Class: SequenceAnnotation

Inherits:
Object
  • Object
show all
Defined in:
lib/bacterial-annotator/sequence-annotation.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(root, outdir, file_ref, type) ⇒ SequenceAnnotation

Initialize then genbank file



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 17

def initialize root, outdir, file_ref, type

  @root = root
  @outdir = outdir
  @coding_seq = {}
  @rna_seq = {}

  case type
  when "refGbk"
    # reference genome use for annotation
    reference_gbk file_ref
  when "db"
    # reference database use for annotation
    reference_db file_ref
  when "fasta"
    # single fasta database for annotation (completion)
    single_fasta file_ref
  when "newGbk"
    # new genbank holder to be annotated
    new_gbk file_ref
  end

end

Instance Attribute Details

#cds_file ⇒ Object

Returns the value of attribute cds_file.



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 14

def cds_file
  @cds_file
end

#coding_seq ⇒ Object

Returns the value of attribute coding_seq.



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 14

def coding_seq
  @coding_seq
end

#gbk ⇒ Object

Returns the value of attribute gbk.



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 14

def gbk
  @gbk
end

#rna_file ⇒ Object

Returns the value of attribute rna_file.



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 14

def rna_file
  @rna_file
end

#rna_seq ⇒ Object

Returns the value of attribute rna_seq.



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 14

def rna_seq
  @rna_seq
end

Instance Method Details

#add_annotation_ref_synteny_prot(synteny_prot, annotations, ref_genome = nil) ⇒ Object

add annotation from reference prot synteny



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 365

def add_annotation_ref_synteny_prot synteny_prot, annotations, ref_genome=nil

  contig = @gbk.definition

  prot_iterator = 0
  @gbk.features.each_with_index do |cds, ft_index|

    next if cds.feature != "CDS"

    prot_iterator+=1
    prot_id = contig+"_"+prot_iterator.to_s

    ftArray = []
    cds.qualifiers = []

    hit = nil

    if ! synteny_prot.has_key? prot_id or
       ! synteny_prot[prot_id].has_key? :homology or
       ! annotations.has_key? synteny_prot[prot_id][:homology][:hits][0] or
       synteny_prot[prot_id][:homology][:assert_cutoff].inject(:+) < 3

      qLocusTag = Bio::Feature::Qualifier.new('locus_tag', "#{prot_id}")
      qProd = Bio::Feature::Qualifier.new('product', "hypothetical protein")

      ftArray.push(qLocusTag)
      ftArray.push(qProd)

      if synteny_prot.has_key? prot_id and
        synteny_prot[prot_id].has_key? :homology and
        synteny_prot[prot_id][:homology][:assert_cutoff] == [1,1,0]
        hit = annotations[synteny_prot[prot_id][:homology][:hits][0]]
        qNote = Bio::Feature::Qualifier.new('note', "possible pseudo gene of #{hit[:locustag]} from #{ref_genome}")
        ftArray.push(qNote)
      end

    else

      hit = annotations[synteny_prot[prot_id][:homology][:hits][0]]

      if synteny_prot.has_key? prot_id

        locus, gene, product, note, inference = nil
        locus = hit[:locustag]
        gene = hit[:gene]
        product = hit[:product]
        note = hit[:note]
        inference = hit[:inference]
        pId = synteny_prot[prot_id][:homology][:pId]
        cov_query = (synteny_prot[prot_id][:homology][:cov_query]*100).round(2)
        cov_subject = (synteny_prot[prot_id][:homology][:cov_subject]*100).round(2)
        reference_prot_id = synteny_prot[prot_id][:homology][:hits][0]

        qLocusTag = Bio::Feature::Qualifier.new('locus_tag', "#{prot_id}")
        ftArray.push(qLocusTag)

        if gene != nil
          qGene = Bio::Feature::Qualifier.new('gene', gene)
          ftArray.push(qGene)
        end

        if product != nil
          qProd = Bio::Feature::Qualifier.new('product', product)
          ftArray.push(qProd)
        end

