Merge pull request #30 from molbiodiv/develop

Version 1.1.0

.travis.yml

@@ -20,7 +20,7 @@ install:
 script: 
  - perl Makefile.PL
  - make
- - PERL5OPT=-MDevel::Cover=-coverage,statement,branch,condition,path,subroutine prove -v
+ - PERL5OPT=-MDevel::Cover=-coverage,statement,branch,condition,path,subroutine travis_wait 30 prove -v
  - cover
 #after_success:
 # - cover -report coveralls

README.org

@@ -166,6 +166,15 @@ Options:
  (as long as they stay unique) so --raxml-p=12345 is equivalent to
  --raxml-p-parsimonyRandomSeed=12345
 
+ [--raxml-aa-substitiution-model "<MODEL>"]
+ The aminoacid substitution model used for the partitions by RAxML.
+ Valid options for RAxML 8.x are: DAYHOFF, DCMUT, JTT, MTREV, WAG,
+ RTREV, CPREV, VT, BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB, HIVB,
+ HIVW, JTTDCMUT, FLU, STMTREV, DUMMY, DUMMY2, AUTO, LG4M, LG4X,
+ PROT_FILE, GTR_UNLINKED, GTR bcgTree will not check whether the
+ provided option is valid but rather pass it to RAxML literally.
+ Default: AUTO
+
  [--raxml-args "<ARGS>"]
  Arbitrary options to pass through to RAxML. The ARGS part should be
  in quotes and is appended to the RAxML command as given.
@@ -211,6 +220,12 @@ The font is from [[fontlibrary.org]]:
  - [[https://fontlibrary.org/en/font/ranchers][Ranchers]] ([[http://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=OFL][SIL Open Font License]])
 ** Changes
 [[https://travis-ci.org/molbiodiv/bcgTree][https://travis-ci.org/molbiodiv/bcgTree.svg?branch=master]]
+*** v1.1.0 <2018-07-19 Do>
+ - Breaking: the default aa substitution model for RAxML changed from WAG to AUTO.
+ This has an impact on performance (it is faster to set this parameter to a fixed value).
+ To get the same behaviour as in earlier versions pass ~--raxml-aa-substitution-model=WAG~
+ - Add parameter ~--raxml-aa-substitution-model~ (#29)
+ - Add HMMs of [[https://www.ezbiocloud.net/tools/ubcg][UBCG]] (#25)
 *** v1.0.10 <2017-03-07 Di>
  - Fix GUI, add scrollbar (#23)
  - Add parameter --raxml-args (#22)

bcgTreeGUI/src/bcgTree/gui/BcgTree.java

@@ -78,6 +78,7 @@ public static void main(String[] args) {
  private JTextField hmmfileTextField;
  private JSpinner minProteomesSpinner;
  private JCheckBox allProteomesCheckbox;
+ private JTextField raxmlAaSubstitutionModelTextField;
  private JTextField raxmlArgsTextField;
 
  public BcgTree(){
@@ -214,7 +215,7 @@ public void actionPerformed(ActionEvent e) {
  }
 
