class Bio::Spidey::Report::Hit

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

Public Class Methods

Source

    # File lib/bio/appl/spidey/report.rb
290 def initialize(data, d0)
291   @data = data
292   @d0 = d0
293 end

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

Public Instance Methods

align ()

Source

    # File lib/bio/appl/spidey/report.rb
465 def align
466   unless defined?(@align); parse_align; end
467   @align
468 end

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

complement? ()

Source

    # File lib/bio/appl/spidey/report.rb
330 def complement?
331   unless defined?(@complement); parse_strand; end
332   @complement
333 end

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

definition ()

Alias for: target_def

each () { |segmentpair| ... }

Source

    # File lib/bio/appl/spidey/report.rb
555 def each(&x) #:yields: segmentpair
556   exons.each(&x)
557 end

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

exons ()

Source

    # File lib/bio/appl/spidey/report.rb
437 def exons
438   unless defined?(@exons); parse_segmentpairs; end
439   @exons
440 end

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

Also aliased as: hsps

genomic ()

Source

    # File lib/bio/appl/spidey/report.rb
373 def genomic
374   unless defined?(@genomic)
375     @genomic = SeqDesc.parse(@d0.find { |x| /^Genomic\:/ =~ x })
376   end
377   @genomic
378 end

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

hit_id ()

Alias for: target_id

hsps ()

Alias for: exons

introns ()

Source

    # File lib/bio/appl/spidey/report.rb
447 def introns
448   unless defined?(@introns); parse_segmentpairs; end
449   @introns
450 end

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.)

len ()

Alias for: target_len

missing_mrna_ends ()

Source

    # File lib/bio/appl/spidey/report.rb
363 def missing_mrna_ends
364   unless defined?(@missing_mrna_ends)
365     @missing_mrna_ends = field_fetch('Missing mRNA ends', @d0)
366   end
367   @missing_mrna_ends
368 end

Returns missing mRNA ends of the hit.

mrna ()

Source

    # File lib/bio/appl/spidey/report.rb
383 def mrna
384   unless defined?(@mrna)
385     @mrna = SeqDesc.parse(@d0.find { |x| /^mRNA\:/ =~ x })
386   end
387   @mrna
388 end

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

number_of_exons ()

Source

    # File lib/bio/appl/spidey/report.rb
336 def number_of_exons
337   unless defined?(@number_of_exons)
338     @number_of_exons = field_fetch('Number of exons', @d0).to_i
339   end
340   @number_of_exons
341 end

Returns number of exons in the hit.

number_of_splice_sites ()

Source

    # File lib/bio/appl/spidey/report.rb
344 def number_of_splice_sites
345   unless defined?(@number_of_splice_sites)
346     @number_of_splice_sites = 
347       field_fetch('Number of splice sites', @d0).to_i
348   end
349   @number_of_splice_sites
350 end

Returns number of splice sites of the hit.

percent_identity ()

Source

    # File lib/bio/appl/spidey/report.rb
353 def percent_identity
354   unless defined?(@percent_identity)
355     x = field_fetch('overall percent identity', @d0)
356     @percent_identity = 
357       (/([\d\.]+)\s*\%/ =~ x.to_s) ? $1 : nil
358   end
359   @percent_identity
360 end

Returns overall percent identity of the hit.

query_def ()

Source

    # File lib/bio/appl/spidey/report.rb
536 def query_def;  mrna.definition; end

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

query_id ()

Source

    # File lib/bio/appl/spidey/report.rb
532 def query_id;   mrna.entry_id;   end

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

query_len ()

Source

    # File lib/bio/appl/spidey/report.rb
528 def query_len;  mrna.len;        end

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

segmentpairs ()

Source

    # File lib/bio/appl/spidey/report.rb
457 def segmentpairs
458   unless defined?(@segmentparis); parse_segmentpairs; end
459   @segmentpairs
460 end

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.)

strand ()

Source

    # File lib/bio/appl/spidey/report.rb
322 def strand
323   unless defined?(@strand); parse_strand; end
324   @strand
325 end

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

target_def ()

Source

    # File lib/bio/appl/spidey/report.rb
545 def target_def; genomic.definition; end

Definition of the genomic (target) sequence.

Also aliased as: definition

target_id ()

Source

    # File lib/bio/appl/spidey/report.rb
542 def target_id;  genomic.entry_id;   end

Identifier of the genomic (target) sequence.

Also aliased as: hit_id

target_len ()

Source

    # File lib/bio/appl/spidey/report.rb
539 def target_len; genomic.len;        end

The genomic (target) sequence length.

Also aliased as: len