Module: Bio::DB::Blast

Defined in:
lib/bio/db/blast.rb

Defined Under Namespace

Classes: BlasteException

Class Method Summary collapse

Class Method Details

.align(opts = {}) ⇒ Object 



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# File 'lib/bio/db/blast.rb', line 79

def self.align(opts={})
  target=opts[:target]
  query=opts[:query]
  max_target_seqs = 6 #TODO: Actually add this as an argument to PolyMarker. 
  max_target_seqs = opts[:max_hits] * 2 if opts[:max_hits]
  cmdline = "blastn -max_target_seqs #{max_target_seqs} -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
  #puts cmdline
  status, stdout, stderr = systemu cmdline
  if status.exitstatus == 0
    alns = Array.new unless block_given?
    stdout.each_line do |e_l|
      #puts e_l
      line = to_exo(e_l)
      #puts line
      arr = line.split("\t")
      aln = Bio::DB::Exonerate::Alignment.parse_custom(line) 
      if aln
        if block_given?
          yield aln
        else
          alns << aln
        end
      end
    end
    return alns unless block_given?
  else
    raise BlasteException.new(), "Error running exonerate. Command line was '#{cmdline}'\n Blast STDERR was:\n#{stderr}"
  end
end

.to_exo(line) ⇒ Object 



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# File 'lib/bio/db/blast.rb', line 69

def self.to_exo(line)
  arr = Array.new
  arr << "RESULT:"
  arr << to_sugar(line)
  arr << line.split("\t")[9..11]
  arr << "."
  arr << to_vulgar(line)
  arr.join("\t")
end

.to_sugar(line) ⇒ Object 



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# File 'lib/bio/db/blast.rb', line 3

def self.to_sugar(line)
  fields = line.split("\t")[0..8]
  
  if  fields[3] =="-1"
    fields[3] = "-"
    fields[2] = fields[2].to_i - 1
  else
    fields[3] = "+"
    fields[1] = fields[1].to_i - 1
  end
  if fields[7] =="-1"
    fields[7] = "-"
    fields[6] = fields[6].to_i - 1
  else
    fields[7] = "+"
    fields[5] = fields[5].to_i - 1
  end
  fields.join(" ")
end

.to_vulgar(line) ⇒ Object 



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# File 'lib/bio/db/blast.rb', line 23

def self.to_vulgar(line)
  qseq, sseq = line.split("\t")[12..13]

  len = qseq.length
  l_status = ""
  l_len = 0
  str = Array.new
  statuses = ""
  for i in 0..len
    if qseq[i] == "-"
      status = "D"
    elsif sseq[i] == "-"
      status = "I"
    else
      status = "M"
    end
    statuses << status
  end
  statuses.split('').each do |e| 
    if l_status != e
      case l_status
      when "M"
        str << ["M", l_len, l_len]
      when "I"
        str << ["G", l_len, 0]
      when "D"
        str << ["G", 0, l_len]
      end
      l_len = 0
    end
    l_status = e
    l_len += 1
  end
  l_len -= 1
  case l_status
  when "M"
    str << ["M", l_len, l_len]
  when "I"
    str << ["G", l_len, 0]
  when "D"
    str << ["G", 0, l_len]
  end

  str.flatten!.join(" ")
end