[biopieces.git] / code_ruby / lib / maasha / align.rb

# Copyright (C) 2007-2011 Martin A. Hansen.

# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

# http://www.gnu.org/copyleft/gpl.html

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# This software is part of the Biopieces framework (www.biopieces.org).

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

require 'pp'
require 'open3'
require 'narray'
require 'maasha/fasta'

class AlignError < StandardError; end;

ALPH_DNA    = %w{A T C G}
ALPH_AMBI   = %w{A T C G M R W S Y K V H D B N}

BIT_INDEL = 0
# BIT_A = 1 << 0
# BIT_T = 1 << 1
# BIT_C = 1 << 2
# BIT_G = 1 << 3

BIT_M = BIT_A | BIT_C
BIT_R = BIT_A | BIT_G
BIT_W = BIT_A | BIT_T
BIT_S = BIT_C | BIT_G
BIT_Y = BIT_C | BIT_T
BIT_K = BIT_G | BIT_T
BIT_V = BIT_A | BIT_C | BIT_G
BIT_H = BIT_A | BIT_C | BIT_T
BIT_D = BIT_A | BIT_G | BIT_T
BIT_B = BIT_C | BIT_G | BIT_T
BIT_N = BIT_G | BIT_A | BIT_T | BIT_C

BITMAP = [
  BIT_A,
  BIT_T,
  BIT_C,
  BIT_G,
  BIT_M,
  BIT_R,
  BIT_W,
  BIT_S,
  BIT_Y,
  BIT_K,
  BIT_V,
  BIT_H,
  BIT_D,
  BIT_B,
  BIT_N
]

TR_NUC = "-"                   + ALPH_AMBI.join("").downcase
TR_HEX = [BIT_INDEL].pack("C") + BITMAP.pack("C*")

ROW_A = 0
ROW_T = 1
ROW_C = 2
ROW_G = 3

class Fasta
  def initialize(io)
    @io = io
  end

  def close
    @io.close
  end
end

# Class for aligning sequences.
class Align
  attr_accessor :options
  attr_reader   :entries

  # Class method to align sequences in a list of Seq objects and
  # return these as a new list of Seq objects.
  def self.muscle(entries, verbose = false)
    result   = []
    index    = {}

    Open3.popen3("muscle", "-quiet") do |stdin, stdout, stderr|
      entries.each do |entry|
        raise AlignError, "Duplicate sequence name: #{entry.seq_name}" if index.has_key? entry.seq_name

        index[entry.seq_name] = entry

        stdin.puts entry.to_fasta
      end

      stdin.close

      stderr.each_line { |line| $stderr.puts line } if verbose

      aligned_entries = Fasta.new(stdout)

      aligned_entries.each do |fa_entry|
        fq_entry = index[fa_entry.seq_name]

        fa_entry.seq.scan(/-+/) do |m|
          fq_entry.seq  = fq_entry.seq[0 ... $`.length]  + ('-' * m.length) + fq_entry.seq[$`.length .. -1]
          fq_entry.qual = fq_entry.qual[0 ... $`.length] + ('@' * m.length) + fq_entry.qual[$`.length .. -1] unless fq_entry.qual.nil?
        end

        result << fq_entry
      end
    end

    self.new(result)
  end

  # Method to initialize an Align object with a list of aligned Seq objects.
  def initialize(entries, options = {})
    @entries = entries
    @options = options
  end

  # Method that returns the length of the alignment.
  def length
    @entries.first.length
  end

  # Method that returns the number of members or sequences in the alignment.
  def members
    @entries.size
  end

  # Method to create a consensus sequence from an Align object and
  # return a new Seq object with the consensus.
  def consensus
    cons = Consensus.new(@entries, @options)
    cons.consensus
  end

  # Method to pretty print an alignment from an Align object.
  def to_s
    cons = Consensus.new(@entries, @options)
    cons.mask_entries!

    max_name = @entries.group_by { |entry| entry.seq_name.length }.max.first

    output = ""

    @entries.each do |entry|
      output << entry.seq_name + (" " * (max_name + 3 - entry.seq_name.length )) + entry.seq + $/
    end

    cons_entry = cons.consensus 

    output << " " * (max_name + 3) + cons_entry.seq
    output << $/ + " " * (max_name + 3) + cons_entry.qual.tr("[@-h]", "           ..........ooooooooooOOOOOOOOOO") unless cons_entry.qual.nil?
    output
  end

  private

  class Consensus
    # Method to initialize a Consensus object given a list of aligned Seq object.
    def initialize(entries, options)
      @entries = entries
      @options = options

      @cols = entries.first.seq.length
      @rows = entries.size

      @has_qual = entries.first.qual.nil? ? false : true

      @na_seq  = NArray.byte(@cols, @rows)
      @na_qual = NArray.byte(@cols, @rows) if @has_qual

      na_add_entries
      consensus_calc
    end

    # Method that lowercase residues that have been removed during
    # the determination of the consensus sequence.
    def mask_entries!
      na_seq = NArray.byte(@cols, @rows)