        # check if there is a reference genome.. reference_locus shouldn't be nil in that case
        if locus != nil

          qNote = Bio::Feature::Qualifier.new('note', "corresponds to #{locus} locus (AA identity: #{pId}%; coverage(q,s): #{cov_query}%,#{cov_subject}%) from #{ref_genome}")
          ftArray.push(qNote)

          db_source = "[DBSource]"
          if reference_prot_id.include? "_"
            db_source = "RefSeq"
          else
            db_source = "INSD"
          end
          qInference = Bio::Feature::Qualifier.new('inference', "similar to AA sequence:#{db_source}:#{reference_prot_id}")
          ftArray.push(qInference)

        end

        if note != nil
          qNote = Bio::Feature::Qualifier.new('note', note)
          ftArray.push(qNote)
        end

        if inference != nil
          qInference = Bio::Feature::Qualifier.new('inference', inference)
          ftArray.push(qInference)
        end

      end

    end

    cds.qualifiers = ftArray

  end


end

#add_annotations(annotations, mode, reference_locus = nil) ⇒ Object

add annotation to a genbank file produced by prodigal



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 471

def add_annotations annotations, mode, reference_locus=nil

  # nb_of_added_ft = 0
  i = 0

  contig = @gbk.definition

  if mode == "inplace"

    # iterate through
    @gbk.features.each_with_index do |cds, ft_index|

      next if cds.feature != "CDS"

      ftArray = []
      cds.qualifiers = []

      i += 1
      prot_id = contig+"_"+i.to_s
      hit = nil

      if annotations.has_key? prot_id
        hit = annotations[prot_id]
      else
        puts "no hit for #{prot_id}"
        next
      end

      if hit != nil

        locus, gene, product, note = nil
        locus = hit[:locustag]
        gene = hit[:gene]
        product = hit[:product]
        note = hit[:note]
        pId = hit[:pId]

        if gene != nil
          qGene = Bio::Feature::Qualifier.new('gene', gene)
          ftArray.push(qGene)
        end

        if product != nil
          qProd = Bio::Feature::Qualifier.new('product', product)
          ftArray.push(qProd)
        end

        # check if there is a reference genome.. reference_locus shouldn't be nil in that case
        if locus != nil
          qNote = Bio::Feature::Qualifier.new('note', "corresponds to #{locus} locus (#{pId}% identity) from #{reference_locus.entry_id}")
          ftArray.push(qNote)
        end

        if note != nil
          qNote = Bio::Feature::Qualifier.new('note', note)
          ftArray.push(qNote)
        end

      end
      cds.qualifiers = ftArray

    end


  elsif mode == "new"

    sorted_annotations = annotations.sort_by { |k, v| v[:query_location][0][0] }

    new_features = {}
    annotations_done = {}
    gbk_features_len = @gbk.features.length

    @gbk.features.each_with_index do |ft, ft_index|

      sorted_annotations.each do |k,v|

        next if annotations_done.has_key? k

        if v[:query_location][0][0] < ft.locations[0].from or ft_index == gbk_features_len-1

          pp v
          if v[:subject_location][0][0] > v[:subject_location][0][1]
            location = "complement(#{v[:query_location][0][0]}..#{v[:query_location][0][1]})"
          else
            location = "#{v[:query_location][0][0]}..#{v[:query_location][0][1]}"
          end

          feature = Bio::Feature.new(v[:feature][0],location)
          feature.qualifiers.push(Bio::Feature::Qualifier.new('product',v[:product][0])) if ! v[:product][0].nil? or v[:product][0] != ""
          if ft_index == gbk_features_len-1
            new_features[gbk_features_len] = feature
          else
            new_features[ft_index] = feature
          end

          annotations_done[k] = 1
          break

        end

      end

    end

    new_features.each do |k,v|
      @gbk.features.insert(k,v)
    end

  end

end

#get_cds ⇒ Object

Prepare CDS/proteins



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 220

def get_cds

  if @coding_seq.empty?

    # Iterate over each CDS
    @gbk.each_cds do |ft|
      ftH = ft.to_hash
      loc = ft.locations
      gene = []
      product = []
      protId = ""
      if ftH.has_key? "pseudo"
        next
      end
      gene = ftH["gene"] if !ftH["gene"].nil?
      product = ftH["product"] if !ftH["product"].nil?
      protId = ftH["protein_id"][0] if !ftH["protein_id"].nil?
      locustag = ftH["locus_tag"][0] if !ftH["locus_tag"].nil?

      dna = get_DNA(ft,@bioseq)
      pep = dna.translate
      pepBioSeq = Bio::Sequence.auto(pep)
      dnaBioSeq = Bio::Sequence.auto(dna)

      if protId.strip == ""
        protId = locustag
      end

      @coding_seq[protId] = {
        protId: protId,
        location: loc,
        locustag: locustag,
        gene: gene[0],
        product: product[0],
        bioseq: pepBioSeq,
        bioseq_gene: dnaBioSeq,
        length: pepBioSeq.length
      }

    end

  end

  @coding_seq

end

#get_rna ⇒ Object

Prepare rRNA tRNA



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 268

def get_rna

  if @rna_seq.empty?

