crowd server action

gistfile1.rb

# Splits up alignemnt into block sized chunks and then render them as html
class RenderAlignment < CloudCrowd::Action
  require 'rubygems'
  require 'bio'
  # Split up alignment
  def split
    fasta_sequences = Bio::FlatFile.open(input_path).to_a
    alignment = Bio::Alignment.new(fasta_sequences)
    block_size = options['block_size']
    number_of_blocks = (alignment.alignment_length/block_size.to_f).ceil
    (1..number_of_blocks).each do |block_number|
      start_of_slice = (block_number-1)*block_size
      end_of_slice = (block_number*block_size)-1
      alignment_slice = alignment.alignment_slice(start_of_slice..end_of_slice)
      slicefile = File.new("alignslice-#{block_number}.fas", "w")
      slicefile.write(alignment_slice.output_fasta)
      slicefile.close
    end
    alignment_files = Dir["alignslice-*"].map {|slice| save(slice) }
    alignment_files.to_json
  end

  # Convert an alignment into html
  def process
    # read in alignment
    fasta_sequences = Bio::FlatFile.open(input_path).to_a
    alignment = Bio::Alignment.new(fasta_sequences)
    alignment.alignment_length


    input_path.match(/alignslice-(\d+)\.fas$/)
    block_number = $1.to_i


    process_options = {'consensus_threshold' => 0.7 ,'block_size' => 81, 'highlight_colour' => "#6666FF", 'draw_ruler' => true, 'translate' => false , 'consensus' => false}.me
rge(options)



    # find maximum sequence
    max_name_length = (alignment.sequence_names.collect{|sequence_name| sequence_name.length}).max
    sequence_names = alignment.sequence_names.collect{|sequence_name| sprintf("%#{max_name_length}s", sequence_name)}
    sequence_names.collect!{|sequence_name| sequence_name.gsub(/\s/, "&nbsp;") + "&nbsp;"}

    html_string =""

    # generate consensus sequence string
    consensus = alignment.consensus_string(process_options['consensus_threshold'])
    if process_options['consensus']
      html_string << sprintf("%#{max_name_length}s", "consensus").gsub(/\s/, "&nbsp;") + "&nbsp;"
      html_string << consensus
      html_string << "<br/>"
    end

    # print out sequences
    sequences = alignment.alignment_collect{|sequence| sequence}
    sequences.each_with_index do |sequence, index|
      #set consensus match to false
      consensus_mismatch = false
      # print sequence name
      html_string << sequence_names[index]
      # loop through sequence blocks
      (0..alignment.alignment_length-1).each do |alignment_position|
        sequence_letter = sequence.slice(alignment_position,1).to_s
        if sequence_letter == "X" or sequence_letter == "Z"# dodgy amino acid or stop
          if consensus_mismatch == true
            consensus_mismatch = false
            html_string << "</span>"
          end
          # add base to html_string
          if sequence_letter == "Z"
            html_string << "<span style='background-color: #FF0000'>*</span>"
          else
            html_string << "<span style='background-color: #FF0000'>" + sequence_letter + "</span>"
          end
        elsif sequence_letter != consensus.slice(alignment_position,1).to_s # not a match
          if consensus_mismatch == false
            consensus_mismatch = true
            html_string << "<span style='background-color: #{process_options['highlight_colour']}'>"
          end
          # add base to html_string
          html_string << sequence_letter
        else  # a match
          if consensus_mismatch == true
            consensus_mismatch = false
            html_string << "</span>"
          end
          # add base to html_string
          if process_options['consensus']
            html_string << "."
          else
            html_string << sequence_letter
          end
        end
      end
      html_string << "</span>" if consensus_mismatch == true
      html_string << "<br/>"
      #translate ?
      if process_options['translate']
        (max_name_length+1).times{html_string << "&nbsp;"}
        (0..alignment.alignment_length-1).each do |alignment_position|
          if alignment_position%3 == 0
            amino_acid =  Bio::CodonTable::TABLES[1][sequence.slice(alignment_position,3).downcase]
            if amino_acid.nil?
              if sequence.slice(alignment_position,3) == "---"
                html_string << "&nbsp;"
              else
                html_string << "X"
              end
            else
              html_string << "#{amino_acid}"
            end
          else
            html_string << "&nbsp;"
          end
        end
        html_string << "<br/>"
      end
    end # end of sequence loop
    
    # ruler drawing
    if process_options['draw_ruler']
      # draw ticks
      (max_name_length+1).times do html_string << "&nbsp;" end
      (((block_number-1)*process_options['block_size'])+1..(block_number*process_options['block_size'])).each do |alignment_position|
        break if alignment_position > ((block_number-1)*process_options['block_size']) + alignment.alignment_length
        if alignment_position%10 == 0
          html_string << "|"
        else
          html_string << "&nbsp;"
        end
      end
      # end
      html_string << "<br/>"
      # draw numbers
      (max_name_length+1).times do html_string << "&nbsp;" end
      alignment_position = ((block_number-1)*process_options['block_size'])+1
      while alignment_position <= (block_number*process_options['block_size']) do
        break if alignment_position > ((block_number-1)*process_options['block_size']) + alignment.alignment_length
        if alignment_position%10 == 0
          html_string << alignment_position.to_s
          alignment_position += alignment_position.to_s.length
        else
          html_string << "&nbsp;"
          alignment_position += 1
        end
      end
      html_string << "<br/>"
    end # end of ruler drawing
    html_string << "<br/>"
    {'block_number'  =>  block_number , 'html_string' => html_string}
  end

  # Merge all resulting htmls into one
  def merge
    all_htmls = Array.new
    input.each do |html_data|
      all_htmls[html_data['block_number']-1] = html_data['html_string']
    end
    final_html_string = ""
    all_htmls.each do |html_string|
      final_html_string << html_string
    end
    final_html_string
  end


end