public final class cladinator {
final static private String PRG_NAME = "cladinator";
- final static private String PRG_VERSION = "1.02";
- final static private String PRG_DATE = "170912";
+ final static private String PRG_VERSION = "1.07";
+ final static private String PRG_DATE = "1711xx";
final static private String PRG_DESC = "clades within clades of annotated labels -- analysis of pplacer-type outputs";
final static private String E_MAIL = "phyloxml@gmail.com";
final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
final static private String EXTRA_PROCESSING_OPTION1 = "x";
final static private String EXTRA_PROCESSING1_SEP_OPTION = "xs";
final static private String EXTRA_PROCESSING1_KEEP_EXTRA_OPTION = "xk";
+ final static private String QUIET_OPTION = "Q";
+ final static private String SPECIAL_PROCESSING_OPTION = "S";
final static private String VERBOSE_OPTION = "v";
- final static private double SPECIFICS_CUTOFF_DEFAULT = 0.8;
+ final static private String REMOVE_ANNOT_SEP_OPTION = "rs";
+ final static private double SPECIFICS_CUTOFF_DEFAULT = 0.7;
final static private String SEP_DEFAULT = ".";
final static private Pattern QUERY_PATTERN_DEFAULT = AnalysisMulti.DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE;
final static private String EXTRA_PROCESSING1_SEP_DEFAULT = "|";
final static private boolean EXTRA_PROCESSING1_KEEP_EXTRA_DEFAULT = false;
- private final static DecimalFormat df = new DecimalFormat( "0.0#######" );
+ private final static DecimalFormat df = new DecimalFormat( "0.0###" );
public static void main( final String args[] ) {
try {
print_help();
System.exit( -1 );
}
- final List<String> allowed_options = new ArrayList<>();
+ final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( SEP_OPTION );
allowed_options.add( QUERY_PATTERN_OPTION );
allowed_options.add( SPECIFICS_CUTOFF_OPTION );
allowed_options.add( EXTRA_PROCESSING_OPTION1 );
allowed_options.add( EXTRA_PROCESSING1_SEP_OPTION );
allowed_options.add( EXTRA_PROCESSING1_KEEP_EXTRA_OPTION );
+ allowed_options.add( SPECIAL_PROCESSING_OPTION );
allowed_options.add( VERBOSE_OPTION );
+ allowed_options.add( QUIET_OPTION );
+ allowed_options.add( REMOVE_ANNOT_SEP_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
ForesterUtil.fatalError( PRG_NAME, "no value for separator option" );
}
}
- Pattern compiled_query_str = null;
+ Pattern compiled_query = null;
if ( cla.isOptionSet( QUERY_PATTERN_OPTION ) ) {
if ( cla.isOptionValueSet( QUERY_PATTERN_OPTION ) ) {
final String query_str = cla.getOptionValue( QUERY_PATTERN_OPTION );
try {
- compiled_query_str = Pattern.compile( query_str );
+ compiled_query = Pattern.compile( query_str );
}
catch ( final PatternSyntaxException e ) {
- ForesterUtil.fatalError( PRG_NAME, "error in regular expression: " + e.getMessage() );
+ ForesterUtil.fatalError( PRG_NAME,
+ "error in regular expression: " + query_str + ": " + e.getMessage() );
}
}
else {
ForesterUtil.fatalError( PRG_NAME, "no value for mapping file" );
}
}
- final Pattern pattern = ( compiled_query_str != null ) ? compiled_query_str : QUERY_PATTERN_DEFAULT;
+ final Pattern pattern = ( compiled_query != null ) ? compiled_query : QUERY_PATTERN_DEFAULT;
final File intreefile = cla.getFile( 0 );
final String error_intreefile = ForesterUtil.isReadableFile( intreefile );
if ( !ForesterUtil.isEmpty( error_intreefile ) ) {
ForesterUtil.fatalError( PRG_NAME, "no value for extra processing separator" );
}
}
- if ( extra_processing1_sep != null && extra_processing1_sep.equals( separator ) ) {
+ if ( ( extra_processing1_sep != null ) && extra_processing1_sep.equals( separator ) ) {
ForesterUtil.fatalError( PRG_NAME,
"extra processing separator must not be the same the annotation-separator" );
}
}