    @rna_seq = {}
    @gbk.features do |ft|

      next if ! ft.feature.to_s.include? "RNA"

      ftH = ft.to_hash
      loc = ft.locations
      # seqBeg = loc[0].from.to_s
      # seqEnd = loc[0].to.to_s
      # strand = loc[0].strand.to_s
      if ftH.has_key? "pseudo"
        next
      end
      # gene = ftH["gene"] if !ftH["gene"].nil?
      # protId = ftH["protein_id"][0] if !ftH["protein_id"].nil?
      product = ""

      if !ftH["product"].nil?
        product = ftH["product"][0]
        # puts ftH["product"].join(",") + "---" + ftH["product"][0]
      end

      locustag = ftH["locus_tag"][0] if !ftH["locus_tag"].nil?

      # puts "#{@accession}\t#{seqBeg}\t#{seqEnd}\t#{strand}\t#{protId}\t#{locustag}\t#{gene[0]}\t#{product[0]}"
      dna = get_DNA(ft,@bioseq)
      dnaBioSeq = Bio::Sequence.auto(dna)

      @rna_seq[locustag] = {
        type: ft.feature.to_s,
        location: loc,
        locustag: locustag,
        product: product,
        bioseq_gene: dnaBioSeq
      }

    end

  end

  @rna_seq

end

#new_gbk(gbk_file) ⇒ Object

New Genbank Holder to add annotation to it



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 197

def new_gbk gbk_file

  if ! File.exists? gbk_file
    fetch_ncbi_genome(gbk_file)
    gbk_file = "#{@outdir}/#{gbk_file}.gbk"
    # gbk_file += ".gbk"
  end

  flat_gbk = Bio::FlatFile.auto(gbk_file)

  # Check if gbk is valid
  if flat_gbk.dbclass != Bio::GenBank
    abort "Aborting : The input #{gbk_file} is not a valid genbank file !"
  else
    @gbk = flat_gbk.next_entry
  end

  @bioseq = @gbk.to_biosequence

end

#reference_db(dir) ⇒ Object

Use a MERGEM database to get annotation from it



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 43

def reference_db dir

  abort "Aborting: Can't find MERGEM db direcotry" if ! File.exists? dir

  @cds_file = "#{dir}/cds.dmnd"
  @rna_file = "#{dir}/rnas.fasta"

  json_genes = {}
  Zlib::GzipReader.open("#{dir}/cds.json.gz") {|gz|
    json_genes = JSON.parse(gz.read)
  }

  json_genes.each do |gene|

    prot_id = gene["cluster_id"]
    @coding_seq[prot_id] = {
      protId: prot_id,
      location: nil,
      product: gene["consensus_name"],
      length: gene["consensus_length"]
    }

  end

  # File.open("#{dir}/cds.txt") do |f|
  #   while l = f.gets
  #     lA = l.chomp.split(" ")
  #     @coding_seq[lA[0].gsub(">","")] = {
  #       protId: lA[0].gsub(">",""),
  #       location: nil,
  #       product: lA[1..-1].join(' '),
  #     }
  #   end
  # end

  File.open("#{dir}/rnas.txt") do |f|
    while l = f.gets
      lA = l.chomp.split(" ")
      @rna_seq[lA[0].gsub(">","")] = {
        protId: lA[0].gsub(">",""),
        location: nil,
        product: lA[1..-1].join(' '),
      }
    end
  end

end

#reference_gbk(gbk_file) ⇒ Object

Use a Genbank Reference and read annotation from it



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 92

def reference_gbk gbk_file

  puts "# Preparing reference genome files.."
  if ! File.exists? gbk_file
    fetch_ncbi_genome(gbk_file)
    gbk_file = "#{@outdir}/#{gbk_file}.gbk"
    # gbk_file += ".gbk"
  end

  flat_gbk = Bio::FlatFile.auto(gbk_file)

