Class | Bio::Sim4::Report::Hit |
In: |
lib/bio/appl/sim4/report.rb
|
Parent: | Object |
Hit object of the sim4 result. Similar to Bio::Blast::Report::Hit but lacks many methods.
seq1 | [R] | Returns sequence informations of ‘seq1’. Returns a Bio::Sim4::Report::SeqDesc object. This would be Bio::Sim4 specific method. |
seq2 | [R] | Returns sequence informations of ‘seq2’. Returns a Bio::Sim4::Report::SeqDesc object. This would be Bio::Sim4 specific method. |
Parses part of sim4 result text and creates a new Hit object. It is designed to be called internally from Bio::Sim4::Report class. Users shall not use it directly.
# File lib/bio/appl/sim4/report.rb, line 273 273: def initialize(str) 274: @data = str.split(/\n(?:\r?\n)+/) 275: parse_seqdesc 276: end
Returns alignments. Returns an Array of arrays. Each array contains sequence of seq1, midline, sequence of seq2, respectively. This would be a Bio::Sim4 specific method.
# File lib/bio/appl/sim4/report.rb, line 432 432: def align 433: unless defined?(@align); parse_align; end 434: @align 435: end
Iterates over each exon of the hit. Yields a Bio::Sim4::Report::SegmentPair object.
# File lib/bio/appl/sim4/report.rb, line 470 470: def each(&x) #:yields: segmentpair 471: exons.each(&x) 472: end
Returns exons of the hit. Each exon is a Bio::Sim4::Report::SegmentPair object.
# File lib/bio/appl/sim4/report.rb, line 402 402: def exons 403: unless defined?(@exons); parse_segmentpairs; end 404: @exons 405: end
Returns introns of the hit. Some of them would contain untranscribed regions. Returns an array of Bio::Sim4::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)
# File lib/bio/appl/sim4/report.rb, line 422 422: def introns 423: unless defined?(@introns); parse_segmentpairs; end 424: @introns 425: end
Definition of the query sequence Same as Bio::Sim4::Report#query_def.
# File lib/bio/appl/sim4/report.rb, line 451 451: def query_def; seq1.definition; end
Identifier of the query sequence. Same as Bio::Sim4::Report#query_id.
# File lib/bio/appl/sim4/report.rb, line 447 447: def query_id; seq1.entry_id; end
Length of the query sequence. Same as Bio::Sim4::Report#query_len.
# File lib/bio/appl/sim4/report.rb, line 443 443: def query_len; seq1.len; end
Returns segment pairs (exons and introns) of the hit. Each segment pair is a Bio::Sim4::Report::SegmentPair object. Returns an array of Bio::Sim4::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)
# File lib/bio/appl/sim4/report.rb, line 412 412: def segmentpairs 413: unless defined?(@segmentpairs); parse_segmentpairs; end 414: @segmentpairs 415: end
Definition of the hit(target) sequence
# File lib/bio/appl/sim4/report.rb, line 460 460: def target_def; seq2.definition; end
Identifier of the hit(target) sequence
# File lib/bio/appl/sim4/report.rb, line 457 457: def target_id; seq2.entry_id; end