      @entries.each_with_index do |entry, i|
        na_seq[true, i]  = NArray.to_na(entry.seq.upcase, "byte")
      end

      na_seq += ((na_seq.ne('-'.ord) - @na_seq.ne(0)) * ' '.ord)

      @entries.each_with_index do |entry, i|
        entry.seq = na_seq[true, i].to_s
      end
    end

    # Method that returns a Sequence object with a consensus sequence
    # for the entries in an Align object.
    def consensus
      new_seq      = Seq.new
      new_seq.seq  = consensus_seq
      new_seq.qual = consensus_qual if @has_qual
      new_seq.type = "dna"

      new_seq
    end

    private

    # Method to add a Seq entry object to the two NArrays; @na_seq and @na_qual
    def na_add_entries
      @entries.each_with_index do |entry, i|
        @na_seq[true, i]  = NArray.to_na(entry.seq.downcase.tr(TR_NUC, TR_HEX), "byte")
        @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - SCORE_ILLUMINA if @has_qual
      end
    end

    # Method to calculate a consensus sequence from a list of sequenced stored in two
    # NArrays.
    def consensus_calc
      if @has_qual
        if @options.has_key? :quality_min
          mask = mask_quality_min

          @na_seq  *= mask
          @na_qual *= mask
        end

        if @options.has_key? :quality_mean
          mask = mask_quality_mean

          @na_seq  *= mask
          @na_qual *= mask
        end
      end

      if @options.has_key? :sequence_min
        mask = mask_sequence_min

        @na_seq  *= mask
        @na_qual *= mask if @has_qual
      end

      if @options.has_key? :gap_max
        mask = mask_gap_max

        @na_seq  *= mask
        @na_qual *= mask if @has_qual
      end

      if @options.has_key? :residue_min
        mask = mask_residue_min

        @na_seq  *= mask
        @na_qual *= mask if @has_qual
      end
    end

    # Mask that indicates which columns have more than sequence_min sequences.
    # Columns with less than sequence_min are 0'ed, otherwise set to 1.
    def mask_sequence_min
      mask  = NArray.byte(@cols, @rows) + 1
      mask *= ((@na_seq > 0).to_type("int").sum(1) >= @options[:sequence_min])
      mask
    end

    # Mask that indicates which residue frequencies that are above the residue_min.
    # The residue frequencies are calculated for each column and residue type as the
    # number of each residue type over the sum of all non-gap residues in that column.
    # Positions with residues above the residue_min are indicated with 1.
    def mask_residue_min
      cons_min = @options[:residue_min]
      factor   = 1 / @na_seq.ne(0).to_type("float").sum(1)

      mask_A = (@na_seq & BIT_A > 0).to_type("int")
      mask_T = (@na_seq & BIT_T > 0).to_type("int")
      mask_C = (@na_seq & BIT_C > 0).to_type("int")
      mask_G = (@na_seq & BIT_G > 0).to_type("int")

      mask_A = (mask_A * mask_A.sum(1)) * factor >= cons_min
      mask_T = (mask_T * mask_T.sum(1)) * factor >= cons_min
      mask_C = (mask_C * mask_C.sum(1)) * factor >= cons_min
      mask_G = (mask_G * mask_G.sum(1)) * factor >= cons_min

      mask_A | mask_T | mask_C | mask_G
    end

    # Mask that indicates which columns contain fewer gaps than max_gap.
    # Columns with more gaps are 0'ed, others are set to 1.
    def mask_gap_max
      mask  = NArray.byte(@cols, @rows) + 1
      mask *= @na_seq.ne(0).to_type("float").sum(1) / @rows > @options[:gap_max]

      mask
    end

    # Mask that indicates which residues in an alignment are above quality_min.
    # Positions with subquality are 0'ed - all others are set to 1.
    def mask_quality_min
      @na_qual > @options[:quality_min]
    end

    # Mask that indicates which columns have a quality mean above quality_mean which
    # is the mean of all non-gap quality residues in that column. Columns with less then
    # quality_mean are 0'ed, otherwise set to 1.
    def mask_quality_mean
      mask     = NArray.byte(@cols, @rows) + 1
      residues = @na_seq.ne(0).to_type("int").sum(1)
      quality  = @na_qual.to_type("float").sum(1)

      mask * (quality / residues).round > @options[:quality_mean]
    end

    # Method to calculate a consensus sequence from a Consensus object.
    def consensus_seq
      cons  = NArray.byte(@cols)
      cons |= (@na_seq & BIT_A).max(1)
      cons |= (@na_seq & BIT_T).max(1)
      cons |= (@na_seq & BIT_C).max(1)
      cons |= (@na_seq & BIT_G).max(1)

      cons.to_s.tr!(TR_HEX, TR_NUC).upcase
    end

    # Method to calculate a consensus quality from a Consensus object.
    def consensus_qual
      (@na_qual.mean(1).round.to_type("byte") + SCORE_ILLUMINA).to_s
    end
  end
end

__END__