  # Check if gbk is valid
  if flat_gbk.dbclass != Bio::GenBank
    abort "Aborting : The input #{gbk_file} is not a valid genbank file !"
  else
    @gbk = flat_gbk.next_entry
  end

  @bioseq = @gbk.to_biosequence

  write_cds_to_file
  write_rna_to_file

end

#save_genbank_to_file ⇒ Object 



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 584

def save_genbank_to_file

  File.open("#{@outdir}/#{@gbk.definition}.gbk", "w") do |f|
    f.write(@gbk.to_biosequence.output(:genbank))
  end

end

#single_fasta(fasta_file) ⇒ Object

Use a Genbank Reference and read annotation from it



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 118

def single_fasta fasta_file

  return "" if ! File.exists? fasta_file

  File.open(fasta_file, "r") do |dbfile|

    while l=dbfile.gets

      if l[0] == ">"

        lA = l.chomp.split("|")

        if lA.length > 1      # refseq, ncbi, trembl, swissprot

          key_gi = l.split(" ")[0][1..-1]
          product_long = lA[-1]

          organism = ""
          product = ""
          db_source = "[DBSource]"

          if product_long.scan(/|/).count >= 5 # FROM BIORUBY SCRIPTS
            product = product_long
            db_source = "RefSeq"
          elsif product_long.include? " [" and product_long.include? "]" # NCBI
            organism = product_long[/\[.*?\]/]
            product = product_long.split(" [")[0].strip
          elsif product_long.include? "OS=" # Swissprot / TrEMBL
            product_tmp = product.split("OS=")
            organism = product_tmp[1].split(/[A-Z][A-Z]=/)[0].strip
            product = product_tmp[0].strip
          elsif product_long.include? "[A-Z][A-Z]=" # NCBI
            product = product_long.split(/[A-Z][A-Z]=/)[0].strip
          else
            product = product_long
          end

          org = organism.gsub("[","").gsub("]","")

          product.lstrip!
          prot_id = nil

          if key_gi.count("|") == 4
            if lA[2] == "ref"
              db_source = "RefSeq"
            end
            prot_id = lA[3]
          elsif key_gi.count("|") == 2
            if lA[0].include? == "sp" or
              lA[0].include? == "tr"
              db_source = "UniProtKB"
            end
            prot_id = lA[1]
          elsif key_gi.count("|") == 5
            db_source = "RefSeq"
            prot_id = lA[2]
          end


        else                  # mergem


        end

        @coding_seq[key_gi] = { product: product,
                                org: org,
                                prot_id: prot_id,
                                db_source: db_source }

      end

    end

  end

end

#write_cds_to_file ⇒ Object

Print CDS to files RETURN : cds_file path



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 318

def write_cds_to_file

  cds_file = "#{@gbk.accession}.pep"
  dna_file = "#{@gbk.accession}.dna"

  if @coding_seq.empty?
    get_cds
  end

  dna_out = File.open("#{@outdir}/#{dna_file}", "w")
  File.open("#{@outdir}/#{cds_file}", "w") do |fwrite|
    @coding_seq.each_key do |k|
      seqout = @coding_seq[k][:bioseq].output_fasta("#{k}",60)
      seqout_dna = @coding_seq[k][:bioseq_gene].output_fasta("#{k}",60)
      fwrite.write(seqout)
      dna_out.write(seqout_dna)
    end
  end
  dna_out.close

  @cds_file = "#{@outdir}/" + cds_file

end

#write_rna_to_file ⇒ Object

Print RNA to files RETURN : rna_file path



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# File 'lib/bacterial-annotator/sequence-annotation.rb', line 344

def write_rna_to_file

  rna_file = "#{@gbk.accession}.rna"

  if @rna_seq.empty?
    get_rna
  end

  File.open("#{@outdir}/#{rna_file}", "w") do |fwrite|
    @rna_seq.each_key do |k|
      seqout_dna = @rna_seq[k][:bioseq_gene].output_fasta("#{k}|#{@rna_seq[k][:type]}|#{@rna_seq[k][:product]}",60)
      fwrite.write(seqout_dna)
    end
  end

  @rna_file = "#{@outdir}/" + rna_file

end