extra_processing1_keep = true;
}
+ Pattern special_pattern = null;
+ boolean special_processing = false;
+ if ( cla.isOptionSet( SPECIAL_PROCESSING_OPTION ) ) {
+ if ( extra_processing1 == true ) {
+ ForesterUtil
+ .fatalError( PRG_NAME,
+ "extra processing cannot be used together with special processing pattern" );
+ }
+ if ( cla.isOptionValueSet( SPECIAL_PROCESSING_OPTION ) ) {
+ final String str = cla.getOptionValue( SPECIAL_PROCESSING_OPTION );
+ try {
+ special_pattern = Pattern.compile( str );
+ }
+ catch ( final PatternSyntaxException e ) {
+ ForesterUtil
+ .fatalError( PRG_NAME,
+ "error in special processing pattern: " + str + ": " + e.getMessage() );
+ }
+ special_processing = true;
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "no value for special processing pattern" );
+ }
+ }
+ final boolean remove_annotation_sep;
+ if ( cla.isOptionSet( REMOVE_ANNOT_SEP_OPTION ) ) {
+ remove_annotation_sep = true;
+ }
+ else {
+ remove_annotation_sep = false;
+ }
final boolean verbose;
if ( cla.isOptionSet( VERBOSE_OPTION ) ) {
verbose = true;
else {
verbose = false;
}
+ final boolean quit;
+ if ( cla.isOptionSet( QUIET_OPTION ) ) {
+ quit = true;
+ }
+ else {
+ quit = false;
+ }
System.out.println( "Input tree : " + intreefile );
System.out.println( "Specific-hit support cutoff: " + cutoff_specifics );
if ( mapping_file != null ) {
+ " rows)" );
}
System.out.println( "Annotation-separator : " + separator );
+ if ( remove_annotation_sep ) {
+ System.out.println( "Remove anno.-sep. in output: " + remove_annotation_sep );
+ }
System.out.println( "Query pattern : " + pattern );
- System.out.println( "Extra processing : " + extra_processing1 );
if ( extra_processing1 ) {
+ System.out.println( "Extra processing : " + extra_processing1 );
System.out.println( "Extra processing separator : " + extra_processing1_sep );
System.out.println( "Keep extra annotations : " + extra_processing1_keep );
}
+ if ( special_processing ) {
+ System.out.println( "Special processing : " + special_processing );
+ System.out.println( "Special processing pattern : " + special_pattern );
+ }
if ( outtablefile != null ) {
System.out.println( "Output table : " + outtablefile );
}
- Phylogeny p = null;
+ Phylogeny phys[] = null;
try {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile, true );
- p = factory.create( intreefile, pp )[ 0 ];
+ phys = factory.create( intreefile, pp );
}
catch ( final IOException e ) {
ForesterUtil.fatalError( PRG_NAME, "Could not read \"" + intreefile + "\" [" + e.getMessage() + "]" );
- System.exit( -1 );
}
- System.out.println( "Ext. nodes in input tree : " + p.getNumberOfExternalNodes() );
- if ( map != null ) {
- AnalysisMulti.performMapping( pattern, map, p, verbose );
+ if ( phys.length == 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "\"" + intreefile + "\" does not contain any trees" );
}
- if ( extra_processing1 ) {
- AnalysisMulti.performExtraProcessing1( pattern,
- p,
- extra_processing1_sep,
- extra_processing1_keep,
- separator,
- verbose );
- }
- final ResultMulti res = AnalysisMulti.execute( p, pattern, separator, cutoff_specifics );
- printResult( res );
+ System.out.println( "Number of input trees : " + phys.length );
+ if ( phys.length == 1 ) {
+ System.out.println( "Ext. nodes in input tree : " + phys[ 0 ].getNumberOfExternalNodes() );
+ }
+ else {
+ System.out.println( "Ext. nodes in input tree 1 : " + phys[ 0 ].getNumberOfExternalNodes() );
+ }
+ final EasyWriter outtable_writer;
if ( outtablefile != null ) {
- writeResultToTable( res, outtablefile );
+ outtable_writer = ForesterUtil.createEasyWriter( outtablefile );
+ outtable_writer.print( "#" + PRG_NAME + " " + PRG_VERSION + " " + PRG_DATE );
+ outtable_writer.print( " Input tree: " + intreefile );
