From: cmzmasek Date: Wed, 6 Sep 2017 18:45:15 +0000 (-0700) Subject: added mapping X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=39252a900803f9bb6349306685ec5ae160fa881e;p=jalview.git added mapping --- diff --git a/forester/java/src/org/forester/application/cladinator.java b/forester/java/src/org/forester/application/cladinator.java index c53d102..d1b4f44 100644 --- a/forester/java/src/org/forester/application/cladinator.java +++ b/forester/java/src/org/forester/application/cladinator.java @@ -30,6 +30,8 @@ import java.io.IOException; import java.text.DecimalFormat; import java.util.ArrayList; import java.util.List; +import java.util.SortedMap; +import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; @@ -39,8 +41,12 @@ import org.forester.clade_analysis.ResultMulti; import org.forester.io.parsers.PhylogenyParser; import org.forester.io.parsers.util.ParserUtils; import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; +import org.forester.phylogeny.iterators.PhylogenyNodeIterator; +import org.forester.util.BasicTable; +import org.forester.util.BasicTableParser; import org.forester.util.CommandLineArguments; import org.forester.util.EasyWriter; import org.forester.util.ForesterUtil; @@ -48,8 +54,8 @@ import org.forester.util.ForesterUtil; public final class cladinator { final static private String PRG_NAME = "cladinator"; - final static private String PRG_VERSION = "1.00"; - final static private String PRG_DATE = "170902"; + final static private String PRG_VERSION = "1.01"; + final static private String PRG_DATE = "170906"; 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"; @@ -58,6 +64,7 @@ public final class cladinator { final static private String SEP_OPTION = "s"; final static private String QUERY_PATTERN_OPTION = "q"; final static private String SPECIFICS_CUTOFF_OPTION = "c"; + final static private String MAPPING_FILE_OPTION = "m"; final static private double SPECIFICS_CUTOFF_DEFAULT = 0.8; final static private String SEP_DEFAULT = "."; final static private Pattern QUERY_PATTERN_DEFAULT = AnalysisMulti.DEFAULT_QUERY_PATTERN_FOR_PPLACER_TYPE; @@ -92,6 +99,7 @@ public final class cladinator { allowed_options.add( SEP_OPTION ); allowed_options.add( QUERY_PATTERN_OPTION ); allowed_options.add( SPECIFICS_CUTOFF_OPTION ); + allowed_options.add( MAPPING_FILE_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); @@ -132,6 +140,20 @@ public final class cladinator { ForesterUtil.fatalError( PRG_NAME, "no value for query pattern option" ); } } + File mapping_file = null; + if ( cla.isOptionSet( MAPPING_FILE_OPTION ) ) { + if ( cla.isOptionValueSet( MAPPING_FILE_OPTION ) ) { + final String mapping_file_str = cla.getOptionValue( MAPPING_FILE_OPTION ); + final String error = ForesterUtil.isReadableFile( mapping_file_str ); + if ( !ForesterUtil.isEmpty( error ) ) { + ForesterUtil.fatalError( PRG_NAME, error ); + } + mapping_file = new File( mapping_file_str ); + } + else { + ForesterUtil.fatalError( PRG_NAME, "no value for mapping file" ); + } + } final Pattern pattern = ( compiled_query_str != null ) ? compiled_query_str : QUERY_PATTERN_DEFAULT; final File intreefile = cla.getFile( 0 ); final String error_intreefile = ForesterUtil.isReadableFile( intreefile ); @@ -149,8 +171,27 @@ public final class cladinator { else { outtablefile = null; } + final BasicTable t; + final SortedMap map; + if ( mapping_file != null ) { + t = BasicTableParser.parse( mapping_file, '\t' ); + if ( t.getNumberOfColumns() != 2 ) { + ForesterUtil.fatalError( PRG_NAME, + "mapping file needs to have 2 tab-separated columns, not " + + t.getNumberOfColumns() ); + } + map = t.getColumnsAsMap( 0, 1 ); + } + else { + t = null; + map = null; + } System.out.println( "Input tree : " + intreefile ); System.out.println( "Specific-hit support cutoff: " + cutoff_specifics ); + if ( mapping_file != null ) { + System.out.println( "Mapping file : " + mapping_file + " (" + t.getNumberOfRows() + + " rows)" ); + } System.out.println( "Annotation-separator : " + separator ); System.out.println( "Query pattern : " + pattern ); if ( outtablefile != null ) { @@ -167,6 +208,9 @@ public final class cladinator { System.exit( -1 ); } System.out.println( "Ext. nodes in input tree : " + p.getNumberOfExternalNodes() ); + if ( map != null ) { + performMapping( pattern, map, p ); + } final ResultMulti res = AnalysisMulti.execute( p, pattern, separator, cutoff_specifics ); printResult( res ); if ( outtablefile != null ) { @@ -185,6 +229,26 @@ public final class cladinator { } } + private final static void performMapping( final Pattern pattern, + final SortedMap map, + Phylogeny p ) { + final PhylogenyNodeIterator it = p.iteratorExternalForward(); + while ( it.hasNext() ) { + final PhylogenyNode node = it.next(); + final String name = node.getName(); + if ( ForesterUtil.isEmpty( name ) ) { + ForesterUtil.fatalError( PRG_NAME, "external node with empty name found" ); + } + final Matcher m = pattern.matcher( name ); + if ( !m.find() ) { + if ( !map.containsKey( name ) ) { + ForesterUtil.fatalError( PRG_NAME, "no mapping for \"" + name + "\" found" ); + } + node.setName( map.get( name ) ); + } + } + } + private final static void printResult( final ResultMulti res ) { System.out.println(); System.out.println( "Result:" ); @@ -292,13 +356,17 @@ public final class cladinator { + ")" ); System.out.println( " -" + SEP_OPTION + "=: the annotation-separator to be used (default: " + SEP_DEFAULT + ")" ); + System.out.println( " -" + MAPPING_FILE_OPTION + + "=: to map node names to appropriate annotations (tab-separated, two columns) (default: no mapping)" ); System.out.println( " -" + QUERY_PATTERN_OPTION + "=: the regular expression for the query (default: \"" + QUERY_PATTERN_DEFAULT + "\" for pplacer output)" ); System.out.println(); - System.out.println( "Example:" ); + 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(); } }