Module: Bio::Alignment::DNASequenceReads

Defined in:
lib/bio/alignment/dna_sequence.rb

Constant Summary collapse

CLUSTALW_OPTS = 
%w(gapopen gapext dnamatrix type)
ALIGN_OPTS = 
{
  :type => 'DNA',
  :gapopen => 20,
  :gapext => 20,
  :dnamatrix => 'IUB',  # "IUB" || "CLUSTALW"
  :fidelity_length => 10,
  :consensus_fidelity => true,
}

Class Method Summary collapse

Class Method Details

.align_pairwise(bioseqs, opt = {}) ⇒ Object

returns high quality pairwise alignments based on the fidelity_length option



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# File 'lib/bio/alignment/dna_sequence.rb', line 87

def align_pairwise(bioseqs, opt={})
  factory = Bio::ClustalW.new
  clustal_opts = hash_opts_to_clustalopts(opt)
  factory.options = clustal_opts
  template = bioseqs.shift
  start_length = []
  pairwise_aligns = bioseqs.map do |bseq|
    clust_al = clustal_align([template, bseq], factory)
    cl_cons = clust_al.consensus
    aligned_string = clust_al[1].to_s
    #(st, len) = find_good_section(aligned_string, opt[:fidelity_length])
    seq_to_use = 
      if opt[:consensus_fidelity]
        cl_cons
      else
        aligned_string
      end
    (st, len) = find_good_section(seq_to_use, opt[:fidelity_length])
    if st
      pristine = aligned_string[st, len].gsub('-','')  # pristine read (ends removed)
      clustal_align([template.to_s, Bio::Sequence::NA.new(pristine)], factory)
    else
      warn "a sequence does not meeting min fidelity! using original alignment" 
      clust_al
    end

  end
end

.clustal_align(bioseqs, factory) ⇒ Object 



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# File 'lib/bio/alignment/dna_sequence.rb', line 71

def clustal_align(bioseqs, factory)
  al = Bio::Alignment.new(bioseqs)
  al.do_align(factory)
end

.consensus_string_and_stats(strings) ⇒ Object

assumes the first is the template



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# File 'lib/bio/alignment/dna_sequence.rb', line 178

def consensus_string_and_stats(strings)
  as_chars = strings.map {|v| v.split("") }
  stats = Array.new(6, 0)
  consensus_string = as_chars.shift.zip(*as_chars).map do |chrs|
    consensus_bool_ar = Array.new(6)
    symbols = [' '] + %w(^ = . ^ ?) 
    all_gaps = 0
    template_gap = 1
    agreement = 2
    gap_below_template = 3
    all_bad_matches = 4
    non_consensus = 5

    first = chrs.shift
    if [first, *chrs].all? {|v| v.nil? or (v == '-') }
      consensus_bool_ar[all_gaps] = true
    elsif first == '-'
      consensus_bool_ar[template_gap] = true
    elsif chrs.all? {|v| v == '-'}
      consensus_bool_ar[gap_below_template] = true
    elsif chrs.all? {|v| (v == '-') or (v == first) }
      consensus_bool_ar[agreement] = true
    elsif chrs.all? {|v| (v == '-') or (v != first) }
      consensus_bool_ar[all_bad_matches] = true
    else
      consensus_bool_ar[non_consensus] = true
    end
    consensus_bool_ar.each_with_index {|v,i| stats[i] += 1 if v }
    symbols[consensus_bool_ar.index(true)]
  end.join
  [consensus_string, stats]
end

.cs_to_s(ar) ⇒ Object 



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# File 'lib/bio/alignment/dna_sequence.rb', line 165

def cs_to_s(ar)
  ar.map {|v| v.nil? ? '-' : v.chr }.join
end

.exactly_chars(string, n) ⇒ Object 



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# File 'lib/bio/alignment/dna_sequence.rb', line 212

def exactly_chars(string, n)
  at_least = "%#{n}s" % string
  at_least[0,n]
end

.find_good_section(iupac_concensus_string, min_length) ⇒ Object

returns (start, length) where min_length reads are correct



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# File 'lib/bio/alignment/dna_sequence.rb', line 29

def find_good_section(iupac_concensus_string, min_length)
  start = find_start_good_section(iupac_concensus_string, min_length)
  from_end = find_start_good_section(iupac_concensus_string.reverse, min_length)
  length = iupac_concensus_string.length - start - from_end
  if length < 0
    nil
  else
    [start, length]
  end
end

.find_start_good_section(iupac_concensus_string, min_length) ⇒ Object

returns the index of the starting run of good chars



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# File 'lib/bio/alignment/dna_sequence.rb', line 11

def find_start_good_section(iupac_concensus_string, min_length)
  good_char_count = 0
  char_index = 0
  iupac_concensus_string.each_char do |char|
    if char =~ /[^\?\-Nn]/
      good_char_count += 1
      if good_char_count >= min_length
        break
      end
    else
      good_char_count = 0
    end
    char_index += 1
  end
  char_index - (good_char_count - 1)
end

