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

new(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.

[Source]

# File lib/bio/appl/blat/report.rb, line 252
        def initialize(str)
          @data = str.chomp.split(/\t/)
        end

block_count()

Number of blocks(exons, segment pairs).

[Source]

# File lib/bio/appl/blat/report.rb, line 309
        def block_count; @data[17].to_i; end

block_sizes()

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

[Source]

# File lib/bio/appl/blat/report.rb, line 313
        def block_sizes
          unless defined?(@block_sizes) then
            @block_sizes = split_comma(@data[18]).collect { |x| x.to_i }
          end
          @block_sizes
        end

blocks()

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

[Source]

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

definition()

Alias for target_def

each() {|segmentpair| ...}

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

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

[Source]

# File lib/bio/appl/blat/report.rb, line 363
        def each(&x) #:yields: segmentpair
          exons.each(&x)
        end

exons()

Alias for blocks

hsps()

Alias for blocks

len()

Alias for target_len

match()

Match nucleotides.

[Source]

# File lib/bio/appl/blat/report.rb, line 291
        def match;       @data[0].to_i;  end

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).

[Source]

# File lib/bio/appl/blat/report.rb, line 377
        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()

Mismatch nucleotides.

[Source]

# File lib/bio/appl/blat/report.rb, line 293
        def mismatch;    @data[1].to_i;  end

n_s()

"N‘s". Number of ‘N’ bases.

[Source]

# File lib/bio/appl/blat/report.rb, line 301
        def n_s;         @data[3].to_i;  end

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).

[Source]

# File lib/bio/appl/blat/report.rb, line 397
        def percent_identity
          100.0 - self.milli_bad * 0.1
        end

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).

[Source]

# File lib/bio/appl/blat/report.rb, line 410
        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()

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

[Source]

# File lib/bio/appl/blat/report.rb, line 269
        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()

Returns the name of query sequence.

[Source]

# File lib/bio/appl/blat/report.rb, line 349
        def query_def;  query.name;  end

query_id()

Alias for query_def

query_len()

Returns the length of query sequence.

[Source]

# File lib/bio/appl/blat/report.rb, line 346
        def query_len;  query.size;  end

rep_match()

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

[Source]

# File lib/bio/appl/blat/report.rb, line 298
        def rep_match;   @data[2].to_i;  end

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).

[Source]

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

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

[Source]

# File lib/bio/appl/blat/report.rb, line 306
        def strand;      @data[8];       end

target()

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

[Source]

# File lib/bio/appl/blat/report.rb, line 281
        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()

Returns the name of the target(subject) sequence.

[Source]

# File lib/bio/appl/blat/report.rb, line 357
        def target_def; target.name; end

target_id()

Alias for target_def

target_len()

Returns the length of the target(subject) sequence.

[Source]

# File lib/bio/appl/blat/report.rb, line 353
        def target_len; target.size; end

Methods

Attributes

Public Class methods

Public Instance methods