Class | Bio::Spidey::Report::Hit |
In: |
lib/bio/appl/spidey/report.rb
|
Parent: | Object |
Hit object of Spidey result. Similar to Bio::Blast::Report::Hit but lacks many methods.
Creates a new Hit object. It is designed to be called internally from Bio::Spidey::Report::* classes. Users shall not call it directly.
# File lib/bio/appl/spidey/report.rb, line 290 290: def initialize(data, d0) 291: @data = data 292: @d0 = d0 293: end
Returns alignments. Returns an Array of arrays. This would be a Bio::Spidey specific method.
# File lib/bio/appl/spidey/report.rb, line 465 465: def align 466: unless defined?(@align); parse_align; end 467: @align 468: end
Returns true if the result reports ‘Reverse complement’. Otherwise, return false or nil. This would be a Bio::Spidey specific method.
# File lib/bio/appl/spidey/report.rb, line 330 330: def complement? 331: unless defined?(@complement); parse_strand; end 332: @complement 333: end
Iterates over each exon of the hit. Yields Bio::Spidey::Report::SegmentPair object.
# File lib/bio/appl/spidey/report.rb, line 555 555: def each(&x) #:yields: segmentpair 556: exons.each(&x) 557: end
Returns exons of the hit. Returns an array of Bio::Spidey::Report::SegmentPair object.
# File lib/bio/appl/spidey/report.rb, line 437 437: def exons 438: unless defined?(@exons); parse_segmentpairs; end 439: @exons 440: end
Returns sequence informations of the ‘Genomic’. Returns a Bio::Spidey::Report::SeqDesc object. This would be a Bio::Spidey specific method.
# File lib/bio/appl/spidey/report.rb, line 373 373: def genomic 374: unless defined?(@genomic) 375: @genomic = SeqDesc.parse(@d0.find { |x| /^Genomic\:/ =~ x }) 376: end 377: @genomic 378: 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.)
# File lib/bio/appl/spidey/report.rb, line 447 447: def introns 448: unless defined?(@introns); parse_segmentpairs; end 449: @introns 450: end
Returns missing mRNA ends of the hit.
# File lib/bio/appl/spidey/report.rb, line 363 363: 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 sequence informations of the mRNA. Returns a Bio::Spidey::Report::SeqDesc object. This would be a Bio::Spidey specific method.
# File lib/bio/appl/spidey/report.rb, line 383 383: def mrna 384: unless defined?(@mrna) 385: @mrna = SeqDesc.parse(@d0.find { |x| /^mRNA\:/ =~ x }) 386: end 387: @mrna 388: end
Returns number of splice sites of the hit.
# File lib/bio/appl/spidey/report.rb, line 344 344: 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 overall percent identity of the hit.
# File lib/bio/appl/spidey/report.rb, line 353 353: 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
Definition of the mRNA (query). Same as Bio::Spidey::Report#query_def.
# File lib/bio/appl/spidey/report.rb, line 536 536: def query_def; mrna.definition; end
Identifier of the mRNA (query). Same as Bio::Spidey::Report#query_id.
# File lib/bio/appl/spidey/report.rb, line 532 532: def query_id; mrna.entry_id; end
Length of the mRNA (query) sequence. Same as Bio::Spidey::Report#query_len.
# File lib/bio/appl/spidey/report.rb, line 528 528: def query_len; mrna.len; 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.)
# File lib/bio/appl/spidey/report.rb, line 457 457: def segmentpairs 458: unless defined?(@segmentparis); parse_segmentpairs; end 459: @segmentpairs 460: end
Returns strand information of the hit. Returns ‘plus’, ‘minus’, or nil. This would be a Bio::Spidey specific method.
# File lib/bio/appl/spidey/report.rb, line 322 322: def strand 323: unless defined?(@strand); parse_strand; end 324: @strand 325: end