bacterial-annotator 0.7.0 → 0.7.1

data/lib/bacterial-annotator/sequence-synteny.rb

@@ -6,15 +6,19 @@
 # version: 	0.0.1
 # licence:  	
 
+require 'json'
+require 'zlib'
 
 class SequenceSynteny
 
   attr_reader :query_file, :subject_file, :aln_hits, :query_sequences, :subject_sequences
 
-  def initialize query_file, subject_file, name, pidentity, min_coverage, type
+  def initialize root, outdir, query_file, subject_file, name, pidentity, min_coverage, type
+
+    @root = root
+    @outdir = outdir
     @query_file = query_file
     @subject_file = subject_file
-
     @query_sequences = get_sequences(query_file)
     @subject_sequences = get_sequences(subject_file)
 
@@ -28,22 +32,47 @@ class SequenceSynteny
 
 
   # get sequences name with length in hash
-  def get_sequences seq_file
+  def get_sequences raw_file
 
     sequences = {}
-    flat = Bio::FlatFile.auto("#{seq_file}")
-    flat.each_entry do |s|
-      s_name = s.definition.chomp.split(" ")[0]
-      sequences[s_name] = {}
-      properties = s.definition.chomp.split(";")
-      partial = false
-      if properties.length >= 2 and properties[1].include? "partial"
-        partial = (properties[1].gsub("partial=","").include? '1')
+
+    if raw_file.include?(".dmnd")
+
+      seq_info_file = raw_file.gsub(".dmnd",".json.gz")
+
+      json_genes = {}
+      Zlib::GzipReader.open(seq_info_file) {|gz|
+        json_genes = JSON.parse(gz.read)
+      }
+
+      json_genes.each do |gene|
+
+        sequences[gene["cluster_id"]] = {}
+        sequences[gene["cluster_id"]][:length] = gene["consensus_length"].to_f
+        sequences[gene["cluster_id"]][:conserved] = false
+        sequences[gene["cluster_id"]][:contig] = gene["cluster_id"].split("_")[0..-2].join("_") if gene["cluster_id"].include? "_"
+
       end
-      sequences[s_name][:partial] = partial
-      sequences[s_name][:length] = s.seq.length
-      sequences[s_name][:conserved] = false
-      sequences[s_name][:contig] = s_name.split("_")[0..-2].join("_") if s_name.include? "_"
+
+    else
+
+      seq_file = raw_file
+      flat = Bio::FlatFile.auto("#{seq_file}")
+      flat.each_entry do |s|
+        s_name = s.definition.chomp.split(" ")[0]
+        sequences[s_name] = {}
+        properties = s.definition.chomp.split(";")
+        partial = false
+        if properties.length >= 2 and properties[1].include? "partial"
+          partial = (properties[1].gsub("partial=","").include? '1')
+        end
+        sequences[s_name][:partial] = partial
+        sequences[s_name][:length] = s.seq.length
+        sequences[s_name][:conserved] = false
+        sequences[s_name][:contig] = s_name.split("_")[0..-2].join("_") if s_name.include? "_"
+
+      end
+
     end
 
