| Class | Bio::Sim4::Report |
| In: |
lib/bio/appl/sim4/report.rb
|
| Parent: | Object |
Bio::Sim4::Report is the sim4 report parser class. Its object may contain some Bio::Sim4::Report::Hit objects.
| DELIMITER | = | RS = nil | Delimiter of each entry. Bio::FlatFile uses it. In Bio::Sim4::Report, it it nil (1 entry 1 file). |
| all_hits | [R] | Returns all hits of the entry. Unlike Bio::Sim4::Report#hits, it returns results of all trials of pairwise alignment. This would be a Bio::Sim4 specific method. Returns an Array of Bio::Sim4::Report::Hit objects. |
| hits | [R] | Returns hits of the entry. Unlike Bio::Sim4::Report#all_hits, it returns hits which have alignments. Returns an Array of Bio::Sim4::Report::Hit objects. |
| seq1 | [R] | Returns sequence informations of ‘seq1’. Returns a Bio::Sim4::Report::SeqDesc object. This would be a Bio::Sim4 specific method. |
Creates new Bio::Sim4::Report object from String. You can use Bio::FlatFile to read a file. Currently, format A=0, A=3, and A=4 are supported. (A=1, A=2, A=5 are NOT supported yet.)
Note that ‘seq1’ in sim4 result is always regarded as ‘query’, and ‘seq2’ is always regarded as ‘subject’(target, hit).
Note that first ‘seq1’ informations are used for Bio::Sim4::Report#query_id, query_def, query_len, and seq1 methods.
# File lib/bio/appl/sim4/report.rb, line 42
42: def initialize(text)
43: @hits = []
44: @all_hits = []
45: overrun = ''
46: text.each("\n\nseq1 = ") do |str|
47: str = str.sub(/\A\s+/, '')
48: str.sub!(/\n(^seq1 \= .*)/m, "\n") # remove trailing hits for sure
49: tmp = $1.to_s
50: hit = Hit.new(overrun + str)
51: overrun = tmp
52: unless hit.instance_eval { @data.empty? } then
53: @hits << hit
54: end
55: @all_hits << hit
56: end
57: @seq1 = @all_hits[0].seq1
58: end
Iterates over each hits of the sim4 result. Same as hits.each. Yields a Bio::Sim4::Report::Hit object.
# File lib/bio/appl/sim4/report.rb, line 453
453: def each_hit(&x) #:yields: hit
454: @hits.each(&x)
455: end
Returns number of hits. Same as hits.size.
# File lib/bio/appl/sim4/report.rb, line 448
448: def num_hits; @hits.size; end
Returns the definition of query sequence. The value will be filename or (first word of) sequence definition according to sim4 run-time options.
# File lib/bio/appl/sim4/report.rb, line 461
461: def query_def; @seq1.definition; end
Returns the identifier of query sequence. The value will be filename or (first word of) sequence definition according to sim4 run-time options.
# File lib/bio/appl/sim4/report.rb, line 466
466: def query_id; @seq1.entry_id; end