Class: GenbankManip

Inherits:
Object
  • Object
show all
Defined in:
lib/bacterial-annotator/genbank-manip.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(gbk_file, outdir) ⇒ GenbankManip

Initialize then genbank file



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# File 'lib/bacterial-annotator/genbank-manip.rb', line 16

def initialize gbk_file, outdir

  @gbk_file = gbk_file
  if ! File.exists? @gbk_file
    fetch_ncbi_genome(@gbk_file, outdir)
    @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

Instance Attribute Details

#cds_file ⇒ Object

Returns the value of attribute cds_file.



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# File 'lib/bacterial-annotator/genbank-manip.rb', line 13

def cds_file
  @cds_file
end

#coding_seq ⇒ Object

Returns the value of attribute coding_seq.



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# File 'lib/bacterial-annotator/genbank-manip.rb', line 13

def coding_seq
  @coding_seq
end

#gbk ⇒ Object

Returns the value of attribute gbk.



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# File 'lib/bacterial-annotator/genbank-manip.rb', line 13

def gbk
  @gbk
end

Instance Method Details

#add_annotation(annotations, outdir, mode, reference_locus) ⇒ Object

add annotation to a genbank file produced by prodigal



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# File 'lib/bacterial-annotator/genbank-manip.rb', line 121

def add_annotation annotations, outdir, mode, reference_locus

  nb_of_added_ft = 0
  i = 0

  contig = @gbk.definition

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

    next if cds.feature != "CDS"

    if mode == 0
      ftArray = []
      cds.qualifiers = []
    else
      ftArray = cds.qualifiers
    end

    i += 1
    prot_id = contig+"_"+i.to_s
    hit = nil
    hit = annotations[prot_id] if annotations.has_key? prot_id

    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

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

  # Bioruby doesn't support gff at this point
  # File.open("#{outdir}/#{contig}.gff", "w") do |f| 
  #   f.write(@gbk.to_biosequence.output(:gff))
  # end

end

#get_cds ⇒ Object

Prepare CDS/proteins



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# File 'lib/bacterial-annotator/genbank-manip.rb', line 40

def get_cds

  if @coding_seq == nil

    @coding_seq = {}

    # 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?

      # if ftH.has_key? "translation"
      #   pep = ftH["translation"][0] if !ftH["translation"].nil?
      # else
      #   dna = get_DNA(ft,@bioseq)
      #   pep = dna.translate
      # end

      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}
    end

  end

  @coding_seq

end

#write_cds_to_file(outdir) ⇒ Object

Print CDS to files RETURN : cds_file path



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# File 'lib/bacterial-annotator/genbank-manip.rb', line 95

def write_cds_to_file outdir

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

  if @coding_seq == nil
    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