     sequences
@@ -51,14 +80,42 @@ class SequenceSynteny
   end
 
   # run blat on proteins
-  def run_blat root, outdir
-    base_cmd = "#{root}/blat.linux -out=blast8 -minIdentity=#{@pidentity} > /dev/null 2>&1"
+  def run_blat
+    base_cmd = "#{@root}/blat.linux -out=blast8 -minIdentity=#{@pidentity} > /dev/null 2>&1"
     if @type == "prot"
-      system("#{base_cmd} -prot #{@subject_file} #{@query_file} #{outdir}/#{@name}.blat8.tsv")
+      system("#{base_cmd} -prot #{@subject_file} #{@query_file} #{@outdir}/#{@name}.blat8.tsv")
+    else
+      system("#{base_cmd} #{@subject_file} #{@query_file} #{@outdir}/#{@name}.blat8.tsv")
+    end
+    @aln_file = "#{@outdir}/#{@name}.blat8.tsv"
+    # extract_hits
+  end                           # end of method
+
+  # run fasta36 on proteins
+  def run_fasta36
+    if @type == "prot"
+      system("#{@root}/fasta36.linux -T 1 -b 3 -E 1e-40 -m 8 #{@query_file} #{@subject_file} > #{@outdir}/#{@name}.fasta36.tsv")
+    else
+      system("#{@root}/glsearch36.linux -T 1 -b 12 -E 1e-40 -m 8 #{@query_file} #{@subject_file} > #{@outdir}/#{@name}.fasta36.tsv")
+    end
+    @aln_file_fasta36 = "#{@outdir}/#{@name}.fasta36.tsv"
+    # extract_hits
+  end                           # end of method
+
+  # run diamond on proteins
+  def run_diamond
+    if @type == "prot"
+      if subject_file.include? ".dmnd"
+        db_file = subject_file
+      else
+        system("#{@root}/diamond.linux makedb --db #{subject_file} --in #{subject_file} > /dev/null 2>&1")
+        db_file = subject_file
+      end
+      system("#{@root}/diamond.linux blastp --db #{db_file} -q #{query_file} -o #{@outdir}/#{@name}.diamond.tsv -f 6 > /dev/null 2>&1")
     else
-      system("#{base_cmd} #{@subject_file} #{@query_file} #{outdir}/#{@name}.blat8.tsv")
+      # system("#{@root}/glsearch36.linux -b 3 -E 1e-25 -m 8 #{@subject_file} #{@query_file} > #{@outdir}/#{@name}.fasta36.tsv")
     end
-    @aln_file = "#{outdir}/#{@name}.blat8.tsv"
+    @aln_file = "#{@outdir}/#{@name}.diamond.tsv"
     # extract_hits
   end                           # end of method
 

data/lib/bacterial-annotator.rb

@@ -23,6 +23,8 @@ class BacterialAnnotator
     @root = root
     @options = options
 
+    abort if ! @options.has_key? :input
+
     @minlength = @options[:minlength].to_i
     @options[:minlength] = @options[:minlength].to_i
     @options[:pidentity] = @options[:pidentity].to_f
@@ -44,12 +46,25 @@ class BacterialAnnotator
     end
     Dir.mkdir(@options[:outdir])
 
-    @query_fasta = SequenceFasta.new(@options[:input], @options[:meta])
+    @query_fasta = SequenceFasta.new(@root,
+                                     options[:outdir],
+                                     @options[:input],
+                                     @options[:meta])
 
     @with_refence_genome = false
+    @with_db = false
     if @options.has_key? :refgenome
       @with_refence_genome = true
-      @ref_genome = SequenceAnnotation.new(@options[:refgenome], @options[:outdir])
+      @ref_genome = SequenceAnnotation.new(@root,
+                                           @options[:outdir],
+                                           @options[:refgenome],
+                                           "refGbk")
+    elsif @options[:mergem]
+      @with_db = true
+      @ref_genome = SequenceAnnotation.new(@root,
+                                           @options[:outdir],
+                                           @options[:mergem],
+                                           "db")
     end
 
     @with_external_db = false
@@ -76,52 +91,12 @@ class BacterialAnnotator
 
   end                           # end of method
 
-  # Prepare files for the annotation
-  # Will run prodigal on the query and prepare reference genome files
-  def prepare_files_for_annotation
-    print "# Running Prodigal on your genome.."
-    start_time = Time.now
-    @query_fasta.run_prodigal @root, @options[:outdir]
-    end_time = Time.now
-    c_time = Helper.sec2str(end_time - start_time)
-    print "done (#{c_time})\n"
-    if @with_refence_genome
-      @ref_genome.write_cds_to_file @options[:outdir]
-      @ref_genome.write_rna_to_file @options[:outdir]
-      # puts "Successfully loaded #{@ref_genome.gbk.definition}"
-    end
-  end                           # end of method
-
-
-  def run_reference_synteny_prot
-
-    ref_synteny_prot = SequenceSynteny.new(@query_fasta.annotation_files[:proteins], @ref_genome.cds_file,
-                                           "Prot-Ref", @options[:pidentity], @options[:pcoverage], "prot")
-
-    print "# Running alignment with Reference Genome CDS (blat).."
-    start_time = Time.now
-    ref_synteny_prot.run_blat @root, @options[:outdir]
-    end_time = Time.now
-    c_time = Helper.sec2str(end_time - start_time)
-    print "done (#{c_time})\n"
-
-    ref_synteny_prot.extract_hits :refgenome
-
-    ref_synteny_prot.query_sequences.each do |k,v|
-      if v.has_key? :homology
-        @contig_annotations_cds[v[:contig]] = [] if ! @contig_annotations_cds.has_key? v[:contig]
-        @contig_annotations_cds[v[:contig]] << k
-      end
-    end
-
-    ref_synteny_prot
-
-  end
-
 