+ outtable_writer.println( " Specific-hit support cutoff: " + cutoff_specifics );
+ }
+ else {
+ outtable_writer = null;
+ }
+ int counter = 0;
+ for( final Phylogeny phy : phys ) {
+ if ( map != null ) {
+ AnalysisMulti.performMapping( pattern, map, phy, verbose );
+ }
+ if ( extra_processing1 ) {
+ AnalysisMulti.performExtraProcessing1( pattern,
+ phy,
+ extra_processing1_sep,
+ extra_processing1_keep,
+ separator,
+ verbose );
+ }
+ else if ( special_processing ) {
+ AnalysisMulti.performSpecialProcessing1( pattern, phy, separator, special_pattern, verbose );
+ }
+ final ResultMulti res = AnalysisMulti.execute( phy, pattern, separator, cutoff_specifics );
+ if ( !quit ) {
+ if ( phys.length == 1 ) {
+ printResult( res, -1, remove_annotation_sep );
+ }
+ else {
+ printResult( res, counter, remove_annotation_sep );
+ }
+ }
+ if ( outtable_writer != null ) {
+ writeResultToTable( res, outtable_writer, remove_annotation_sep );
+ outtable_writer.flush();
+ }
+ ++counter;
+ }
+ if ( outtable_writer != null ) {
+ outtable_writer.flush();
+ outtable_writer.close();
}
}
catch ( final UserException e ) {
}
}
- private final static void printResult( final ResultMulti res ) {
- System.out.println();
- System.out.println( "Result:" );
+ private final static void printResult( final ResultMulti res,
+ final int counter,
+ final boolean remove_annotation_sep ) {
System.out.println();
+ if ( counter == -1 ) {
+ System.out.println( "Result for " + res.getQueryNamePrefix() );
+ }
+ else {
+ System.out.println( "Result for " + res.getQueryNamePrefix() + " [tree " + counter + "]" );
+ }
if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
- System.out.println( "No match to query pattern!" );
+ System.out.println( " No match to query pattern!" );
}
else {
- System.out.println( "Matching Clade(s):" );
+ System.out.println( " Matching Clade(s):" );
for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
- System.out.println( prefix );
+ if ( remove_annotation_sep ) {
+ System.out.println( " " + prefix.toStringRemovSeparator() );
+ }
+ else {
+ System.out.println( " " + prefix );
+ }
}
if ( res.isHasSpecificMultiHitsPrefixes() ) {
System.out.println();
- System.out.println( "Specific-hit(s):" );
+ System.out.println( " Specific-hit(s):" );
for( final Prefix prefix : res.getSpecificMultiHitPrefixes() ) {
- System.out.println( prefix );
+ if ( remove_annotation_sep ) {
+ System.out.println( " " + prefix.toStringRemovSeparator() );
+ }
+ else {
+ System.out.println( " " + prefix );
+ }
}
System.out.println();
- System.out.println( "Matching Clade(s) with Specific-hit(s):" );
+ System.out.println( " Matching Clade(s) with Specific-hit(s):" );
for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
- System.out.println( prefix );
+ if ( remove_annotation_sep ) {
+ System.out.println( " " + prefix.toStringRemovSeparator() );
+ }
+ else {
+ System.out.println( " " + prefix );
+ }
for( final Prefix spec : res.getSpecificMultiHitPrefixes() ) {
if ( spec.getPrefix().startsWith( prefix.getPrefix() ) ) {
- System.out.println( " " + spec );
+ if ( remove_annotation_sep ) {
+ System.out.println( " " + spec.toStringRemovSeparator() );
+ }
+ else {
+ System.out.println( " " + spec );
+ }
}
}
}
}
if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesDown() ) ) {
System.out.println();
- System.out.println( "Matching Down-tree Bracketing Clade(s):" );
+ System.out.println( " Matching Down-tree Bracketing Clade(s):" );
for( final Prefix prefix : res.getCollapsedMultiHitPrefixesDown() ) {
- System.out.println( prefix );
+ if ( remove_annotation_sep ) {
+ System.out.println( " " + prefix.toStringRemovSeparator() );
+ }
+ else {
+ System.out.println( " " + prefix );
+ }
}
}
