From: cmzmasek Date: Thu, 30 Mar 2017 05:03:07 +0000 (-0700) Subject: in progress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9355a2b6f0e6b0192ceef9fa31b11a9233b298ab;p=jalview.git in progress --- diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index a77ac2d..22d91ba 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -26,6 +26,7 @@ package org.forester.application; import java.io.File; +import java.io.FilenameFilter; import java.io.IOException; import java.text.SimpleDateFormat; import java.util.ArrayList; @@ -62,6 +63,7 @@ public final class gsdi { final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION = "g"; final static private String GSDIR_OPTION = "r"; final static private String MOST_PARSIMONIOUS_OPTION = "m"; + final static private String SUFFIX_FOR_DIR_OPTION = "s"; final static private String GUESS_FORMAT_OF_SPECIES_TREE = "q"; final static private String TRANSFER_TAXONOMY_OPTION = "t"; final static private String HELP_OPTION_1 = "help"; @@ -71,9 +73,9 @@ public final class gsdi { final static private String REMAPPED_SUFFIX = "_gsdi_remapped.txt"; final static private String PRG_NAME = "gsdi"; final static private String PRG_VERSION = "1.001"; - final static private String PRG_DATE = "130325"; + final static private String PRG_DATE = "170327"; final static private String PRG_DESC = "general speciation duplication inference"; - final static private String E_MAIL = "phylosoft@gmail.com"; + final static private String E_MAIL = "phyloxml@gmail.com"; final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"; public static void main( final String args[] ) { @@ -92,12 +94,12 @@ public final class gsdi { catch ( final Exception e ) { ForesterUtil.fatalError( PRG_NAME, e.getMessage() ); } - if ( cla.isOptionSet( gsdi.HELP_OPTION_1 ) || cla.isOptionSet( gsdi.HELP_OPTION_2 ) ) { + if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) { System.out.println(); gsdi.print_help(); System.exit( 0 ); } - else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 3 ) ) { + else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() != 2 && cla.getNumberOfNames() != 3 ) ) { System.out.println(); System.out.println( "Wrong number of arguments." ); System.out.println(); @@ -105,14 +107,15 @@ public final class gsdi { System.exit( -1 ); } final List allowed_options = new ArrayList(); - allowed_options.add( gsdi.GSDIR_OPTION ); - allowed_options.add( gsdi.GUESS_FORMAT_OF_SPECIES_TREE ); - allowed_options.add( gsdi.MOST_PARSIMONIOUS_OPTION ); - allowed_options.add( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ); + allowed_options.add( GSDIR_OPTION ); + allowed_options.add( GUESS_FORMAT_OF_SPECIES_TREE ); + allowed_options.add( MOST_PARSIMONIOUS_OPTION ); + allowed_options.add( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ); allowed_options.add( TRANSFER_TAXONOMY_OPTION ); + allowed_options.add( SUFFIX_FOR_DIR_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "unknown option(s): " + dissallowed_options ); + ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options ); } execute( cla ); } @@ -125,18 +128,18 @@ public final class gsdi { ALGORITHM base_algorithm = ALGORITHM.GSDI; boolean most_parsimonous_duplication_model = false; boolean allow_stripping_of_gene_tree = false; - if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) { + if ( cla.isOptionSet( GSDIR_OPTION ) ) { base_algorithm = ALGORITHM.GSDIR; } - if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) { + if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) { if ( base_algorithm == ALGORITHM.SDI ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" ); + ForesterUtil.fatalError( PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" ); } most_parsimonous_duplication_model = true; } - if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) { + if ( cla.isOptionSet( ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) { if ( base_algorithm == ALGORITHM.SDI ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" ); + ForesterUtil.fatalError( PRG_NAME, "Cannot allow stripping of gene tree with SDI" ); } allow_stripping_of_gene_tree = true; } @@ -144,22 +147,92 @@ public final class gsdi { if ( cla.isOptionSet( TRANSFER_TAXONOMY_OPTION ) ) { transfer_taxonomy = true; } - Phylogeny species_tree = null; - Phylogeny gene_tree = null; + boolean use_gene_tree_dir = false; + final String gene_tree_suffix; + if ( cla.isOptionSet( SUFFIX_FOR_DIR_OPTION ) ) { + gene_tree_suffix = cla.getOptionValue( SUFFIX_FOR_DIR_OPTION ); + use_gene_tree_dir = true; + } + else { + gene_tree_suffix = null; + } File gene_tree_file = null; File species_tree_file = null; File out_file = null; File log_file = null; - EasyWriter log_writer = null; try { gene_tree_file = cla.getFile( 0 ); species_tree_file = cla.getFile( 1 ); - out_file = cla.getFile( 