   # run_alignment of reference genome proteins and the query
   def run_annotation
 
+    prepare_files_for_annotation
+
     # process reference genome synteny
     if @with_refence_genome        # Annotation with the Reference Genome
 
@@ -153,23 +128,69 @@ class BacterialAnnotator
       dump_ref_synteny_to_file
 
       # run RNA annotation
-      @rna_synteny = SequenceSynteny.new(@query_fasta.fasta_file, @ref_genome.rna_file,
-                                         "RNA-Ref", @options[:pidentity], @options[:pcoverage], "dna")
+      @rna_synteny = SequenceSynteny.new(@root,
+                                         @options[:outdir],
+                                         @query_fasta.fasta_file,
+                                         @ref_genome.rna_file,
+                                         "RNA-Ref",
+                                         @options[:pidentity],
+                                         @options[:pcoverage],
+                                         "dna")
+
       print "# Running alignment with Reference Genome RNA (blat).."
       start_time = Time.now
-      @rna_synteny.run_blat @root, @options[:outdir]
+      @rna_synteny.run_blat
       end_time = Time.now
       c_time = Helper.sec2str(end_time-start_time)
       print "done (#{c_time})\n"
+
+      # # takes too long
+      # print "# Running alignment with Reference Genome RNA (fasta36).."
+      # start_time = Time.now
+      # @rna_synteny.run_fasta36
+      # end_time = Time.now
+      # c_time = Helper.sec2str(end_time-start_time)
+      # print "done (#{c_time})\n"
+
       @rna_synteny.extract_hits_dna :rna
       @contig_annotations_rna = {}
       @query_fasta.annotation_files[:contigs].each_with_index do |contig, contig_index|
         @contig_annotations_rna[contig] = @rna_synteny.get_annotation_for_contig contig
       end
 
+
+    elsif @with_db
+
+      @prot_synteny_refgenome = run_mergem_synteny_prot
+      # iterate over each contig
+      #     discard short contig
+      #     cumulate statistics of homolog CDS
+      @query_fasta.annotation_files[:contigs].each_with_index do |contig, contig_index|
+
+        # Skip short contigs
+        if @query_fasta.annotation_files[:contigs_length][contig_index] < @minlength
+          @annotation_stats[:short_contigs] << contig
+          next
+        end
+
+        remaining_cds = cumulate_annotation_stats_reference contig
+
+        if remaining_cds != []
+          @contig_foreign_cds[contig] = remaining_cds
+        end
+
+      end
+
+      # dump foreign proteins to file
+      foreign_cds_file = dump_cds
+
+      # dump reference CDS synteny to file
+      dump_ref_synteny_to_file
+
+
     else                        # no reference genome
 
-      # no reference genome .. will process all the CDS
+      # no reference genome .. will process all the CDS as foreign for the external db
       foreign_cds_file = @query_fasta.annotation_files[:proteins]
 
     end
@@ -187,6 +208,99 @@ class BacterialAnnotator
   end                           # end of method
 
