class Bio::Spidey::Report
Spidey report parser class. Please see bio/appl/spidey/report.rb for details.
Its object may contain some Bio::Spidey::Report::Hit objects.
Constants
- DELIMITER
Delimiter of each entry. Bio::FlatFile uses it.
- DELIMITER_OVERRUN
(Integer) excess read size included in DELIMITER.
Attributes
Returns an Array of Bio::Spidey::Report::Hit objects. Unlike #hits, the method returns results of all trials of pairwise alignment. This would be a Bio::Spidey specific method.
piece of next entry. Bio::FlatFile uses it.
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.
Public Class Methods
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 def initialize(str) str = str.sub(/\A\s+/, '') str.sub!(/\n(^\-\-SPIDEY .*)/m, '') # remove trailing entries for sure @entry_overrun = $1 data = str.split(/\r?\n(?:\r?\n)+/) d0 = data.shift.to_s.split(/\r?\n/) @hit = Hit.new(data, d0) @all_hits = [ @hit ] if d0.empty? or /\ANo alignment found\.\s*\z/ =~ d0[-1] then @hits = [] else @hits = [ @hit ] end end
Public Instance Methods
Iterates over each hits. Same as hits.each. Yields a Bio::Spidey::Report::Hit object.
# File lib/bio/appl/spidey/report.rb, line 576 def each_hit(&x) #:yields: hit @hits.each(&x) 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 def mrna; @hit.mrna; end
Returns number of hits. Same as hits.size.
# File lib/bio/appl/spidey/report.rb, line 571 def num_hits; @hits.size; end
Returns definition of the mRNA (query) sequence.
# File lib/bio/appl/spidey/report.rb, line 582 def query_def; @hit.mrna.definition; end
Returns identifier of the mRNA (query) sequence.
# File lib/bio/appl/spidey/report.rb, line 585 def query_id; @hit.mrna.entry_id; end
Returns the length of the mRNA (query) sequence.
# File lib/bio/appl/spidey/report.rb, line 588 def query_len; @hit.mrna.len; end