Class: SequenceSynteny

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(root, outdir, query_file, subject_file, name, pidentity, min_coverage, type) ⇒ SequenceSynteny

Returns a new instance of SequenceSynteny.



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 16

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)

  @name = name
  @pidentity = pidentity
  @min_coverage = min_coverage
  @aln_file = nil
  @type = type

end

Instance Attribute Details

#aln_hits ⇒ Object (readonly)

Returns the value of attribute aln_hits.



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

def aln_hits
  @aln_hits
end

#query_file ⇒ Object (readonly)

Returns the value of attribute query_file.



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

def query_file
  @query_file
end

#query_sequences ⇒ Object (readonly)

Returns the value of attribute query_sequences.



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

def query_sequences
  @query_sequences
end

#subject_file ⇒ Object (readonly)

Returns the value of attribute subject_file.



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

def subject_file
  @subject_file
end

#subject_sequences ⇒ Object (readonly)

Returns the value of attribute subject_sequences.



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

def subject_sequences
  @subject_sequences
end

Instance Method Details

#choose_best_hit(i, prots, ref_cds) ⇒ Object

Choose Best Hit base on neighbor hits



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 337

def choose_best_hit i, prots, ref_cds

  hit_index = 0
  p = prots[i]
  hit_locus_tags = []

  @aln_hits[p][:hits].each do |h|
    hit_locus_tags << ref_cds[h][:locustag].downcase.split("_")[-1].gsub(/[a-z]/,"").to_i
  end

  continue=true
  offset=1

  while continue
    fwd_end = false
    bcw_end = false
    found = false

    if (i+offset) < (prots.length-1)
      fwd_p = prots[i+offset]
      next_prot_hits = @aln_hits[fwd_p][:hits]
      if next_prot_hits.length < 2
        n = ref_cds[next_prot_hits[0]][:locustag].downcase.split("_")[-1].gsub(/[a-z]/,"").to_i
        closest = 10000
        current_ltag_i = 0
        hit_locus_tags.each_with_index do |ltag,ltag_i|
          if (ltag-n).abs < closest
            current_ltag_i = ltag_i
            closest = (ltag-n).abs
          end
        end
        hit_index = current_ltag_i
        found = true
      end
    else
      fwd_end = true
    end

    if (i-offset) >= 0 and !found
      bcw_p = prots[i-offset]
      next_prot_hits = @aln_hits[bcw_p][:hits]
      if next_prot_hits.length < 2
        n = ref_cds[next_prot_hits[0]][:locustag].downcase.split("_")[-1].gsub(/[a-z]/,"").to_i
        closest = 10000
        current_ltag_i = 0
        hit_locus_tags.each_with_index do |ltag,ltag_i|
          if (ltag-n).abs < closest
            current_ltag_i = ltag_i
            closest = (ltag-n).abs
          end
        end
        hit_index = current_ltag_i
        found = true
      end
    else
      bcw_end = true
    end

    offset += 1
    continue = (!fwd_end and !bcw_end and !found)
  end

  hit_index

end

#extract_hits(mode) ⇒ Object

Extract Hit from blast8 file and save it in hash contig-0_1 ABJ71957.1 96.92 65 2 0 1 65 1 65 9.2e-31 131.0



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 125

def extract_hits mode

  feature = ""
  File.open(@aln_file,"r") do |fread|
    while l = fread.gets

      lA = l.chomp!.split("\t")
      key = lA[0]

      # extraction of hit id depends on mode ..
      if mode == :refgenome
        hit = lA[1]
        feature = "cds"
      elsif mode == :externaldb
        # hit = lA[1].chomp.split("|")[3]
        hit = lA[1]
        feature = "cds"
        # decrease min. % identity for foreign proteins
        @pidentity = 60.0
      end

      # compute coverage based on sequences length
      cov_query = (lA[3].to_f/@query_sequences[key][:length]).round(2)
      cov_subject = (lA[3].to_f/@subject_sequences[hit][:length]).round(2)

      # assert cutoff on identity and coverage
      # 1 -> pass cutoff, 0 under cutoff
      assert_cutoff = [1,1,1]
      assert_cutoff[0] = 0 if lA[2].to_f < @pidentity
      assert_cutoff[1] = 0 if cov_query < @min_coverage
      assert_cutoff[2] = 0 if cov_subject < @min_coverage and @query_sequences[key][:partial] == false