 
+  # Prepare files for the annotation
+  # Will run prodigal on the query and prepare reference genome files
+  def prepare_files_for_annotation
+    print "# Running Prodigal on your genome.."
+    start_time = Time.now
+    @query_fasta.run_prodigal
+    end_time = Time.now
+    c_time = Helper.sec2str(end_time - start_time)
+    print "done (#{c_time})\n"
+  end                           # end of method
+
+
+  def run_mergem_synteny_prot
+
+
+    ref_synteny_prot = SequenceSynteny.new(@root,
+                                           @options[:outdir],
+                                           @query_fasta.annotation_files[:proteins],
+                                           @ref_genome.cds_file,
+                                           "Prot-Ref",
+                                           @options[:pidentity],
+                                           @options[:pcoverage],
+                                           "prot")
+
+    print "# Running alignment with Reference Genome CDS (diamond).."
+    start_time = Time.now
+    ref_synteny_prot.run_diamond
+    end_time = Time.now
+    c_time = Helper.sec2str(end_time - start_time)
+    print "done (#{c_time})\n"
+
+    ref_synteny_prot.extract_hits :refgenome
+
+    ref_synteny_prot.query_sequences.each do |k,v|
+      if v.has_key? :homology
+        @contig_annotations_cds[v[:contig]] = [] if ! @contig_annotations_cds.has_key? v[:contig]
+        @contig_annotations_cds[v[:contig]] << k
+      end
+    end
+
+    ref_synteny_prot
+
+
+  end
+
+
+
+  def run_reference_synteny_prot
+
+    ref_synteny_prot = SequenceSynteny.new(@root,
+                                           @options[:outdir],
+                                           @query_fasta.annotation_files[:proteins],
+                                           @ref_genome.cds_file,
+                                           "Prot-Ref",
+                                           @options[:pidentity],
+                                           @options[:pcoverage],
+                                           "prot")
+
+    print "# Running alignment with Reference Genome CDS (diamond).."
+    start_time = Time.now
+    ref_synteny_prot.run_diamond
+    end_time = Time.now
+    c_time = Helper.sec2str(end_time - start_time)
+    print "done (#{c_time})\n"
+
+    # print "# Running alignment with Reference Genome CDS (blat).."
+    # start_time = Time.now
+    # ref_synteny_prot.run_blat
+    # end_time = Time.now
+    # c_time = Helper.sec2str(end_time - start_time)
+    # print "done (#{c_time})\n"
+
+    # print "# Running alignment with Reference Genome CDS (fasta36).."
+    # start_time = Time.now
+    # ref_synteny_prot.run_fasta36
+    # end_time = Time.now
+    # c_time = Helper.sec2str(end_time - start_time)
+    # print "done (#{c_time})\n"
+
+    ref_synteny_prot.extract_hits :refgenome
+
+    ref_synteny_prot.query_sequences.each do |k,v|
+      if v.has_key? :homology
+        @contig_annotations_cds[v[:contig]] = [] if ! @contig_annotations_cds.has_key? v[:contig]
+        @contig_annotations_cds[v[:contig]] << k
+      end
+    end
+
+    ref_synteny_prot
+
+  end
+
+
   # Finishing the annotation of the remaining CDS
   def finish_annotation remaining_cds_file
 
@@ -194,15 +308,25 @@ class BacterialAnnotator
     if @options.has_key? :external_db	# from an external DB
 
       db_file = @options[:external_db]
-      ref_cds = extract_externaldb_prot_info db_file
-
-      @externaldb_synteny = SequenceSynteny.new(remaining_cds_file, db_file,
-                                                "Prot-ExternalDB", @options[:pidentity],
-                                                @options[:pcoverage], "prot")
+      ref_cds = SequenceAnnotation.new(@root,
+                                       @options[:outdir],
+                                       db_file,
+                                      "fasta")
+
+      # ref_cds = extract_externaldb_prot_info db_file
+
+      @externaldb_synteny = SequenceSynteny.new(@root,
+                                                @options[:outdir],
+                                                remaining_cds_file,
+                                                db_file,
+                                                "Prot-ExternalDB",
+                                                @options[:pidentity],
+                                                @options[:pcoverage],
+                                                "prot")
 
       print "# Running BLAT alignment with External Database.."
       start_time = Time.now
-      @externaldb_synteny.run_blat @root, @options[:outdir]
+      @externaldb_synteny.run_blat
       end_time = Time.now
       c_time = Helper.sec2str(end_time-start_time)
       print "done (#{c_time})\n"
@@ -228,18 +352,18 @@ class BacterialAnnotator
         # note = "Protein homology (#{v[:pId]}% identity) with gi:#{hit_gi}"
         cov_query = (v[:homology][:cov_query]*100).round(2)
         cov_subject = (v[:homology][:cov_subject]*100).round(2)
-        note = "Protein homology (AA identity: #{v[:homology][:pId]}%; coverage (q,s): #{cov_query}%,#{cov_subject}%) with #{ref_cds[hit_gi][:prot_id]}"
-        inference = "similar to AA sequence:#{ref_cds[hit_gi][:db_source]}:#{ref_cds[hit_gi][:prot_id]}"
+        note = "Protein homology (AA identity: #{v[:homology][:pId]}%; coverage (q,s): #{cov_query}%,#{cov_subject}%) with #{ref_cds.coding_seq[hit_gi][:prot_id]}"
+        inference = "similar to AA sequence:#{ref_cds.coding_seq[hit_gi][:db_source]}:#{ref_cds.coding_seq[hit_gi][:prot_id]}"
 
-        if ref_cds[hit_gi][:org] != ""
-          note +=  " from #{ref_cds[hit_gi][:org]}"
+        if ref_cds.coding_seq[hit_gi][:org] != ""
+          note +=  " from #{ref_cds.coding_seq[hit_gi][:org]}"
         end
 