if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesUp() ) ) {
System.out.println();
- System.out.println( "Matching Up-tree Bracketing Clade(s):" );
+ System.out.println( " Matching Up-tree Bracketing Clade(s):" );
for( final Prefix prefix : res.getCollapsedMultiHitPrefixesUp() ) {
- System.out.println( prefix );
+ if ( remove_annotation_sep ) {
+ System.out.println( " " + prefix.toStringRemovSeparator() );
+ }
+ else {
+ System.out.println( " " + prefix );
+ }
}
}
+ System.out.println();
+ System.out.println( " Total Number of Matches: " + res.getNumberOfMatches() + "/"
+ + res.getReferenceTreeNumberOfExternalNodes() );
}
System.out.println();
}
- private final static void writeResultToTable( final ResultMulti res, final File outtablefile ) throws IOException {
- final EasyWriter w = ForesterUtil.createEasyWriter( outtablefile );
+ private final static void writeResultToTable( final ResultMulti res,
+ final EasyWriter w,
+ final boolean remove_annotation_sep )
+ throws IOException {
if ( ( res.getAllMultiHitPrefixes() == null ) | ( res.getAllMultiHitPrefixes().size() < 1 ) ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
w.println( "No match to query pattern!" );
}
else {
for( final Prefix prefix : res.getCollapsedMultiHitPrefixes() ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
w.print( "Matching Clades" );
w.print( "\t" );
- w.print( prefix.getPrefix() );
+ if ( remove_annotation_sep ) {
+ w.print( prefix.getPrefixRemovSeparator() );
+ }
+ else {
+ w.print( prefix.getPrefix() );
+ }
w.print( "\t" );
w.print( df.format( prefix.getConfidence() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getNumberOfMatches() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
w.println();
}
if ( res.isHasSpecificMultiHitsPrefixes() ) {
for( final Prefix prefix : res.getSpecificMultiHitPrefixes() ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
w.print( "Specific-hits" );
w.print( "\t" );
- w.print( prefix.getPrefix() );
+ if ( remove_annotation_sep ) {
+ w.print( prefix.getPrefixRemovSeparator() );
+ }
+ else {
+ w.print( prefix.getPrefix() );
+ }
w.print( "\t" );
w.print( df.format( prefix.getConfidence() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getNumberOfMatches() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
w.println();
}
}
if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesDown() ) ) {
for( final Prefix prefix : res.getCollapsedMultiHitPrefixesDown() ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
w.print( "Matching Down-tree Bracketing Clades" );
w.print( "\t" );
- w.print( prefix.getPrefix() );
+ if ( remove_annotation_sep ) {
+ w.print( prefix.getPrefixRemovSeparator() );
+ }
+ else {
+ w.print( prefix.getPrefix() );
+ }
w.print( "\t" );
w.print( df.format( prefix.getConfidence() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getNumberOfMatches() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
w.println();
}
}
if ( !ForesterUtil.isEmpty( res.getAllMultiHitPrefixesUp() ) ) {
for( final Prefix prefix : res.getCollapsedMultiHitPrefixesUp() ) {
+ w.print( res.getQueryNamePrefix() );
+ w.print( "\t" );
w.print( "Matching Up-tree Bracketing Clades" );
w.print( "\t" );
- w.print( prefix.getPrefix() );
+ if ( remove_annotation_sep ) {
+ w.print( prefix.getPrefixRemovSeparator() );
+ }
+ else {
+ w.print( prefix.getPrefix() );
+ }
w.print( "\t" );
w.print( df.format( prefix.getConfidence() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getNumberOfMatches() ) );
+ w.print( "\t" );
+ w.print( String.valueOf( res.getReferenceTreeNumberOfExternalNodes() ) );
w.println();
}
}
}
- w.flush();
- w.close();
}
private final static void print_help() {
System.out.println( "Usage:" );
System.out.println();