.first_non_dash_char(string) ⇒ Object 



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# File 'lib/bio/alignment/dna_sequence.rb', line 60

def first_non_dash_char(string)
  char_cnt = 0
  string.each_char do |char|
    if char != '-'
      break
    end
    char_cnt += 1
  end
  char_cnt
end

.hash_opts_to_clustalopts(hash) ⇒ Object 



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# File 'lib/bio/alignment/dna_sequence.rb', line 40

def hash_opts_to_clustalopts(hash)
  array = []
  hash.each do |k,v|
    if CLUSTALW_OPTS.include?(k.to_s)
      array << "-#{k}=#{v}"
    end
  end
  array
end

.lstrip_dash(string) ⇒ Object 



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# File 'lib/bio/alignment/dna_sequence.rb', line 50

def lstrip_dash(string)
  chr = first_non_dash_char(string)
  string[chr..-1]
end

.merge_pairwise(aligns) ⇒ Object

assumes all were aligned to the same template (the first of a pair)



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# File 'lib/bio/alignment/dna_sequence.rb', line 117

def merge_pairwise(aligns)
  ps = aligns.map do |align| 
    seqs = []
    align.each do |bioseq|
      seqs << bioseq.to_s
    end
    seqs
  end
  template = []
  #m,x,n
  x = 2
  ftemp = ps.first.first
  nmax = ps.map {|pair| pair.first.size }.max
  mmax = ps.size
  mar = (0...mmax).to_a
  others = mar.map { [] }
  ns = mar.map { 0 }
  tn = 0
  on = 0
  (0...nmax).each do |n|
    (t_dsh, t_no_dsh) = mar.partition do |m| 
      # this is RUBY 1.8 ONLY!!
      ps[m][0][ns[m]] == 45  # '-' is ascii 45
    end

    # if a template has a dash, all other off-templates need a dash
    if t_dsh.size > 0
      template[tn] = 45
      t_no_dsh.each do |m|
        # don't update these guys counter
        others[m][tn] = 45
      end
      t_dsh.each do |m|
        others[m][tn] = ps[m][1][ns[m]]
        ns[m] += 1
      end
    else # no dashes in the template
      t_no_dsh.each do |m|
        others[m][tn] = ps[m][1][ns[m]]
      end
      template[tn] = ps[0][0][ns[0]]
      ns.map!{|v| v+1 } 
    end
    tn += 1
  end
  [cs_to_s(template), others.map! {|ar| cs_to_s(ar) } ]
end

.print_align(io, sequences, labels, opts = {}) ⇒ Object

all gaps <blank>

template gap              ^
gap below template        .
agreement                 =
all bad matches           ^
non-consensus             ?

accepts :template => template_sequence



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# File 'lib/bio/alignment/dna_sequence.rb', line 226

def print_align(io, sequences, labels, opts={})
  opts = {:cutoff => 70, :start => 0, :chars => 20}.merge(opts)
  (start, length, chars) = opts.values_at(:start, :cutoff, :chars)
  spacer = "  "

  if opts[:template]
    sequences.unshift(opts[:template])
    labels.unshift(opts[:template_label])
  end

  all_stats = Array.new(6,0)
  loop do
    fin = false

    max_length = 0
    lines = []
    consensus_line = ""
    fragments = sequences.map do |string|
      fin = (start >= string.length )
      break if fin

      string_frag = string[start, length]

      string_frag
    end ; break if fin

    doubles = fragments.zip(labels)

    doubles = doubles.select {|frag, _| (frag.size > 0) && (frag =~ /[^-]/) }

    max_length = doubles.map {|frag, _| frag.size }.max

    (cs, stats) = consensus_string_and_stats( doubles.map {|frag,_| frag } )
    all_stats = all_stats.zip(stats).map {|a,b| a + b }

    doubles.push( [cs, "<CONSENSUS>"] )

    lines = doubles.map {|frag, label| [exactly_chars(label, chars),spacer,frag].join }

    ## the counters at the top of the line
    start_s = start.to_s
    finish_s = (start + max_length).to_s
    count_line_gap = max_length - (start_s.size + finish_s.size)
    count_line = [start_s, spacer]
    unless count_line_gap < 1
      count_line << " " * count_line_gap
    end
    io.puts [exactly_chars("", chars), spacer, count_line.join].join

    io.puts lines.join("\n")

    io.puts " "  # separator between lines
    start += length
  end
end

.strip_dash(string) ⇒ Object 



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# File 'lib/bio/alignment/dna_sequence.rb', line 55

def strip_dash(string)
  ls = lstrip_dash(string)
  lstrip_dash(ls.reverse).reverse
end