Class: FastaManip

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fasta_file, meta) ⇒ FastaManip

Initialize fasta holder



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

def initialize fasta_file, meta

  @fasta_file = fasta_file
  @fasta_flat = Bio::FlatFile.auto(@fasta_file)
  @meta = meta
  @prodigal_files = nil
  @single_fasta = nil
  @seq_info = nil

  if @fasta_flat.dbclass != Bio::FastaFormat
    abort "Aborting : The input sequence is not a fasta file !"
  end

end

Instance Attribute Details

#fasta_file ⇒ Object (readonly)

Returns the value of attribute fasta_file.



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

def fasta_file
  @fasta_file
end

#fasta_flat ⇒ Object (readonly)

Returns the value of attribute fasta_flat.



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

def fasta_flat
  @fasta_flat
end

#prodigal_files ⇒ Object (readonly)

Returns the value of attribute prodigal_files.



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

def prodigal_files
  @prodigal_files
end

Instance Method Details

Utility function to print the sequence to the end of a gbk file



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# File 'lib/bacterial-annotator/fasta-manip.rb', line 106

def print_sequence_for_gbk seq

  outseq = "ORIGIN\n"
  # puts "ORIGIN"

  ntNum = 0
  sequence = seq.seq.downcase

  nt_left = true
  it = 0

  while nt_left

    if sequence.length > it+60
      nt_to_add = sequence[it..(it+59)]
      # printf "%9s ", (ntNum - l.size + 2)
      outseq += "%9s " % (it+1)
      outseq += nt_to_add.scan(/.{1,10}/).join(" ")
      outseq += "\n"
      it += 60
    else
      nt_to_add = sequence[it..sequence.length-1]
      outseq += "%9s " % (it+1)
      outseq += nt_to_add.scan(/.{1,10}/).join(" ")
      outseq += "\n"
      outseq += "//"
      nt_left = false
    end

  end

  return outseq, sequence.length

end

#run_prodigal(root, outdir) ⇒ Object

Run prodigal on the genome to annotate



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# File 'lib/bacterial-annotator/fasta-manip.rb', line 32

def run_prodigal root, outdir
  @prodigal_files = {}
  Dir.mkdir "#{outdir}" if ! Dir.exists? "#{outdir}"
  if @meta
    system("#{root}/prodigal.linux -p meta -i #{@fasta_file} -a #{outdir}/Proteins.fa -d #{outdir}/Genes.fa -o #{outdir}/Genbanks.gbk -q")
  else
    system("#{root}/prodigal.linux -i #{@fasta_file} -a #{outdir}/Proteins.fa -d #{outdir}/Genes.fa -o #{outdir}/Genbanks.gbk -q")
  end

  @prodigal_files = {multiGBK: "#{outdir}/Genbanks.gbk",
                     contigs: [],
                     contigs_length: [],
                     genes: "#{outdir}/Genes.fa",
                     proteins: "#{outdir}/Proteins.fa",
                     prot_ids_by_contig: {},
                     fasta_path: "#{outdir}/single-fasta/",
                     gbk_path: "#{outdir}/single-genbank/"}
  split_fasta outdir
  split_genbank outdir, "#{outdir}/Genbanks.gbk"
  extract_cds_names
  @prodigal_files
end

#split_fasta(outdir) ⇒ Object

Split Multi Genbanks file RETURN : array of fasta files



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# File 'lib/bacterial-annotator/fasta-manip.rb', line 58

def split_fasta outdir
  @single_fasta = {}
  Dir.mkdir("#{outdir}/single-fasta") if ! Dir.exists?("#{outdir}/single-fasta")
  @fasta_flat.each_entry do |seq|
    file_name = seq.definition.chomp.split(" ")[0]
    @prodigal_files[:contigs] << "#{file_name}"
    @prodigal_files[:contigs_length] << seq.seq.length
    File.open("#{outdir}/single-fasta/#{file_name}.fasta", "w") do |fwrite|
      fwrite.write(seq)
    end
    @single_fasta[file_name] = seq
  end
end

#split_genbank(outdir, multigbk) ⇒ Object

Split Multi Genbanks file RETURN : array of genbank files



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# File 'lib/bacterial-annotator/fasta-manip.rb', line 75

def split_genbank outdir, multigbk

  Dir.mkdir("#{outdir}/single-genbank")if ! Dir.exists?("#{outdir}/single-genbank")
  File.open(multigbk,"r") do |f|
    fopen = nil
    while l = f.gets
      if l[0..9] == "DEFINITION"
        file_name = l.chomp.split(";")[2].gsub("seqhdr","").delete("\"").delete("=").split(" ")[0]
        outseq, seq_length = print_sequence_for_gbk @single_fasta[file_name]
        spacer = " " * (20-seq_length.to_s.length)
        date = DateTime.now
        month = Date::ABBR_MONTHNAMES[date.month]
        day = "%02d" % date.day
        year = date.year
        locus = "LOCUS       #{file_name}#{spacer}#{seq_length.to_s} bp    DNA     linear   BCT #{day}-#{month}-#{year}\n"
        locus += "DEFINITION  #{file_name}\n"
        fopen = File.open("#{outdir}/single-genbank/#{file_name}.gbk", "w")
        fopen.write(locus)
      elsif l[0..1] == "//"
        fopen.write(outseq)
        fopen.close
      elsif ! l.include? "                     /note="
        fopen.write(l)
      end
    end
  end

end