X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fmsa_compactor.java;h=e60d88697c79b236184bc2b4b04553cc5262221e;hb=154955274422ff0b34ff51fb40c2d621269368ca;hp=4e5167583f163cb24f11310134c8bb9fe52dacb9;hpb=e49ac25b5d578ea326900b7b56495ee33c3cb92c;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 4e51675..e60d886 100644 --- a/forester/java/src/org/forester/application/msa_compactor.java +++ b/forester/java/src/org/forester/application/msa_compactor.java @@ -46,6 +46,12 @@ 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 private static NumberFormat NF_1 = new DecimalFormat( "0.#" ); @@ -61,6 +67,7 @@ public class msa_compactor { 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"; @@ -70,7 +77,7 @@ public class msa_compactor { 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"; @@ -124,6 +131,7 @@ public class msa_compactor { 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 ); @@ -137,6 +145,11 @@ public class msa_compactor { 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 ) ) ); @@ -145,7 +158,7 @@ public class msa_compactor { } 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 ); } @@ -169,7 +182,7 @@ public class msa_compactor { if ( length >= msa.getLength() ) { ForesterUtil.fatalError( PRG_NAME, "target length is out of range [longer than MSA (" + msa.getLength() - + ")]: " + length ); + + ")]: " + length ); } else if ( length < initial_msa_stats.getMin() ) { ForesterUtil.fatalError( PRG_NAME, @@ -269,8 +282,8 @@ public class msa_compactor { 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)" ); + .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, @@ -281,34 +294,14 @@ public class msa_compactor { 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, - 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( " Normalized Shannon Entropy (entn21): " - + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, msa ) ) ); + "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 ); } - else { - System.out.println( "Output : n/a" ); - } + if ( removed_seqs_out_base != null ) { System.out.println( "Write removed sequences to : " + removed_seqs_out_base ); } @@ -401,6 +394,9 @@ public class msa_compactor { msa_props = mc.chart( step, realign, norm ); } Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() ); + System.out.println(); + System.out.println( "Final MSA properties" ); + printMsaInfo( msa, MsaMethods.calculateEffectiveLengthStatistics( msa )); } } catch ( final IllegalArgumentException iae ) { @@ -416,13 +412,43 @@ public class msa_compactor { } } + 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 ); + printMsaInfo( msa, initial_msa_stats ); + } + + private static void printMsaInfo( DeleteableMsa msa, final DescriptiveStatistics msa_stats ) { + System.out.println( "MSA length : " + msa.getLength() ); + System.out.println( "Number of sequences : " + msa.getNumberOfSequences() ); + System.out.println( "Median sequence length : " + NF_1.format( msa_stats.median() ) ); + System.out.println( "Mean sequence length : " + + NF_1.format( msa_stats.arithmeticMean() ) ); + System.out.println( "Max sequence length : " + ( ( int ) msa_stats.getMax() ) ); + System.out.println( "Min sequence length : " + ( ( int ) msa_stats.getMin() ) ); + System.out.println( "Gap ratio : " + + NF_4.format( MsaMethods.calcGapRatio( msa ) ) ); + System.out.println( "Mean gap count per sequence : " + + NF_1.format( MsaMethods.calcNumberOfGapsStats( 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 ) ) { } 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 + "\"" ); @@ -448,30 +474,32 @@ 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" ); + + "= 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)" ); + + "= step for diagnostics reports (default: 1)" ); System.out.println( " -" + REPORT_ENTROPY - + " to calculate normalized Shannon Entropy (not recommended for very large alignments)" ); + + " 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" ); + + "= 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)" ); + + "= 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)" ); + + "= 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)" ); + + " to calculate a simple phylogenetic tree (Kimura distances, NJ)" ); System.out.println(); System.out.println(); System.out.println();