         @contig_annotations_externaldb[contig_of_protein][v[:homology][:hits][0]] = {
-          product: ref_cds[hit_gi][:product],
+          product: ref_cds.coding_seq[hit_gi][:product],
           feature: "cds",
           gene: nil,
-          prot_id: ref_cds[hit_gi][:prot_id],
+          prot_id: ref_cds.coding_seq[hit_gi][:prot_id],
           locustag: nil,
           note: note,
           inference: inference
@@ -260,7 +384,10 @@ class BacterialAnnotator
     @contig_annotations_cds.each do |contig, contig_prots|
 
       gbk_path = @query_fasta.annotation_files[:gbk_path]
-      gbk_to_annotate = SequenceAnnotation.new("#{gbk_path}/#{contig}.gbk", "#{gbk_path}")
+      gbk_to_annotate = SequenceAnnotation.new(@root,
+                                               "#{gbk_path}",
+                                               "#{gbk_path}/#{contig}.gbk",
+                                               "newGbk")
 
       if @with_external_db and @with_refence_genome
         gbk_to_annotate.add_annotation_ref_synteny_prot(
@@ -273,6 +400,11 @@ class BacterialAnnotator
           @externaldb_synteny.query_sequences,
           @contig_annotations_externaldb[contig]
         )
+      elsif @with_db
+        gbk_to_annotate.add_annotation_ref_synteny_prot(
+          @prot_synteny_refgenome.query_sequences,
+          @ref_genome.coding_seq
+        )
       else
         gbk_to_annotate.add_annotation_ref_synteny_prot(
           @prot_synteny_refgenome.query_sequences,
@@ -286,7 +418,7 @@ class BacterialAnnotator
         gbk_to_annotate.add_annotations @contig_annotations_rna[contig], "new"
       end
 
-      gbk_to_annotate.save_genbank_to_file gbk_path
+      gbk_to_annotate.save_genbank_to_file
 
     end
     end_time = Time.now
@@ -579,9 +711,14 @@ class BacterialAnnotator
         partial = ref_annotated[ref_v[:protId]][:partial]
       end
 
+      _locus_tag = ref_v[:locustag] || ""
+      _seq_len = "NA"
+      # _seq_len = ref_v[:bioseq].seq.length.to_s if ! ref_v[:bioseq].nil?
+      _seq_len = ref_v[:length].to_s if ! ref_v[:length].nil?
+
       synteny_file.write(ref_v[:protId])
-      synteny_file.write("\t"+ref_v[:locustag])
-      synteny_file.write("\t"+ref_v[:bioseq].seq.length.to_s)
+      synteny_file.write("\t"+_locus_tag)
+      synteny_file.write("\t"+_seq_len)
       synteny_file.write("\t"+coverage_ref.to_s)
       synteny_file.write("\t"+pId.to_s)
       synteny_file.write("\t"+gene)

data/lib/bacterial-comparator.rb

@@ -34,15 +34,31 @@ class BacterialComparator
       min_pid = min_pid/100
     end
 
+    @aln_opt = options[:align].downcase
+    @run_phylo = 0
+    if options[:phylogeny] == 1
+      @bootstrap = options[:bootstrap]
+      @run_phylo = 1
+    end
+
     @ref_prot = get_ref_prot
     @synteny = read_prot_synteny
     @stats = extract_syntenic_fasta min_cov, min_pid
 
   end
 
+
+  def run_comparison
+
+    run_mafft_aln
+    run_raxml_phylo if @run_phylo != 0
+
+  end
+
+
   def read_prot_synteny
 
-    print "# Reading genome synteny files - from genome annotations.."
+    puts "# Reading genome synteny files START.."
     start_time = Time.now
     synteny = {}
     @genomes_list.each do |g|
@@ -65,7 +81,8 @@ class BacterialComparator
     end
     end_time = Time.now
     c_time = Helper.sec2str(end_time-start_time)
-    print "done (#{c_time})\n"
+
+    puts "# Reading genome synteny files [DONE] (in #{c_time})"
 
     synteny
 
@@ -146,7 +163,7 @@ class BacterialComparator
   # extract and dump multifasta for syntenic genes and proteins
   def extract_syntenic_fasta min_cov, min_pid
 
