| Class | Bio::Spidey::Report |
| In: |
lib/bio/appl/spidey/report.rb
|
| Parent: | Object |
Spidey report parser class. Please see bio/appl/spidey/report.rb for details.
Its object may contain some Bio::Spidey::Report::Hit objects.
| DELIMITER | = | RS = "\n--SPIDEY " | Delimiter of each entry. Bio::FlatFile uses it. | |
| DELIMITER_OVERRUN | = | 9 | (Integer) excess read size included in DELIMITER. |
| all_hits | [R] | Returns an Array of Bio::Spidey::Report::Hit objects. Unlike Bio::Spidey::Report#hits, the method returns results of all trials of pairwise alignment. This would be a Bio::Spidey specific method. |
| entry_overrun | [R] | piece of next entry. Bio::FlatFile uses it. |
| hits | [R] | Returns an Array of Bio::Spidey::Report::Hit objects. Because current version of SPIDEY supports only 1 genomic sequences, the number of hits is 1 or 0. |
Creates a new Bio::Spidey::Report object from String. You can use Bio::FlatFile to read a file.
# File lib/bio/appl/spidey/report.rb, line 47
47: def initialize(str)
48: str = str.sub(/\A\s+/, '')
49: str.sub!(/\n(^\-\-SPIDEY .*)/m, '') # remove trailing entries for sure
50: @entry_overrun = $1
51: data = str.split(/\r?\n(?:\r?\n)+/)
52: d0 = data.shift.to_s.split(/\r?\n/)
53: @hit = Hit.new(data, d0)
54: @all_hits = [ @hit ]
55: if d0.empty? or /\ANo alignment found\.\s*\z/ =~ d0[-1] then
56: @hits = []
57: else
58: @hits = [ @hit ]
59: end
60: end
Iterates over each hits. Same as hits.each. Yields a Bio::Spidey::Report::Hit object.
# File lib/bio/appl/spidey/report.rb, line 576
576: def each_hit(&x) #:yields: hit
577: @hits.each(&x)
578: end
Returns sequence informationsof 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 563
563: def mrna; @hit.mrna; end
Returns number of hits. Same as hits.size.
# File lib/bio/appl/spidey/report.rb, line 571
571: def num_hits; @hits.size; end
Returns definition of the mRNA (query) sequence.
# File lib/bio/appl/spidey/report.rb, line 582
582: def query_def; @hit.mrna.definition; end
Returns identifier of the mRNA (query) sequence.
# File lib/bio/appl/spidey/report.rb, line 585
585: def query_id; @hit.mrna.entry_id; end