From c0439ed8b088887ffea2faf11bc7897333287cb3 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Thu, 18 May 2017 11:51:06 -0700 Subject: [PATCH] in progress... --- forester/java/src/org/forester/application/fasta_split.java | 10 ++++++---- forester/java/src/org/forester/application/surfacing.java | 8 ++++---- .../org/forester/surfacing/MinimalDomainomeCalculator.java | 2 +- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/forester/java/src/org/forester/application/fasta_split.java b/forester/java/src/org/forester/application/fasta_split.java index 16999c7..f71d0a1 100644 --- a/forester/java/src/org/forester/application/fasta_split.java +++ b/forester/java/src/org/forester/application/fasta_split.java @@ -51,7 +51,7 @@ public final class fasta_split { final static private String PRG_NAME = "fasta_split"; final static private String PRG_VERSION = "1.00"; - final static private String PRG_DATE = "150331"; + final static private String PRG_DATE = "170516"; public static void main( final String args[] ) { ForesterUtil.printProgramInformation( fasta_split.PRG_NAME, fasta_split.PRG_VERSION, fasta_split.PRG_DATE ); @@ -98,9 +98,8 @@ public final class fasta_split { } System.out.println( "Read " + seqs.size() + " sequences" ); final Map> output = new HashMap>(); - int cc = 0; + for( final MolecularSequence seq : seqs ) { - ++cc; final Matcher m = pa.matcher( seq.getIdentifier() ); if ( m.find() ) { final String key = m.group( 1 ); @@ -139,7 +138,10 @@ public final class fasta_split { private static void argumentsError() { System.out.println( PRG_NAME + " " ); - System.out.println( "Example: " + PRG_NAME + " \"v-germ=(\\S+)\" tt.fasta outdir" ); + System.out.println(); + System.out.println( "Examples: " ); + System.out.println( " " + PRG_NAME + " \"v-germ=(\\S+)\" tt.fasta outdir" ); + System.out.println( " " + PRG_NAME + " \"(\\S+?)\\|\" seqs.fasta outdir" ); System.out.println(); System.exit( -1 ); } diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 9326929..fc87a96 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -217,8 +217,8 @@ public class surfacing { final static private String INPUT_GENOMES_FILE_OPTION = "genomes"; final static private String INPUT_SPECIES_TREE_OPTION = "species_tree"; final static private String SEQ_EXTRACT_OPTION = "prot_extract"; - final static private String PRG_VERSION = "2.502"; - final static private String PRG_DATE = "170511"; + final static private String PRG_VERSION = "2.503"; + final static private String PRG_DATE = "170518"; 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; @@ -1776,7 +1776,7 @@ public class surfacing { ForesterUtil .programMessage( PRG_NAME, "Wrote domain promiscuities to: " + per_genome_domain_promiscuity_statistics_file ); - final int LEVEL = 2; + final int LEVEL = 0; try { MinimalDomainomeCalculator.calc( false, intrees[ 0 ], @@ -2315,7 +2315,7 @@ public class surfacing { .println( "Example 3: surfacing -species_tree=master_tree.xml -no_eo -ie=1e-6 -mrel=0.5 -mo=10 -dufs -genomes=genomes.txt -out_dir=a605 -o=a605" ); System.out.println(); System.out - .println("[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" ); + .println( "[next step for phylogenomic analysis pipeline (example, in \"DAS\" dir): % mse.rb .prot . FL_seqs DA_seqs path/to/genome_locations.txt]" ); System.out.println(); } } diff --git a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java index d48cc2b..0c9ca73 100644 --- a/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java +++ b/forester/java/src/org/forester/surfacing/MinimalDomainomeCalculator.java @@ -85,7 +85,7 @@ public final class MinimalDomainomeCalculator { final String rank = node.getNodeData().isHasTaxonomy() ? node.getNodeData().getTaxonomy().getRank() : ""; final List external_descs = node.getAllExternalDescendants(); if ( ( target_level < 1 ) || ( node_level >= target_level ) ) { - out.write( species_name + " " + node_level); + out.write( species_name ); if ( !ForesterUtil.isEmpty( common ) ) { out.write( "\t" + common ); } -- 1.7.10.2