Class: Bio::MAF::Sequence

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/maf/maf.rb

Overview

A sequence within an alignment block.

Direct Known Subclasses

EmptySequence

Constant Summary collapse

I_STATUS =
{
  'C' => :contiguous,
  'I' => :intervening,
  'N' => :first,
  'n' => :first_bridged,
  'M' => :missing_data,
  'T' => :tandem
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(source, start, size, strand, src_size, text) ⇒ Sequence

Returns a new instance of Sequence



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# File 'lib/bio/maf/maf.rb', line 277

def initialize(source, start, size, strand, src_size, text)
  @source = source
  @start = start
  @size = size
  @strand = strand
  @src_size = src_size
  @text = text
end

Instance Attribute Details

#i_dataArray<String>

Array of raw synteny information from 'i' line.

Returns:

  • (Array<String>)


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# File 'lib/bio/maf/maf.rb', line 271

def i_data
  @i_data
end

#qualityString

Quality string from 'q' line.

Returns:

  • (String)


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# File 'lib/bio/maf/maf.rb', line 274

def quality
  @quality
end

#sizeInteger (readonly)

Returns Size of aligning region in source sequence.

Returns:

  • (Integer)

    Size of aligning region in source sequence.



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# File 'lib/bio/maf/maf.rb', line 258

def size
  @size
end

#sourceString (readonly)

Returns Source sequence name.

Returns:

  • (String)

    Source sequence name.



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# File 'lib/bio/maf/maf.rb', line 254

def source
  @source
end

#src_sizeInteger (readonly) Also known as: source_size

Size of the entire source sequence, not just the aligning region.

Returns:

  • (Integer)


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# File 'lib/bio/maf/maf.rb', line 265

def src_size
  @src_size
end

#startInteger (readonly)

Returns Zero-based start position.

Returns:

  • (Integer)

    Zero-based start position.



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# File 'lib/bio/maf/maf.rb', line 256

def start
  @start
end

#strandSymbol (readonly)

:+ or :-, indicating which strand the alignment is to.

Returns:

  • (Symbol)


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# File 'lib/bio/maf/maf.rb', line 261

def strand
  @strand
end

#textString (readonly)

Sequence data for the alignment, including insertions.

Returns:

  • (String)


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# File 'lib/bio/maf/maf.rb', line 268

def text
  @text
end

Instance Method Details

#decode_status_char(c) ⇒ Object



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# File 'lib/bio/maf/maf.rb', line 332

def decode_status_char(c)
  I_STATUS[c] || raise("Unsupported status character #{c}!")
end

#delete_text(offset, len) ⇒ Object



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# File 'lib/bio/maf/maf.rb', line 365

def delete_text(offset, len)
  unless empty?
    text.slice!(offset, len)
    if quality
      quality.slice!(offset, len)
    end
  end
end

#empty?Boolean

Whether this sequence is empty. Only true for EmptySequence instances from 'e' lines.

Returns:

  • (Boolean)


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# File 'lib/bio/maf/maf.rb', line 315

def empty?
  false
end

#endObject



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# File 'lib/bio/maf/maf.rb', line 286

def end
  start + size
end

#fasta_descObject



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# File 'lib/bio/maf/maf.rb', line 382

def fasta_desc
  "#{source}:#{start}-#{start + size}"
end

#gapped?Boolean

Returns:

  • (Boolean)


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# File 'lib/bio/maf/maf.rb', line 319

def gapped?
  size != text.size
end

#intervalObject



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# File 'lib/bio/maf/maf.rb', line 290

def interval
  GenomicInterval.zero_based(self.source, self.start, self.end)
end

#join(o) ⇒ Object



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# File 'lib/bio/maf/maf.rb', line 392

def join(o)
  s2 = Sequence.new(source,
                    start,
                    size + o.size,
                    strand,
                    src_size,
                    text + o.text)
  if quality && o.quality
    s2.quality = quality + o.quality
  end
  s2
end

#joinable_with?(o) ⇒ Boolean

Returns:

  • (Boolean)


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# File 'lib/bio/maf/maf.rb', line 386

def joinable_with?(o)
  (self.end == o.start) \
  && (self.strand == o.strand) \
  && (self.empty? == o.empty?)
end

#left_countObject



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# File 'lib/bio/maf/maf.rb', line 344

def left_count
  i_data && i_data[1].to_i
end

#left_statusObject



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# File 'lib/bio/maf/maf.rb', line 340

def left_status
  i_data && decode_status_char(left_status_char())
end

#left_status_charObject



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# File 'lib/bio/maf/maf.rb', line 336

def left_status_char
  i_data && i_data[0]
end

#right_countObject



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# File 'lib/bio/maf/maf.rb', line 356

def right_count
  i_data && i_data[3].to_i
end

#right_statusObject



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# File 'lib/bio/maf/maf.rb', line 352

def right_status
  i_data && decode_status_char(right_status_char())
end

#right_status_charObject



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# File 'lib/bio/maf/maf.rb', line 348

def right_status_char
  i_data && i_data[2]
end

#slice(range) ⇒ Object



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# File 'lib/bio/maf/maf.rb', line 294

def slice(range)
  before = text.slice(0...(range.begin))
  non_gap_prev = before.delete("-").size
  new_text = text.slice(range)
  unless new_text
    raise "could not extract slice #{range} from #{self.inspect}!"
  end
  non_gap_text = new_text.delete("-").size
  s2 = Sequence.new(source,
                    start + non_gap_prev,
                    non_gap_text,
                    strand,
                    src_size,
                    new_text)
  s2.quality = quality.slice(range) if quality
  # TODO: what to do with synteny data?
  s2
end

#speciesObject



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# File 'lib/bio/maf/maf.rb', line 360

def species
  parts = source.split('.', 2)
  parts.size == 2 ? parts[0] : nil
end

#text_range(range) ⇒ Object

Maps the given zero-based genomic range onto a range of string offsets, suitable for extracting the text for the given range from #text.

See Also:

  • String#slice


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# File 'lib/bio/maf/maf.rb', line 410

def text_range(range)
  r_end = range.exclude_end? ? range.end : range.end + 1
  r_size = r_end - range.begin
  if range.begin == start && r_size == size
    # special case, entire text
    0...text.size
  else
    if range.begin < start || r_end > self.end
      raise "Range #{range} outside sequence bounds; start #{start}, size #{size}"
    end
    if ! gapped?
      # no gaps, can map indexes directly
      (range.begin - start)...(r_end - start)
    else
      # gaps present
      g_start = start     # genomic position of the start
      t_start = 0         # text position of the start
      m_begin = nil       # beginning of match
      match = nil
      text.scan(/(\w+|-+)/) do |parts|
        part = parts[0]
        if part[0] != '-'
          # sequence text
          g_end = g_start + part.size
          if g_start <= range.begin && range.begin < g_end
            offset_in_part = range.begin - g_start
            m_begin = offset_in_part + t_start
          end
          if g_start <= r_end && r_end <= g_end
            raise "reached end before start!" unless m_begin
            offset_in_part = r_end - g_start
            m_end = offset_in_part + t_start
            match = m_begin...m_end
            break
          end
          g_start = g_end
        else
          # gap
        end
        t_start += part.size
      end
      raise "no match found!" unless match
      return match
    end
  end
end

#to_bio_alignmentObject



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# File 'lib/bio/maf/maf.rb', line 378

def to_bio_alignment
  Bio::BioAlignment::Sequence.new(source, text)
end

#upcase!Object



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# File 'lib/bio/maf/maf.rb', line 374

def upcase!
  text.upcase!
end