Class: Bio::Spidey::Report::Hit

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

Overview

Hit object of Spidey result. Similar to Bio::Blast::Report::Hit but lacks many methods.

Instance Method Summary (collapse)

Constructor Details

- (Hit) initialize(data, d0)

Creates a new Hit object. It is designed to be called internally from Bio::Spidey::Report::* classes. Users shall not call it directly.



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# File 'lib/bio/appl/spidey/report.rb', line 290

def initialize(data, d0)
  @data = data
  @d0 = d0
end

Instance Method Details

- (Object) align

Returns alignments. Returns an Array of arrays. This would be a Bio::Spidey specific method.



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# File 'lib/bio/appl/spidey/report.rb', line 465

def align
  unless defined?(@align); parse_align; end
  @align
end

- (Boolean) complement?

Returns true if the result reports 'Reverse complement'. Otherwise, return false or nil. This would be a Bio::Spidey specific method.

Returns:

  • (Boolean)


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# File 'lib/bio/appl/spidey/report.rb', line 330

def complement?
  unless defined?(@complement); parse_strand; end
  @complement
end

- (Object) each(&x)

Iterates over each exon of the hit. Yields Bio::Spidey::Report::SegmentPair object.



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# File 'lib/bio/appl/spidey/report.rb', line 555

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

- (Object) exons Also known as: hsps

Returns exons of the hit. Returns an array of Bio::Spidey::Report::SegmentPair object.



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# File 'lib/bio/appl/spidey/report.rb', line 437

def exons
  unless defined?(@exons); parse_segmentpairs; end
  @exons
end

- (Object) genomic

Returns sequence informations of the 'Genomic'. Returns a Bio::Spidey::Report::SeqDesc object. This would be a Bio::Spidey specific method.



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# File 'lib/bio/appl/spidey/report.rb', line 373

def genomic
  unless defined?(@genomic)
    @genomic = SeqDesc.parse(@d0.find { |x| /^Genomic\:/ =~ x })
  end
  @genomic
end

- (Object) introns

Returns introns of the hit. Some of them would contain untranscribed regions. Returns an array of Bio::Spidey::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)



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# File 'lib/bio/appl/spidey/report.rb', line 447

def introns
  unless defined?(@introns); parse_segmentpairs; end
  @introns
end

- (Object) missing_mrna_ends

Returns missing mRNA ends of the hit.



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

def missing_mrna_ends
  unless defined?(@missing_mrna_ends)
    @missing_mrna_ends = field_fetch('Missing mRNA ends', @d0)
  end
  @missing_mrna_ends
end

- (Object) mrna

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



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# File 'lib/bio/appl/spidey/report.rb', line 383

def mrna
  unless defined?(@mrna)
    @mrna = SeqDesc.parse(@d0.find { |x| /^mRNA\:/ =~ x })
  end
  @mrna
end

- (Object) number_of_exons

Returns number of exons in the hit.



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# File 'lib/bio/appl/spidey/report.rb', line 336

def number_of_exons
  unless defined?(@number_of_exons)
    @number_of_exons = field_fetch('Number of exons', @d0).to_i
  end
  @number_of_exons
end

- (Object) number_of_splice_sites

Returns number of splice sites of the hit.



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# File 'lib/bio/appl/spidey/report.rb', line 344

def number_of_splice_sites
  unless defined?(@number_of_splice_sites)
    @number_of_splice_sites = 
      field_fetch('Number of splice sites', @d0).to_i
  end
  @number_of_splice_sites
end

- (Object) percent_identity

Returns overall percent identity of the hit.



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# File 'lib/bio/appl/spidey/report.rb', line 353

def percent_identity
  unless defined?(@percent_identity)
    x = field_fetch('overall percent identity', @d0)
    @percent_identity = 
      (/([\d\.]+)\s*\%/ =~ x.to_s) ? $1 : nil
  end
  @percent_identity
end

- (Object) query_def

Definition of the mRNA (query). Same as Bio::Spidey::Report#query_def.



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# File 'lib/bio/appl/spidey/report.rb', line 536

def query_def;  mrna.definition; end

- (Object) query_id

Identifier of the mRNA (query). Same as Bio::Spidey::Report#query_id.



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# File 'lib/bio/appl/spidey/report.rb', line 532

def query_id;   mrna.entry_id;   end

- (Object) query_len

Length of the mRNA (query) sequence. Same as Bio::Spidey::Report#query_len.



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# File 'lib/bio/appl/spidey/report.rb', line 528

def query_len;  mrna.len;        end

- (Object) segmentpairs

Returns segment pairs (exons and introns) of the hit. Each segment pair is a Bio::Spidey::Report::SegmentPair object. Returns an array of Bio::Spidey::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)



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# File 'lib/bio/appl/spidey/report.rb', line 457

def segmentpairs
  unless defined?(@segmentparis); parse_segmentpairs; end
  @segmentpairs
end

- (Object) strand

Returns strand information of the hit. Returns 'plus', 'minus', or nil. This would be a Bio::Spidey specific method.



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

def strand
  unless defined?(@strand); parse_strand; end
  @strand
end

- (Object) target_def Also known as: definition

Definition of the genomic (target) sequence.



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# File 'lib/bio/appl/spidey/report.rb', line 545

def target_def; genomic.definition; end

- (Object) target_id Also known as: hit_id

Identifier of the genomic (target) sequence.



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# File 'lib/bio/appl/spidey/report.rb', line 542

def target_id;  genomic.entry_id;   end

- (Object) target_len Also known as: len

The genomic (target) sequence length.



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# File 'lib/bio/appl/spidey/report.rb', line 539

def target_len; genomic.len;        end