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No matching classes.

# Bio::Blat::Report::Hit

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.

### Attributes

data[R]

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

### Public Class Methods

new(str) click to toggle source

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.

    # File lib/bio/appl/blat/report.rb, line 293
    def initialize(str)
      @data = str.chomp.split(/\t/)
    end

### Public Instance Methods

block_count() click to toggle source

Number of blocks(exons, segment pairs).

    # File lib/bio/appl/blat/report.rb, line 350
    def block_count; @data[17].to_i; end

block_sizes() click to toggle source

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

    # 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

blocks() click to toggle source

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

    # 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

Also aliased as: exons, hsps
definition() click to toggle source
Alias for: target_def
each() click to toggle source

Iterates over each block(exon, segment pair) of the hit.

    Yields a Bio::Blat::Report::SegmentPair object.

    # File lib/bio/appl/blat/report.rb, line 404
    def each(&x) #:yields: segmentpair
      exons.each(&x)
    end

exons() click to toggle source
Alias for: blocks
hsps() click to toggle source
Alias for: blocks
len() click to toggle source
Alias for: target_len
match() click to toggle source

Match nucleotides.

    # File lib/bio/appl/blat/report.rb, line 332
    def match;       @data[0].to_i;  end

milli_bad() click to toggle source

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).

    # 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

mismatch() click to toggle source

Mismatch nucleotides.

    # File lib/bio/appl/blat/report.rb, line 334
    def mismatch;    @data[1].to_i;  end

n_s() click to toggle source

"N's". Number of 'N' bases.

    # File lib/bio/appl/blat/report.rb, line 342
    def n_s;         @data[3].to_i;  end

percent_identity() click to toggle source

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).

    # File lib/bio/appl/blat/report.rb, line 438
    def percent_identity
      100.0 - self.milli_bad * 0.1
    end

protein?() click to toggle source

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).

    # 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

query() click to toggle source

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

    # 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

query_def() click to toggle source

Returns the name of query sequence.

    # File lib/bio/appl/blat/report.rb, line 390
    def query_def;  query.name;  end

Also aliased as: query_id
query_id() click to toggle source
Alias for: query_def
query_len() click to toggle source

Returns the length of query sequence.

    # File lib/bio/appl/blat/report.rb, line 387
    def query_len;  query.size;  end

rep_match() click to toggle source

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

    # File lib/bio/appl/blat/report.rb, line 339
    def rep_match;   @data[2].to_i;  end

score() click to toggle source

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).

    # 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

strand() click to toggle source

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

    # File lib/bio/appl/blat/report.rb, line 347
    def strand;      @data[8];       end

target() click to toggle source

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

    # 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

target_def() click to toggle source

Returns the name of the target(subject) sequence.

    # File lib/bio/appl/blat/report.rb, line 398
    def target_def; target.name; end

Also aliased as: target_id, definition
target_id() click to toggle source
Alias for: target_def
target_len() click to toggle source

Returns the length of the target(subject) sequence.

    # File lib/bio/appl/blat/report.rb, line 394
    def target_len; target.size; end

Also aliased as: len

[Validate]

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