  private JPanel getAdvancedSettingsPanel(){
- JPanel advancedSettingsPanel = new JPanel(new GridLayout(8, 2));
+ JPanel advancedSettingsPanel = new JPanel(new GridLayout(9, 2));
  advancedSettingsPanel.add(new JLabel("--bootstraps"));
  bootstrapSpinner = new JSpinner(new SpinnerNumberModel(10, 1, 1000, 1));
  advancedSettingsPanel.add(bootstrapSpinner);
@@ -227,6 +228,9 @@ private JPanel getAdvancedSettingsPanel(){
  advancedSettingsPanel.add(new JLabel("--raxml-p-parsimonyRandomSeed"));
  randomSeedPTextField = new JTextField("", DEFAULT_TEXTFIELD_COLUMNS);
  advancedSettingsPanel.add(randomSeedPTextField);
+ advancedSettingsPanel.add(new JLabel("--raxml-aa-substitution-model"));
+ raxmlAaSubstitutionModelTextField = new JTextField("AUTO", DEFAULT_TEXTFIELD_COLUMNS);
+ advancedSettingsPanel.add(raxmlAaSubstitutionModelTextField);
  advancedSettingsPanel.add(new JLabel("--raxml-args"));
  raxmlArgsTextField = new JTextField("", DEFAULT_TEXTFIELD_COLUMNS);
  advancedSettingsPanel.add(raxmlArgsTextField);
@@ -289,6 +293,10 @@ public void actionPerformed(ActionEvent e) {
  if(! xSeed.equals("")){
  writer.println("--raxml-x-rapidBootstrapRandomNumberSeed="+xSeed);
  }
+ String raxmlAaSubstitutionModel = raxmlAaSubstitutionModelTextField.getText();
+ if(! raxmlAaSubstitutionModel.equals("")){
+ writer.println("--raxml-aa-substitution-model=\""+raxmlAaSubstitutionModel+"\"");
+ }
  String raxmlArgs = raxmlArgsTextField.getText();
  if(! raxmlArgs.equals("")){
  writer.println("--raxml-args=\""+raxmlArgs+"\"");

bin/bcgTree.pl

@@ -198,6 +198,23 @@ =head1 OPTIONS
 
 =back
 
+=item [--raxml-aa-substitiution-model "<MODEL>"]
+
+The aminoacid substitution model used for the partitions by RAxML.
+Valid options for RAxML 8.x are:
+DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, LG,
+MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, STMTREV, DUMMY, DUMMY2, AUTO,
+LG4M, LG4X, PROT_FILE, GTR_UNLINKED, GTR
+bcgTree will not check whether the provided option is valid but rather pass
+it to RAxML literally.
+Default: AUTO
+
+=cut
+
+$options{'raxml-aa-substitution-model=s'} = \( my $opt_raxml_aa_subst = "AUTO");
+
+=back
+
 =item [--raxml-args "<ARGS>"]
 
 Arbitrary options to pass through to RAxML.
@@ -254,6 +271,7 @@ =head1 CODE
  'raxml-p' => $opt_raxml_p,
  'raxml-x' => $opt_raxml_x,
  'min-proteomes' => $opt_min_proteomes,
+ 'raxml-aa-substitution-model' => $opt_raxml_aa_subst,
  'raxml-args' => $opt_raxml_args
 });
 $bcgTree->check_existence_of_fasta_files();

lib/bcgTree.pm

@@ -11,7 +11,7 @@ use File::Path qw(make_path);
 use File::Spec;
 use Fasta::Parser;
 
-our $VERSION = '1.0.10';
+our $VERSION = '1.1.0';
 
 my $L = Log::Log4perl::get_logger();
 
@@ -248,7 +248,7 @@ sub complete_and_concat_alignments{
  $seq{$seq->id} = $seq->seq;
  $length = length($seq->seq);
  }
- print PART "WAG, $gene = ".($totalpos+1)."-";
+ print PART $self->{'raxml-aa-substitution-model'}.", $gene = ".($totalpos+1)."-";
  $totalpos += $length;
  print PART $totalpos."\n";
  open(OUT, ">$out/$gene.aln-gb.comp") or $L->logdie("Error opening $out/$gene.aln-gb.comp. $!");

t/11_run_raxml.t

@@ -17,7 +17,8 @@ my $script_args = ['bin/bcgTree.pl',
  '--proteome', 'Filifactor=t/data/NC_016630.faa',
 # '--proteome', 'Acholeplasma=t/data/NC_022549.faa',
  '--outdir', $tmpdir,
- '--bootstrap', 10
+ '--bootstrap', 10,
+ '--raxml-aa-substitution-model', 'WAG'
  ];
 
 script_runs($script_args, \%options, "Test if script executes raxml");