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 262 262: def initialize(str) 263: @data = str.split(/\n(?:\r?\n)+/) 264: parse_seqdesc 265: 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 399 399: def align 400: unless defined?(@align); parse_align; end 401: @align 402: end
Iterates over each exon of the hit. Yields a Bio::Sim4::Report::SegmentPair object.
# File lib/bio/appl/sim4/report.rb, line 437 437: def each(&x) #:yields: segmentpair 438: exons.each(&x) 439: end
Returns exons of the hit. Each exon is a Bio::Sim4::Report::SegmentPair object.
# File lib/bio/appl/sim4/report.rb, line 369 369: def exons 370: unless defined?(@exons); parse_segmentpairs; end 371: @exons 372: 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 389 389: def introns 390: unless defined?(@introns); parse_segmentpairs; end 391: @introns 392: end
Definition of the query sequence Same as Bio::Sim4::Report#query_def.
# File lib/bio/appl/sim4/report.rb, line 418 418: 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 414 414: 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 410 410: 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 379 379: def segmentpairs 380: unless defined?(@segmentpairs); parse_segmentpairs; end 381: @segmentpairs 382: end
Definition of the hit(target) sequence
# File lib/bio/appl/sim4/report.rb, line 427 427: def target_def; seq2.definition; end
Identifier of the hit(target) sequence
# File lib/bio/appl/sim4/report.rb, line 424 424: def target_id; seq2.entry_id; end