From: cmzmasek Date: Mon, 21 Aug 2017 18:56:31 +0000 (-0700) Subject: in progress... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cb49ee5684c6907b3161db82ff9aea72961b8548;p=jalview.git in progress... --- diff --git a/forester/.classpath b/forester/.classpath index 4437209..baf7e77 100644 --- a/forester/.classpath +++ b/forester/.classpath @@ -2,8 +2,8 @@ - + diff --git a/forester/.gitignore b/forester/.gitignore index ae3c172..7b24670 100644 --- a/forester/.gitignore +++ b/forester/.gitignore @@ -1 +1,12 @@ -/bin/ +.metadata +bin/ +tmp/ +java/classes/ +*.class +*.tmp +*.bak +*.swp +local.properties +.project + + diff --git a/forester/java/forester.jar b/forester/java/forester.jar index 399915a..bbb00f9 100644 Binary files a/forester/java/forester.jar and b/forester/java/forester.jar differ diff --git a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java index 207b57c..5a5afea 100644 --- a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java +++ b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java @@ -32,7 +32,15 @@ public class CladeAnalysisTest { failed = true; } if ( !testCladeAnalysis4() ) { - System.out.println( "Clade analysis 3 failed" ); + System.out.println( "Clade analysis 4 failed" ); + failed = true; + } + if ( !testCladeAnalysis5() ) { + System.out.println( "Clade analysis 5 failed" ); + failed = true; + } + if ( !testCladeAnalysis6() ) { + System.out.println( "Clade analysis 6 failed" ); failed = true; } if ( !failed ) { @@ -53,6 +61,12 @@ public class CladeAnalysisTest { if ( !testCladeAnalysis4() ) { return false; } + if ( !testCladeAnalysis5() ) { + return false; + } + if ( !testCladeAnalysis6() ) { + return false; + } return true; } @@ -761,4 +775,88 @@ public class CladeAnalysisTest { } return true; } + + private static boolean testCladeAnalysis5() { + try { + final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_3.xml" ); + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true ); + final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ]; + Pattern query = Pattern.compile(".+#\\d+_M=(.+)"); + Result2 res = Analysis2.execute( p1, query, "." ); + + res.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + // Result res = Analysis.execute( p1, "A.1.1.1", "." ); + /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 4 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + }*/ + + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testCladeAnalysis6() { + try { + final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_4.xml" ); + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true ); + final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ]; + Pattern query = Pattern.compile(".+#\\d+_M=(.+)"); + Result2 res = Analysis2.execute( p1, query, "." ); + + res.analyzeGreatestCommonPrefixes( 0.45 ); + System.out.print( res.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + // Result res = Analysis.execute( p1, "A.1.1.1", "." ); + /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 4 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + }*/ + + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } } diff --git a/forester/java/src/org/forester/clade_analysis/Result2.java b/forester/java/src/org/forester/clade_analysis/Result2.java index 2bd4911..1cfc3ff 100644 --- a/forester/java/src/org/forester/clade_analysis/Result2.java +++ b/forester/java/src/org/forester/clade_analysis/Result2.java @@ -258,8 +258,7 @@ public final class Result2 { @Override public int compare( final Prefix x, final Prefix y ) { - final int start_comparison = compare( x.getConfidence(), y.getConfidence() ); - return start_comparison; + return compare( x.getConfidence(), y.getConfidence() ); } private int compare( final double a, final double b ) { diff --git a/forester/perl/phylo_pl.pl b/forester/perl/phylo_pl.pl index 39d6e20..77c603d 100755 --- a/forester/perl/phylo_pl.pl +++ b/forester/perl/phylo_pl.pl @@ -762,13 +762,13 @@ if ( $use_raxml == 1 ) { } # NOTE. RaxML does its own bootstrapping. - &executeRaxml( "align", $RAXML_MODEL_BASE.