- System.out.println( PRG_NAME + " [options] <input tree file> [output table file]" );
+ System.out.println( PRG_NAME + " [options] <input tree(s) file> [output table file]" );
System.out.println();
System.out.println( " options:" );
System.out.println( " -" + SPECIFICS_CUTOFF_OPTION
- + "=<double> : the cutoff for \"specific-hit\" support values (default: "
+ + "=<double> : the minimal confidence value for \"specific-hits\" to be reported (default: "
+ SPECIFICS_CUTOFF_DEFAULT + ")" );
- System.out.println( " -" + SEP_OPTION + "=<separator> : the annotation-separator to be used (default: "
- + SEP_DEFAULT + ")" );
+ System.out.println( " -" + SEP_OPTION + "=<separator> : the annotation-separator to be used (default: \""
+ + SEP_DEFAULT + "\")" );
System.out.println( " -" + MAPPING_FILE_OPTION
- + "=<mapping table>: to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)" );
- System.out.println( " -" + QUERY_PATTERN_OPTION
- + "=<query pattern>: the regular expression for the query (default: \"" + QUERY_PATTERN_DEFAULT
- + "\" for pplacer output)" );
+ + "=<mapping table> : to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)" );
System.out.println( " -" + EXTRA_PROCESSING_OPTION1
- + " : to enable extra processing of annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1\")" );
+ + " : to enable extra processing of annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1\")" );
System.out.println( " -" + EXTRA_PROCESSING1_SEP_OPTION
- + "=<separator> : the separator for extra annotations (default: \"" + EXTRA_PROCESSING1_SEP_DEFAULT
+ + "=<separator> : the separator for extra annotations (default: \"" + EXTRA_PROCESSING1_SEP_DEFAULT
+ "\")" );
System.out.println( " -" + EXTRA_PROCESSING1_KEEP_EXTRA_OPTION
- + " : to keep extra annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1.Q16611\")" );
- System.out.println( " -" + VERBOSE_OPTION + " : verbose" );
+ + " : to keep extra annotations (e.g. \"Q16611|A.1.1\" becomes \"A.1.1.Q16611\")" );
+ System.out.println( " -" + SPECIAL_PROCESSING_OPTION
+ + "=<pattern> : special processing with pattern (e.g. \"(\\d+)([a-z]+)_.+\" for changing \"6q_EF42\" to \"6.q\")" );
+ System.out.println( " -" + REMOVE_ANNOT_SEP_OPTION
+ + " : to remove the annotation-separator in the output (e.g. the \"" + SEP_DEFAULT
+ + "\")" );
+ System.out.println( " -" + VERBOSE_OPTION + " : verbose" );
+ System.out.println( " -" + QUIET_OPTION
+ + " : quiet (no output to console, for when used in a pipeline)" );
+ System.out.println( " --" + QUERY_PATTERN_OPTION
+ + "=<pattern> : expert option: the regular expression pattern for the query (default: \""
+ + QUERY_PATTERN_DEFAULT + "\" for pplacer output)" );
System.out.println();
System.out.println( "Examples:" );
System.out.println();
- System.out.println( " " + PRG_NAME + " my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -c=0.5 -s=. my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -c=0.9 -s=_ -m=map.tsv my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -x -xs=& -xk my_tree.nh result.tsv" );
- System.out.println( " " + PRG_NAME + " -x -xs=\"|\" my_tree.nh result.tsv" );
+ System.out.println( " " + PRG_NAME + " pp_out_tree.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -c=0.5 -s=. pp_out_tree.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -c=0.9 -s=_ -m=map.tsv pp_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xs=& -xk pp_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xs=\"|\" pp_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -x -xk -m=map.tsv pp_out_trees.sing.tre result.tsv" );
+ System.out.println( " " + PRG_NAME + " -m=map.tsv -S='(\\d+)([a-z?]*)_.+' pp_out_trees.sing.tre result.tsv" );
System.out.println();
}
}
git://source.jalview.org / jalview.git / blobdiff