2 ); - log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX ); + if ( cla.getNumberOfNames() == 3 ) { + out_file = cla.getFile( 2 ); + log_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + LOGFILE_SUFFIX ); + } } catch ( final IllegalArgumentException e ) { - ForesterUtil.fatalError( gsdi.PRG_NAME, "error in command line: " + e.getMessage() ); + ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() ); } + if ( use_gene_tree_dir ) { + final File dir = new File( gene_tree_file.toString() ); + final File gene_tree_files[] = dir.listFiles( new FilenameFilter() { + + @Override + public boolean accept( final File dir, final String name ) { + return name.endsWith( gene_tree_suffix ); + } + } ); + for( final File file : gene_tree_files ) { + System.out.println( file ); + } + execute( base_algorithm, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + transfer_taxonomy, + gene_tree_files, + species_tree_file ); + } + else { + execute( base_algorithm, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + transfer_taxonomy, + gene_tree_file, + species_tree_file, + out_file, + log_file ); + } + } + + private static void execute( final ALGORITHM base_algorithm, + final boolean most_parsimonous_duplication_model, + final boolean allow_stripping_of_gene_tree, + final boolean transfer_taxonomy, + final File gene_tree_files[], + final File species_tree_file ) + throws IOException { + for( final File gene_tree_file : gene_tree_files ) { + if (gene_tree_file.getName().equals( species_tree_file.getName() )) { + continue; + } + execute( base_algorithm, + most_parsimonous_duplication_model, + allow_stripping_of_gene_tree, + transfer_taxonomy, + gene_tree_file, + species_tree_file, + new File( gene_tree_file + "gsdi" ), + new File( gene_tree_file + "gsdi_log" ) ); + } + } + + private static void execute( final ALGORITHM base_algorithm, + final boolean most_parsimonous_duplication_model, + final boolean allow_stripping_of_gene_tree, + final boolean transfer_taxonomy, + final File gene_tree_file, + final File species_tree_file, + final File out_file, + final File log_file ) + throws IOException { if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) { ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) ); } @@ -172,12 +245,15 @@ public final class gsdi { if ( ForesterUtil.isWritableFile( log_file ) != null ) { ForesterUtil.fatalError( gsdi.PRG_NAME, ForesterUtil.isWritableFile( log_file ) ); } + EasyWriter log_writer = null; try { log_writer = ForesterUtil.createEasyWriter( log_file ); } catch ( final IOException e ) { ForesterUtil.fatalError( gsdi.PRG_NAME, "Failed to create [" + log_file + "]: " + e.getMessage() ); } + Phylogeny species_tree = null; + Phylogeny gene_tree = null; try { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); gene_tree = factory.create( gene_tree_file, PhyloXmlParser.createPhyloXmlParserXsdValidating() )[ 0 ]; @@ -210,7 +286,7 @@ public final class gsdi { gene_tree.setRooted( true ); species_tree.setRooted( true ); if ( !gene_tree.isCompletelyBinary() ) { - fatalError( "user error", "gene tree is not completely binary", log_writer ); + fatalError( "user error", "gene tree [" + gene_tree_file + "] is not completely binary", log_writer ); } if ( base_algorithm == ALGORITHM.SDI ) { if ( !species_tree.isCompletelyBinary() ) { @@ -283,9 +359,9 @@ public final class gsdi { fatalError( "unexpected error", e.toString(), log_writer ); } System.out.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time ) - + "ms" ); + + "ms" ); log_writer.println( "Running time (excluding I/O) : " + ( new Date().getTime() - start_time ) - + "ms" ); + + "ms" ); System.out.println( "Mapping based on : " + gsdii.getTaxCompBase() ); log_writer.println( "Mapping based on : " + gsdii.getTaxCompBase() ); try { @@ -304,14 +380,15 @@ public final class gsdi { System.out.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() ); log_writer.println( "Wrote resulting gene tree to : " + out_file.getCanonicalPath() ); final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() ) - + SUFFIX_FOR_SPECIES_TREE_USED ); + + SUFFIX_FOR_SPECIES_TREE_USED ); try { final PhylogenyWriter writer = new PhylogenyWriter(); writer.toPhyloXML( species_tree_used_file, species_tree, 0 ); } catch ( final IOException e ) { - ForesterUtil.fatalError( PRG_NAME, "Failed to write to [" + species_tree_used_file.getCanonicalPath() - + "]: " + e.getMessage() ); + ForesterUtil.fatalError( PRG_NAME, + "Failed to write to [" + species_tree_used_file.getCanonicalPath() + "]: " + + e.getMessage() ); } System.out.println( "Wrote (stripped) species tree to : " + species_tree_used_file.getCanonicalPath() ); log_writer.println( "Wrote (stripped) species tree to : " + species_tree_used_file.getCanonicalPath() ); @@ -334,8 +411,10 @@ public final class gsdi { + gsdii.getStrippedExternalGeneTreeNodes().size() ); log_writer.println( "External nodes stripped from gene tree : " + gsdii.getStrippedExternalGeneTreeNodes().size() ); - System.out.println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() ); - log_writer.println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() ); + System.out + .