@ 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.DeleteableMsa; +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; + +/* +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 = "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 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 = "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 { @@ -71,10 +103,18 @@ public class msa_compactor { 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 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 allowed_options = new ArrayList(); allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION ); allowed_options.add( AV_GAPINESS_OPTION ); @@ -83,6 +123,15 @@ public class msa_compactor { 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 ); @@ -95,9 +144,21 @@ public class msa_compactor { 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 ) ) { + 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 ); } @@ -118,8 +179,31 @@ public class msa_compactor { 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( 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 ) ) { @@ -141,40 +225,223 @@ public class msa_compactor { 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( 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 ); } if ( worst_remove > 0 ) { - MsaCompactor.removeWorstOffenders( msa, worst_remove, step, realign, norm, path_to_mafft, out ); + System.out.println( "Number of worst offenders to remove : " + worst_remove ); + } + if ( av_gap > 0 ) { + System.out.println( "Target gap-ratio : " + av_gap ); + } + if ( length > 0 ) { + System.out.println( "Target MSA length : " + length ); + } + 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.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 ( !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 ); } - else if ( av_gap > 0 ) { - MsaCompactor.reduceGapAverage( msa, av_gap, step, realign, norm, path_to_mafft, out ); + System.out.println(); + final int initial_number_of_seqs = msa.getNumberOfSequences(); + List 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 ); } - else if ( length > 0 ) { - // TODO if < shortest seq -> error - MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out ); + if ( min_length != -1 ) { + mc.removeSequencesByMinimalLength( min_length ); } else { - MsaCompactor.chart( msa, step, realign, norm, path_to_mafft ); + 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() ); } } + 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 ); + 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() ) ); + System.out.println( " Gap ratio : " + + NF_4.format( MsaMethods.calcGapRatio( msa ) ) ); + System.out.println( " Mean gap count per 100 residues : " + + NF_1.format( MsaMethods.calcNumberOfGapsPer100Stats( 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 ) ) { - 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 - + "=\" option" ); + + "=\" option" ); } else { ForesterUtil.fatalError( PRG_NAME, "no MAFFT executable at \"" + path_to_mafft + "\"" ); @@ -200,16 +467,32 @@ public class msa_compactor { } System.out.println( "Usage:" ); System.out.println(); - System.out.println( PRG_NAME + " " ); + System.out.println( PRG_NAME + " [options] [output file base]" ); System.out.println(); System.out.println( " options: " ); System.out.println(); + System.out.println( " -" + INFO_ONLY_OPTION + + " to only display same basic information about the MSA" ); System.out.println( " -" + REMOVE_WORST_OFFENDERS_OPTION - + "= number of worst offender sequences to remove" ); - System.out.println( " -" + LENGTH_OPTION + "= target MSA length" ); - System.out.println( " -" + AV_GAPINESS_OPTION + "= target gap-ratio (0.0-1.0)" ); - System.out.println( " -" + STEP_OPTION + "= step (for output and re-aligning)" ); - System.out.println( " -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment ); + + "= number of worst offender sequences to remove" ); + System.out.println( " -" + LENGTH_OPTION + "= target MSA length" ); + System.out.println( " -" + AV_GAPINESS_OPTION + "= target gap-ratio (0.0-1.0)" ); + System.out.println( " -" + REALIGN_OPTION + " to realign using MAFFT" + mafft_comment ); + System.out.println( " -" + MAFFT_OPTIONS + "= options for MAFFT (default: --auto)" ); + 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_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();