      # first hit for query
      if ! @query_sequences[key].has_key? :homology
        @query_sequences[key][:conserved] = true
        # @subject_sequences[key][:conserved] = true
        @query_sequences[key][:homology] = {
          pId: lA[2].to_f.round(2),
          cov_query: cov_query,
          cov_subject: cov_subject,
          evalue: lA[10],
          score: lA[11].to_f,
          hits: [hit],
          length: [lA[3].to_i],
          query_location: [[lA[6].to_i,lA[7].to_i]],
          subject_location: [[lA[8].to_i,lA[9].to_i]],
          feature: feature,
          assert_cutoff: assert_cutoff
        }
        @subject_sequences[hit][:hits] = [key]

      # query already got at least 1 hit and new_score > last_score
      elsif lA[11].to_f > @query_sequences[key][:homology][:score]
        @query_sequences[key][:conserved] = true
        # @subject_sequences[key][:conserved] = true
        @query_sequences[key][:homology] = {
          pId: lA[2].to_f.round(2),
          cov_query: cov_query,
          cov_subject: cov_subject,
          evalue: lA[10],
          score: lA[11].to_f,
          hits: [hit],
          length: [lA[3].to_i],
          query_location: [[lA[6].to_i,lA[7].to_i]],
          subject_location: [[lA[8].to_i,lA[9].to_i]],
          feature: feature,
          assert_cutoff: assert_cutoff
        }
        @subject_sequences[hit][:hits] =  [key]

      # query already got at least 1 hit and score == last_score
      elsif lA[11].to_f == @query_sequences[key][:homology][:score]
        @query_sequences[key][:homology][:hits] << hit
        @query_sequences[key][:homology][:length] << lA[3].to_i
        @query_sequences[key][:homology][:query_location] << [lA[6].to_i,lA[7].to_i]
        @query_sequences[key][:homology][:subject_location] << [lA[8].to_i,lA[9].to_i]
        if @subject_sequences[hit].has_key? :hits
          @subject_sequences[hit][:hits] << key
        else
          @subject_sequences[hit][:hits] = [key]
        end
      end
    end
  end

end

#extract_hits_dna(mode) ⇒ Object

Extract Hit from blast8 file and save it in hash prpa PA0668.4|rRNA|23S 99.97 2891 1 0 705042 707932 1 2891 0.0e+00 5671.0



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 215

def extract_hits_dna mode

  @aln_hits = {}
  feature = ""
  File.open(@aln_file,"r") do |fread|
    while l = fread.gets
      lA = l.chomp!.split("\t")
      key = lA[0]+"_"+lA[6]+"_"+lA[7]
      if mode == :rna
        hit_split = lA[1].chomp.split("|")
        hit = hit_split[0]
        feature = hit_split[1]
        product = hit_split[2]
      end
      next if lA[2].to_f < @pidentity
      if ! @aln_hits.has_key? key
        @aln_hits[key] = {
          pId: lA[2].to_f.round(2),
          # cov_query: (@query_sequences[key][:length]/lA[3].to_f).round(2),
          # cov_subject: (@subject_sequences[hit][:length]/lA[3].to_f).round(2),
          evalue: lA[10],
          score: lA[11].to_f,
          hits: [hit],
          product: [product],
          length: [lA[3].to_i],
          query_location: [[lA[6].to_i,lA[7].to_i]],
          subject_location: [[lA[8].to_i,lA[9].to_i]],
          feature: [feature]
        }
      elsif lA[11].to_f > @aln_hits[key][:score]
        @aln_hits[key] = {
          pId: lA[2].to_f.round(2),
          # cov_query: (@query_sequences[key][:length]/lA[3].to_f).round(2),
          # cov_subject: (@subject_sequences[hit][:length]/lA[3].to_f).round(2),
          evalue: lA[10],
          score: lA[11].to_f,
          hits: [hit],
          product: [product],
          length: [lA[3].to_i],
          query_location: [[lA[6].to_i,lA[7].to_i]],
          subject_location: [[lA[8].to_i,lA[9].to_i]],
          feature: [feature]
        }
      elsif lA[11].to_f == @aln_hits[key][:score]
        @aln_hits[key][:hits] << hit
        @aln_hits[key][:length] << lA[3].to_i
        @aln_hits[key][:query_location] << [lA[6].to_i,lA[7].to_i]
        @aln_hits[key][:subject_location] << [lA[8].to_i,lA[9].to_i]
        @aln_hits[key][:feature] << feature
        @aln_hits[key][:product] << product
      end
    end
  end

  prune_aln_hits @aln_hits

end

#get_annotation_for_contig(contig_to_annotate, prots_to_annotate = nil, ref_cds = nil) ⇒ Object