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() ); + log_writer + .println( "External nodes stripped from species tree: " + gsdii.getStrippedSpeciesTreeNodes().size() ); System.out.println(); System.out.println( "Number of speciations : " + gsdii.getSpeciationsSum() ); log_writer.println( "Number of speciations : " + gsdii.getSpeciationsSum() ); @@ -379,31 +458,36 @@ public final class gsdi { } private static void print_help() { - System.out.println( "Usage: " + gsdi.PRG_NAME - + " [-options] " ); + System.out.println( "Usage: " + PRG_NAME + + " [-options] [outfile]" ); System.out.println(); System.out.println( "Options:" ); - System.out.println( " -" + gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION - + ": to allow stripping of gene tree nodes without a matching species" ); - System.out.println( " -" + gsdi.MOST_PARSIMONIOUS_OPTION - + ": use most parimonious duplication model for GSDI: " ); - System.out.println( " assign nodes as speciations which would otherwise be assiged" ); - System.out.println( " as potential duplications due to polytomies in the species tree" ); - System.out.println( " -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE - + ": to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); - System.out.println( " -" + gsdi.GSDIR_OPTION - + ": to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" ); + System.out.println( " -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + + " : to allow stripping of gene tree nodes without a matching species" ); + System.out.println( " -" + MOST_PARSIMONIOUS_OPTION + + " : use most parimonious duplication model for GSDI: " ); + System.out.println( " assign nodes as speciations which would otherwise be assiged" ); + System.out.println( " as potential duplications due to polytomies in the species tree" ); + System.out.println( " -" + GUESS_FORMAT_OF_SPECIES_TREE + + " : to allow species tree in other formats than phyloXML (i.e. Newick, NHX, Nexus)" ); + System.out.println( " -" + GSDIR_OPTION + + " : to use GSDIR algorithm instead of GSDI algorithm (re-rooting)" ); System.out.println( " -" + TRANSFER_TAXONOMY_OPTION - + ": to transfer taxonomic data from species tree to gene tree\n" ); + + " : to transfer taxonomic data from species tree to gene tree" ); + System.out.println( " -" + SUFFIX_FOR_DIR_OPTION + + "=: suffix for gene trees for analyzing entire directory of trees" ); System.out.println(); - System.out.println( "Gene tree:" ); + System.out.println(); + System.out.println( "Gene tree(s):" ); System.out.println( " in phyloXM format, with taxonomy and sequence data in appropriate fields" ); System.out.println(); System.out.println( "Species tree:" ); - System.out.println( " in phyloXML format (unless option -" + gsdi.GUESS_FORMAT_OF_SPECIES_TREE + " is used)" ); + System.out.println( " in phyloXML format (unless option -" + GUESS_FORMAT_OF_SPECIES_TREE + " is used)" ); System.out.println(); - System.out.println( "Example: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION - + " gene_tree.xml tree_of_life.xml out.xml" ); + System.out.println( "Examples: gsdi -" + ALLOW_STRIPPING_OF_GENE_TREE_OPTION + + " gene_tree.xml tree_of_life.xml out.xml" ); + System.out.println( " gsdi -" + SUFFIX_FOR_DIR_OPTION + " -" + SUFFIX_FOR_DIR_OPTION + "=.xml" + + " gene_tree_dir tree_of_life.xml" ); System.out.println(); } @@ -444,7 +528,8 @@ public final class gsdi { private static void writeToRemappedFile( final File out_file, final SortedSet remapped, - final EasyWriter log_writer ) throws IOException { + final EasyWriter log_writer ) + throws IOException { final File file = new File( ForesterUtil.removeSuffix( out_file.toString() ) + REMAPPED_SUFFIX ); final EasyWriter remapped_writer = ForesterUtil.createEasyWriter( file ); for( final String s : remapped ) { diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index c8ea6d3..b9d544c 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -219,7 +219,7 @@ public class surfacing { final static private String SEQ_EXTRACT_OPTION = "prot_extract"; final static private String PRG_VERSION = "2.501"; final static private String PRG_DATE = "170327"; - final static private String E_MAIL = "czmasek@burnham.org"; + final static private String E_MAIL = "phyloxml@gmail.com"; final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester/surfacing"; final static private boolean IGNORE_DUFS_DEFAULT = true; final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;