Class: Bio::Blat::Report::Hit

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/blat/report.rb

Overview

Hit class for the BLAT result parser. Similar to Bio::Blast::Report::Hit but lacks many methods. Its object may contain some Bio::Blat::Report::SegmentPair objects.

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (Hit) initialize(str)

Creates a new Hit object from a piece of BLAT result text. It is designed to be called internally from Bio::Blat::Report object. Users shall not use it directly.



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# File 'lib/bio/appl/blat/report.rb', line 293

def initialize(str)
  @data = str.chomp.split(/\t/)
end

Instance Attribute Details

- (Object) data (readonly)

Raw data of the hit. (Note that it doesn't add 1 to position numbers.)



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# File 'lib/bio/appl/blat/report.rb', line 299

def data
  @data
end

Instance Method Details

- (Object) block_count

Number of blocks(exons, segment pairs).



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# File 'lib/bio/appl/blat/report.rb', line 350

def block_count; @data[17].to_i; end

- (Object) block_sizes

Sizes of all blocks(exons, segment pairs). Returns an array of numbers.



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# File 'lib/bio/appl/blat/report.rb', line 354

def block_sizes
  unless defined?(@block_sizes) then
    @block_sizes = split_comma(@data[18]).collect { |x| x.to_i }
  end
  @block_sizes
end

- (Object) blocks Also known as: exons, hsps

Returns blocks(exons, segment pairs) of the hit. Returns an array of Bio::Blat::Report::SegmentPair objects.



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# File 'lib/bio/appl/blat/report.rb', line 363

def blocks
  unless defined?(@blocks)
    bs    = block_sizes
    qst   = query.starts
    tst   = target.starts
    qseqs = query.seqs
    tseqs = target.seqs
    pflag = self.protein?
    @blocks = (0...block_count).collect do |i|
      SegmentPair.new(query.size, target.size, strand, bs[i],
                      qst[i], tst[i], qseqs[i], tseqs[i],
                      pflag)
    end
  end
  @blocks
end

- (Object) each(&x)

Iterates over each block(exon, segment pair) of the hit. Yields a Bio::Blat::Report::SegmentPair object.



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# File 'lib/bio/appl/blat/report.rb', line 404

def each(&x) #:yields: segmentpair
  exons.each(&x)
end

- (Object) match

Match nucleotides.



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# File 'lib/bio/appl/blat/report.rb', line 332

def match;       @data[0].to_i;  end

- (Object) milli_bad

Calculates the pslCalcMilliBad value defined in the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

The algorithm is taken from the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).



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# File 'lib/bio/appl/blat/report.rb', line 418

def milli_bad
  w = (self.protein? ? 3 : 1)
  qalen = w * (self.query.end - self.query.start)
  talen = self.target.end - self.target.start
  alen = (if qalen < talen then qalen; else talen; end)
  return 0 if alen <= 0
  d = qalen - talen
  d = 0 if d < 0
  total = w * (self.match + self.rep_match + self.mismatch)
  return 0 if total == 0
  return (1000 * (self.mismatch * w + self.query.gap_count +
                    (3 * Math.log(1 + d)).round) / total)
end

- (Object) mismatch

Mismatch nucleotides.



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# File 'lib/bio/appl/blat/report.rb', line 334

def mismatch;    @data[1].to_i;  end

- (Object) n_s

“N's”. Number of 'N' bases.



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# File 'lib/bio/appl/blat/report.rb', line 342

def n_s;         @data[3].to_i;  end

- (Object) percent_identity

Calculates the percent identity compatible with the BLAT web server as described in the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

The algorithm is taken from the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).



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# File 'lib/bio/appl/blat/report.rb', line 438

def percent_identity
  100.0 - self.milli_bad * 0.1
end

- (Boolean) protein?

When the output data comes from the protein query, returns true. Otherwise (nucleotide query), returns false. It returns nil if this cannot be determined.

The algorithm is taken from the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

Note: It seems that it returns true only when protein query with nucleotide database (blat options: -q=prot -t=dnax).

Returns:

  • (Boolean)


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# File 'lib/bio/appl/blat/report.rb', line 451

def protein?
  return nil if self.block_sizes.empty?
  case self.strand[1,1]
  when '+'
    if self.target.end == self.target.starts[-1] +
        3 * self.block_sizes[-1] then
      true
    else
      false
    end
  when '-'
    if self.target.start == self.target.size -
        self.target.starts[-1] - 3 * self.block_sizes[-1] then
      true
    else
      false
    end
  else
    nil
  end
end

- (Object) query

Returns sequence informations of the query. Returns a Bio::Blat::Report::SeqDesc object. This would be Bio::Blat specific method.



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# File 'lib/bio/appl/blat/report.rb', line 310

def query
  unless defined?(@query)
    d = @data
    @query = SeqDesc.new(d[4], d[5], d[9], d[10], d[11], d[12],
                         split_comma(d[19]), split_comma(d[21]))
  end
  @query
end

- (Object) query_def Also known as: query_id

Returns the name of query sequence.



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# File 'lib/bio/appl/blat/report.rb', line 390

def query_def;  query.name;  end

- (Object) query_len

Returns the length of query sequence.



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# File 'lib/bio/appl/blat/report.rb', line 387

def query_len;  query.size;  end

- (Object) rep_match

“rep. match”. Number of bases that match but are part of repeats. Note that current version of BLAT always set 0.



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# File 'lib/bio/appl/blat/report.rb', line 339

def rep_match;   @data[2].to_i;  end

- (Object) score

Calculates the score compatible with the BLAT web server as described in the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

The algorithm is taken from the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).



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# File 'lib/bio/appl/blat/report.rb', line 479

def score
  w = (self.protein? ? 3 : 1)
  w * (self.match + (self.rep_match >> 1)) -
    w * self.mismatch - self.query.gap_count - self.target.gap_count
end

- (Object) strand

Returns strand information of the hit. Returns '+' or '-'. This would be a Bio::Blat specific method.



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# File 'lib/bio/appl/blat/report.rb', line 347

def strand;      @data[8];       end

- (Object) target

Returns sequence informations of the target(hit). Returns a Bio::Blat::Report::SeqDesc object. This would be Bio::Blat specific method.



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# File 'lib/bio/appl/blat/report.rb', line 322

def target
  unless defined?(@target)
    d = @data
    @target = SeqDesc.new(d[6], d[7], d[13], d[14], d[15], d[16],
                          split_comma(d[20]), split_comma(d[22]))
  end
  @target
end

- (Object) target_def Also known as: target_id, definition

Returns the name of the target(subject) sequence.



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# File 'lib/bio/appl/blat/report.rb', line 398

def target_def; target.name; end

- (Object) target_len Also known as: len

Returns the length of the target(subject) sequence.



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# File 'lib/bio/appl/blat/report.rb', line 394

def target_len; target.size; end