X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=24acfe8b3d51fb09a41c4f93f38b7ebaff572017;hb=b5fe992f707cdad84255eb85040effbee97d61b3;hp=aa5063925570eee0c3d3e3ac91a217cfb34e5dfd;hpb=975cabe8898d1fa574380f5800c2d69d8f632b0d;p=jalview.git diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index aa50639..24acfe8 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -47,13 +47,6 @@ public class rio { 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 HELP_OPTION_1 = "help"; - final static private String LOGFILE_SUFFIX = "_RIO_log.tsv"; - final static private String STRIPPED_SPECIES_TREE_SUFFIX = "_RIO_sst.xml"; - final static private String ORTHO_OUTTABLE_SUFFIX = "_RIO_orthologies.tsv"; - final static private String ORTHO_OUTTABLE_WITH_MAP_SUFFIX = "_RIO_orthologies_ext_map.tsv"; - final static private String OUT_MIN_DUP_GENE_TREE_SUFFIX = "_RIO_gene_tree_min_dup_"; - final static private String OUT_MED_DUP_GENE_TREE_SUFFIX = "_RIO_gene_tree_med_dup_"; - final static private String ORTHOLOG_GROUPS_SUFFIX = "_RIO_ortholog_groups.tsv"; final static private String HELP_OPTION_2 = "h"; final static private String GT_FIRST = "f"; final static private String GT_LAST = "l"; @@ -63,7 +56,10 @@ public class rio { final static private String GENE_TREES_SUFFIX_OPTION = "g"; final static private String MAPPINGS_DIR_OPTION = "m"; final static private String MAPPINGS_SUFFIX_OPTION = "ms"; + final static private String CONSENSUS_TREES_DIR_OPTION = "co"; + final static private String CONSENSUS_TREES_SUFFIX_OPTION = "cos"; final static private String MAPPINGS_SUFFIX_DEFAULT = ".nim"; + final static private String CONSENSUS_TREE_SUFFIX_DEFAULT = ".xml"; final static private String ORTHOLOG_GROUPS_CUTOFF_OPTION = "c"; final static private String GENE_TREES_SUFFIX_DEFAULT = ".mlt"; final static private double ORTHOLOG_GROUPS_CUTOFF_DEFAULT = 0.5; @@ -102,6 +98,8 @@ public class rio { allowed_options.add( ORTHOLOG_GROUPS_CUTOFF_OPTION ); allowed_options.add( MAPPINGS_DIR_OPTION ); allowed_options.add( MAPPINGS_SUFFIX_OPTION ); + allowed_options.add( CONSENSUS_TREES_DIR_OPTION ); + allowed_options.add( CONSENSUS_TREES_SUFFIX_OPTION ); final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options ); if ( dissallowed_options.length() > 0 ) { ForesterUtil.fatalError( "unknown option(s): " + dissallowed_options ); @@ -325,6 +323,49 @@ public class rio { else { id_mapping_suffix = MAPPINGS_SUFFIX_DEFAULT; } + boolean perform_gsdir_on_best_tree; + final File best_trees_indir; + if ( cla.isOptionSet( CONSENSUS_TREES_DIR_OPTION ) ) { + best_trees_indir = new File( cla.getOptionValue( CONSENSUS_TREES_DIR_OPTION ) ); + perform_gsdir_on_best_tree = true; + if ( !use_dir ) { + ForesterUtil + .fatalError( "no consensus (\"best\") gene tree GSDIR analysis when operating on individual gene trees" ); + } + if ( !best_trees_indir.exists() ) { + ForesterUtil.fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + + "\" does not exist" ); + } + if ( !best_trees_indir.isDirectory() ) { + ForesterUtil.fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + + "\" is not a directory" ); + } + if ( best_trees_indir.listFiles().length < 1 ) { + ForesterUtil + .fatalError( "consensus (\"best\") gene tree directory \"" + best_trees_indir + "\" is empty" ); + } + } + else { + best_trees_indir = null; + perform_gsdir_on_best_tree = false; + } + final String best_trees_suffix; + if ( cla.isOptionSet( CONSENSUS_TREES_SUFFIX_OPTION ) ) { + if ( !use_dir ) { + ForesterUtil + .fatalError( "no consensus (\"best\") gene tree suffix option when operating on individual gene trees" ); + } + if ( !perform_gsdir_on_best_tree ) { + ForesterUtil.fatalError( "no consensus (\"best\") gene tree directory given" ); + } + if ( !cla.isOptionHasAValue( CONSENSUS_TREES_SUFFIX_OPTION ) ) { + ForesterUtil.fatalError( "no value for -" + CONSENSUS_TREES_SUFFIX_OPTION ); + } + best_trees_suffix = cla.getOptionValueAsCleanString( CONSENSUS_TREES_SUFFIX_OPTION ); + } + else { + best_trees_suffix = CONSENSUS_TREE_SUFFIX_DEFAULT; + } ForesterUtil.fatalErrorIfFileNotReadable( species_tree_file ); if ( !use_dir && orthology_outtable.exists() ) { ForesterUtil.fatalError( "\"" + orthology_outtable + "\" already exists" ); @@ -352,6 +393,15 @@ public class rio { } System.out.println( "Id mappings suffix :\t" + id_mapping_suffix ); } + if ( perform_gsdir_on_best_tree ) { + try { + System.out.println( "Consensus (\"best\") gene trees in-dir:\t" + best_trees_indir.getCanonicalPath() ); + } + catch ( IOException e ) { + ForesterUtil.fatalError( e.getLocalizedMessage() ); + } + System.out.println( "Consensus (\"best\") gene trees suffix:\t" + best_trees_suffix ); + } if ( use_dir ) { System.out.println( "Out-dir :\t" + outdir ); } @@ -466,6 +516,26 @@ public class rio { log.print( "\t" ); log.print( species_tree_file.getCanonicalPath() ); log.println(); + if ( perform_id_mapping ) { + log.print( "# Id mappings in-dir" ); + log.print( "\t" ); + log.print( id_mapping_dir.getCanonicalPath() ); + log.println(); + log.print( "# Id mappings suffix" ); + log.print( "\t" ); + log.print( id_mapping_suffix ); + log.println(); + } + if ( perform_gsdir_on_best_tree ) { + log.print( "# Consensus (\"best\") gene tree dir" ); + log.print( "\t" ); + log.print( best_trees_indir.getCanonicalPath() ); + log.println(); + log.print( "# Consensus (\"best\") gene tree suffix" ); + log.print( "\t" ); + log.print( best_trees_suffix ); + log.println(); + } log.print( "# Out-dir" ); log.print( "\t" ); log.print( outdir.getCanonicalPath() ); @@ -520,9 +590,11 @@ public class rio { log.print( "\t" ); log.print( "0.95 O GROUPS" ); log.print( "\t" ); - if ( true ) { //TODO + if ( perform_gsdir_on_best_tree ) { log.print( "BEST TREE DUP" ); log.print( "\t" ); + log.print( "MEDIAN DUP - BEST TREE DUP" ); + log.print( "\t" ); } log.print( "MEDIAN DUP" ); log.print( "\t" ); @@ -556,22 +628,23 @@ public class rio { RIOUtil.executeAnalysis( gf, species_tree_file, new File( outdir.getCanonicalFile() + "/" + outname - + ORTHO_OUTTABLE_SUFFIX ), + + RIOUtil.ORTHO_OUTTABLE_SUFFIX ), new File( outdir.getCanonicalFile() + "/" + outname - + ORTHO_OUTTABLE_WITH_MAP_SUFFIX ), + + RIOUtil.ORTHO_OUTTABLE_WITH_MAP_SUFFIX ), new File( outdir.getCanonicalFile() + "/" + outname - + ORTHOLOG_GROUPS_SUFFIX ), - new File( outdir.getCanonicalFile() + "/" + outname + LOGFILE_SUFFIX ), + + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ), + new File( outdir.getCanonicalFile() + "/" + outname + + RIOUtil.LOGFILE_SUFFIX ), outgroup, rerooting, gt_first, gt_last, new File( outdir.getCanonicalFile() + "/" + outname - + STRIPPED_SPECIES_TREE_SUFFIX ), + + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ), new File( outdir.getCanonicalFile() + "/" + outname - + OUT_MIN_DUP_GENE_TREE_SUFFIX ), + + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ), new File( outdir.getCanonicalFile() + "/" + outname - + OUT_MED_DUP_GENE_TREE_SUFFIX ), + + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ), true, algorithm, true, @@ -579,7 +652,11 @@ public class rio { ortholog_group_cutoff, perform_id_mapping, id_mapping_dir, - id_mapping_suffix ); + id_mapping_suffix, + perform_gsdir_on_best_tree, + outdir, + best_trees_indir, + best_trees_suffix ); } catch ( IOException e ) { ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() ); @@ -590,23 +667,20 @@ public class rio { System.out.println(); } else { - String outname = orthology_outtable.toString(); - if ( outname.indexOf( "." ) > 0 ) { - outname = outname.substring( 0, outname.lastIndexOf( "." ) ); - } + String outname = ForesterUtil.removeFileExtension( orthology_outtable.toString() ); RIOUtil.executeAnalysis( gene_trees_file, species_tree_file, orthology_outtable, null, - new File( outname + ORTHOLOG_GROUPS_SUFFIX ), + new File( outname + RIOUtil.ORTHOLOG_GROUPS_SUFFIX ), logfile, outgroup, rerooting, gt_first, gt_last, - new File( outname + STRIPPED_SPECIES_TREE_SUFFIX ), - new File( outname + OUT_MIN_DUP_GENE_TREE_SUFFIX ), - new File( outname + OUT_MED_DUP_GENE_TREE_SUFFIX ), + new File( outname + RIOUtil.STRIPPED_SPECIES_TREE_SUFFIX ), + new File( outname + RIOUtil.OUT_MIN_DUP_GENE_TREE_SUFFIX ), + new File( outname + RIOUtil.OUT_MED_DUP_GENE_TREE_SUFFIX ), algorithm == ALGORITHM.GSDIR, algorithm, false, @@ -614,6 +688,10 @@ public class rio { ortholog_group_cutoff, false, null, + null, + false, + null, + null, null ); } if ( !use_dir ) { @@ -661,6 +739,11 @@ public class rio { System.out.println( " -" + MAPPINGS_DIR_OPTION + "= : directory for id mapping files" ); System.out.println( " -" + MAPPINGS_SUFFIX_OPTION + "= : suffix for id mapping files (default: " + MAPPINGS_SUFFIX_DEFAULT + ")" ); + System.out.println( " -" + CONSENSUS_TREES_DIR_OPTION + + "= : directory with consenus (\"best\") gene trees to be analyzed with GSDIR" ); + System.out.println( " -" + CONSENSUS_TREES_SUFFIX_OPTION + + "= : suffix for consenus (\"best\") gene trees (default: " + CONSENSUS_TREE_SUFFIX_DEFAULT + + ")" ); System.out.println(); System.out.println( " Formats" ); System.out @@ -678,6 +761,8 @@ public class rio { System.out.println( " rio -g=.xml gene_trees_dir species.xml out_dir log.tsv" ); System.out.println( " rio -g=.mlt -m=id_maps_dir -ms=.nim -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); System.out.println( " rio -m=id_maps_dir -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); + System.out + .println( " rio -m=id_maps_dir -co=consensus_dir -cos=.xml -c=0.8 gene_trees_dir species.xml out_dir log.tsv" ); System.out.println(); System.exit( -1 ); }