Get the annotations for a contig for RerenceGenome



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 275

def get_annotation_for_contig contig_to_annotate, prots_to_annotate=nil, ref_cds=nil

  annotations = {}

  if prots_to_annotate != nil

    # contig_to_annotate = prots_to_annotate[0].split("_")[0..-2].join("_")
    prots = []

    @aln_hits.each_key do |k|
      contig = k.split("_")[0..-2].join("_")
      if contig == contig_to_annotate
        prots << k
      end
    end

    # sorting the prot by their appearance in the contig
    prots.sort! { |a,b| a.split("_")[-1].to_i <=> b.split("_")[-1].to_i }

    i = 0
    prots_to_annotate.each do |p|

      if @aln_hits.has_key? p

        hit_index = 0

        if @aln_hits[p][:hits].length > 1
          hit_index = choose_best_hit i, prots, ref_cds
        end

        h = @aln_hits[p][:hits][hit_index]
        hit = ref_cds[h]
        annotations[p] = hit
        annotations[p][:pId] = @aln_hits[p][:pId]
        annotations[p][:length] = @aln_hits[p][:length][hit_index]
        i+=1

      else

        annotations[p] = nil

      end

    end

  elsif ! @aln_hits.empty?

    @aln_hits.each_key do |k|
      contig = k.split("_")[0..-3].join("_")
      if contig == contig_to_annotate
        annotations[k] = @aln_hits[k]
      end
    end

  end

  annotations                 # return

end

#get_sequences(raw_file) ⇒ Object

get sequences name with length in hash



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 35

def get_sequences raw_file

  sequences = {}

  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

  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

end

#prune_aln_hits(aln_hits) ⇒ Object

end of method



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 403

def prune_aln_hits aln_hits

  keys_to_delete = []

  aln_hits.each do |key1,val1|

    aln_hits.each do |key2,val2|

      next if key1==key2
      next if keys_to_delete.include? key1
      next if keys_to_delete.include? key2

      if val1[:query_location][0][0] >= val2[:query_location][0][0] and
        val1[:query_location][0][0] < val2[:query_location][0][1]
        overlap_len = val2[:query_location][0][1] - val1[:query_location][0][0]
        val1_len = val1[:query_location][0][1]-val1[:query_location][0][0]
        val2_len = val2[:query_location][0][1]-val2[:query_location][0][0]
        if overlap_len.to_f/val1_len > 0.2 and overlap_len.to_f/val2_len > 0.2
          if val1[:score] < val2[:score]
            keys_to_delete << key1
          else
            keys_to_delete << key2
          end
        end
      elsif val2[:query_location][0][0] >= val1[:query_location][0][0] and
           val2[:query_location][0][0] < val1[:query_location][0][1]
        overlap_len = val1[:query_location][0][1] - val2[:query_location][0][0]
        val1_len = val1[:query_location][0][1]-val1[:query_location][0][0]
        val2_len = val2[:query_location][0][1]-val2[:query_location][0][0]
        if overlap_len.to_f/val1_len > 0.2 and overlap_len.to_f/val2_len > 0.2
          if val1[:score] < val2[:score]
            keys_to_delete << key1
          else
            keys_to_delete << key2
          end
        end
      end

    end

  end

  keys_to_delete.each do |k|
    aln_hits.delete(k)
  end

end

#run_blat ⇒ Object

run blat on proteins



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 83

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")
  else
    system("#{base_cmd} #{@subject_file} #{@query_file} #{@outdir}/#{@name}.blat8.tsv")
  end
  @aln_file = "#{@outdir}/#{@name}.blat8.tsv"
  # extract_hits
end

#run_diamond ⇒ Object

run diamond on proteins



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 106

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 --masking none --db #{db_file} -q #{query_file} -o #{@outdir}/#{@name}.diamond.tsv -f 6 > /dev/null 2>&1")
  else
    # system("#{@root}/glsearch36.linux -b 3 -E 1e-25 -m 8 #{@subject_file} #{@query_file} > #{@outdir}/#{@name}.fasta36.tsv")
  end
  @aln_file = "#{@outdir}/#{@name}.diamond.tsv"
  # extract_hits
end

#run_fasta36 ⇒ Object

run fasta36 on proteins



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# File 'lib/bacterial-annotator/sequence-synteny.rb', line 95

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