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

Inherits:

Object

• Object
• Bio::Spidey::Report::Hit

show all

Defined in:

lib/bio/appl/spidey/report.rb

Overview

Instance Method Summary (collapse)

• - (Object) align

  Returns alignments.

• - (Boolean) complement?

  Returns true if the result reports 'Reverse complement'.

• - (Object) each(&x)

  Iterates over each exon of the hit.

• - (Object) exons (also: #hsps)

  Returns exons of the hit.

• - (Object) genomic

  Returns sequence informations of the 'Genomic'.

• - (Hit) initialize(data, d0) constructor

  Creates a new Hit object.

• - (Object) introns

  Returns introns of the hit.

• - (Object) missing_mrna_ends

  Returns missing mRNA ends of the hit.

• - (Object) mrna

  Returns sequence informations of the mRNA.

• - (Object) number_of_exons

  Returns number of exons in the hit.

• - (Object) number_of_splice_sites

  Returns number of splice sites of the hit.

• - (Object) percent_identity

  Returns overall percent identity of the hit.

• - (Object) query_def

  Definition of the mRNA (query).

• - (Object) query_id

  Identifier of the mRNA (query).

• - (Object) query_len

  Length of the mRNA (query) sequence.

• - (Object) segmentpairs

  Returns segment pairs (exons and introns) of the hit.

• - (Object) strand

  Returns strand information of the hit.

• - (Object) target_def (also: #definition)

  Definition of the genomic (target) sequence.

• - (Object) target_id (also: #hit_id)

  Identifier of the genomic (target) sequence.

• - (Object) target_len (also: #len)

  The genomic (target) sequence length.

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

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

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

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

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

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

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

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

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

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

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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

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

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

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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

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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

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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

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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

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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

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

def query_def;  mrna.definition; end

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

def query_id;   mrna.entry_id;   end

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

def query_len;  mrna.len;        end

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

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

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

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

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

def target_def; genomic.definition; end

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

def target_id;  genomic.entry_id;   end

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

def target_len; genomic.len;        end