$invar.$model."F", $bootstraps, $seed, "xxx", $RAXML_ALGORITHM ); + &executeRaxml( "align", $RAXML_MODEL_BASE.$invar.$model."X", $bootstraps, $seed, "xxx", $RAXML_ALGORITHM ); print( "\n========== RAxML end =========\n\n" ); &rm( "RAxML_log.xxx" ); &rm( "RAxML_parsimonyTree.xxx" ); &mv( "RAxML_info.xxx", $outfile."_raxml_info" ); - if ( $bootstraps > 1 ) { + # if ( $bootstraps > 1 ) { &rm( "RAxML_bestTree.xxx" ); &mv( "RAxML_bipartitions.xxx", $CONSENSUS_RAXML ); &append( "RAxML_bootstrap.xxx", $OUTTREES_ALL ); @@ -779,10 +779,10 @@ if ( $use_raxml == 1 ) { &rm( "RAxML_bootstrap.xxx" ); } $all_count++; - } - else { - &mv( "RAxML_result.xxx", $OUTTREE_RAXML ); - } + # } + # else { + # &mv( "RAxML_result.xxx", $OUTTREE_RAXML ); + # } } @@ -1226,7 +1226,8 @@ else { &to_phyloxml( $OUTTREE_WEIGHBOR, $weighbor_outtree, 0, 1 ); } if ( $use_raxml == 1 ) { - &to_phyloxml( $OUTTREE_RAXML, $raxml_outtree, 0, 1 ); + # &to_phyloxml( $OUTTREE_RAXML, $raxml_outtree, 0, 1 ); + &to_phyloxml( $CONSENSUS_RAXML, $raxml_outtree, 1, 1 ); } if ( $use_phyml == 1 ) { &to_phyloxml( $OUTTREE_PHYML, $phyml_outtree, 0, 1 ); @@ -1324,7 +1325,7 @@ chdir( $current_dir ) rmdir( $temp_dir ) || print "\n\n$0: Warning: Could not remove <<$temp_dir>>: $!\n\n"; -print "\n\n\n$0 successfully comleted.\n\n"; +print "\n\n\n$0 successfully completed.\n\n"; exit( 0 ); @@ -1350,8 +1351,10 @@ sub executeRaxml { my $outfile_suffix = $_[ 4 ]; my $algo = $_[ 5 ]; + $replicates = 100; + &testForTextFilePresence( $msa ); - my $command = "$RAXML -m $model -s $msa -n $outfile_suffix"; + my $command = "$RAXML -p 27 -m $model -s $msa -n $outfile_suffix"; if ( $replicates > 1 ) { $command = $command . " -x $seed -N $replicates"; @@ -1444,7 +1447,7 @@ sub dieIfFileExists { sub dieIfFileNotExists { my $file = $_[ 0 ]; unless ( ( -s $file ) && ( -f $file ) ) { - die( "\n\n$0: \"$file\" does not exist or is empty" ); + die( "\n\n$0: \"$file\" does not exist or is empty" ); } } diff --git a/forester/ruby/evoruby/lib/evo/tool/domains_to_forester.rb b/forester/ruby/evoruby/lib/evo/tool/domains_to_forester.rb index a090d52..51398ed 100644 --- a/forester/ruby/evoruby/lib/evo/tool/domains_to_forester.rb +++ b/forester/ruby/evoruby/lib/evo/tool/domains_to_forester.rb @@ -184,9 +184,12 @@ module Evoruby original_sequences_file = cla.get_file_name( 1 ) else hmmscan_index = domains_list_file.index(Constants::HMMSCAN) + puts domains_list_file if ( hmmscan_index != nil ) prefix = domains_list_file[0 .. hmmscan_index-1 ] + puts prefix suffix = Constants::ID_NORMALIZED_FASTA_FILE_SUFFIX + puts suffix files = Dir.entries( "." ) matching_files = Util.get_matching_files( files, prefix, suffix) if matching_files.length < 1 diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index b2f6446..3b51469 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -22,7 +22,7 @@ module Evoruby DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -mp -or' DECORATOR_OPTIONS_DOMAINS = '-p -t' SLEEP_TIME = 0.01 - REMOVE_NI = true + REMOVE_NI = false TMP_FILE_1 = '___PD1___' TMP_FILE_2 = '___PD2___' LOG_FILE = '00_phylogenies_decorator.log' diff --git a/forester/ruby/evoruby/lib/evo/util/constants.rb b/forester/ruby/evoruby/lib/evo/util/constants.rb index c9e15f9..4866f69 100644 --- a/forester/ruby/evoruby/lib/evo/util/constants.rb +++ b/forester/ruby/evoruby/lib/evo/util/constants.rb @@ -14,7 +14,7 @@ module Evoruby ID_NORMALIZED_FASTA_FILE_SUFFIX = "_ni.fasta" ID_MAP_FILE_SUFFIX = ".nim" DOMAIN_TABLE_SUFFIX = "_domain_table" - HMMSCAN = "_hmmscan_" + HMMSCAN = "_hmmscan" DOMAINS_TO_FORESTER_OUTFILE_SUFFIX = ".dff" DOMAINS_TO_FORESTER_EVALUE_CUTOFF_SUFFIX = "_dtfE"