-    print "# Extracting Proteins and Genes multifasta.."
+    puts "# Extracting Proteins and Genes multifasta  START.."
     start_time = Time.now
 
     nb_of_syntenic = 0
@@ -216,14 +233,13 @@ class BacterialComparator
 
     end_time = Time.now
     c_time = Helper.sec2str(end_time-start_time)
-    print "done (#{c_time})\n"
+    puts "# Extracting Proteins and Genes multifasta  [DONE] (in #{c_time})"
 
     stats[:nb_of_syntenic] = nb_of_syntenic
     #puts "   Syntenic genes : " + nb_of_syntenic.to_s + " / " + @ref_prot.length.to_s
 
   end
 
-
   def mafft_align f
 
     trying = 0
@@ -252,7 +268,7 @@ class BacterialComparator
 
   def mafft_align_all_pep
 
-    print "# Sequence alignments - conserved single proteins a.a. (MAFFT).."
+    puts "# Sequence alignments - individual proteins a.a. (MAFFT)  START.."
     start_time = Time.now
 
     ori_dir = Dir.pwd
@@ -277,7 +293,7 @@ class BacterialComparator
 
     end_time = Time.now
     c_time = Helper.sec2str(end_time-start_time)
-    print "done (#{c_time})\n"
+    puts "# Sequence alignments - individual proteins a.a. (MAFFT)  [DONE] (in #{c_time})"
 
     # FIXME ugly hack to find out the reference genome
     ref_id = Dir["#{ori_dir}/#{@genomes_list[0]}/*.pep"][0].split('/')[-1].gsub(".pep","")
@@ -290,7 +306,7 @@ class BacterialComparator
 
   def mafft_align_all_dna
 
-    print "# Sequence alignments - conserved single genes dna (MAFFT).."
+    puts "# Sequence alignments - individual genes dna (MAFFT)  START.."
     start_time = Time.now
 
     ori_dir = Dir.pwd
@@ -313,12 +329,12 @@ class BacterialComparator
       }
     end
 
-    # ugly hack to find out the reference genome
+    # ugly hack to find out the reference genome FIXME
     ref_id = Dir["#{ori_dir}/#{@genomes_list[0]}/*.pep"][0].split('/')[-1].gsub(".pep","")
 
     end_time = Time.now
     c_time = Helper.sec2str(end_time-start_time)
-    print "done (#{c_time})\n"
+    puts "# Sequence alignments - individual genes dna (MAFFT)  [DONE] (in #{c_time})"
 
     concat_alignments "align-genes-dna.all.fasta", ref_id
 
@@ -377,21 +393,21 @@ class BacterialComparator
 
   end
 
-  def mafft_aln aln_opt
+  def run_mafft_aln
 
-    if aln_opt == "both"
+    if @aln_opt == "both"
       mafft_align_all_pep
       mafft_align_all_dna
-    elsif aln_opt == "prot"
+    elsif @aln_opt == "prot"
       mafft_align_all_pep
-    elsif aln_opt == "dna"
+    elsif @aln_opt == "dna"
       mafft_align_all_dna
     end
 
   end
 
   def raxml_tree_dna bt
-    print "# Genes DNA tree creation (RAXML).."
+    puts "# Genes DNA tree creation (RAXML)  START.."
     start_time = Time.now
     ori_dir = Dir.pwd
     Dir.chdir(@outdir)
@@ -405,11 +421,11 @@ class BacterialComparator
     Dir.chdir(ori_dir)
     end_time = Time.now
     c_time = Helper.sec2str(end_time-start_time)
-    print "done (#{c_time})\n"
+    puts "# Genes DNA tree creation (RAXML)  [DONE] (in #{c_time})"
   end
 
   def raxml_tree_pep bt
-    print "# Proteins AA tree creation (RAXML).."
+    puts "# Proteins AA tree creation (RAXML)  START.."
     start_time = Time.now
     ori_dir = Dir.pwd
     Dir.chdir(@outdir)
@@ -423,18 +439,18 @@ class BacterialComparator
     Dir.chdir(ori_dir)
     end_time = Time.now
     c_time = Helper.sec2str(end_time-start_time)
-    print "done (#{c_time})\n"
+    puts "# Proteins AA tree creation (RAXML)  [DONE] (in #{c_time})"
   end
 
-  def raxml_tree aln_opt, bt
+  def run_raxml_phylo
 
-    if aln_opt == "both"
-      raxml_tree_dna bt
-      raxml_tree_pep bt
-    elsif aln_opt == "prot"
-      raxml_tree_pep bt
-    elsif aln_opt == "dna"
-      raxml_tree_dna bt
+    if @aln_opt == "both"
+      raxml_tree_dna @bootstrap
+      raxml_tree_pep @bootstrap
+    elsif @aln_opt == "prot"
+      raxml_tree_pep @bootstrap
+    elsif @aln_opt == "dna"
+      raxml_tree_dna @bootstrap
     end
 
   end