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

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.

Public Class Methods

new(str) click to toggle source

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
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

Public Instance Methods

each()

Alias for: each_hit

each_hit() { |hit| ... } click to toggle source

Iterates over each hits. Same as hits.each. Yields a Bio::Spidey::Report::Hit object.

    # File lib/bio/appl/spidey/report.rb
576 def each_hit(&x) #:yields: hit
577   @hits.each(&x)
578 end

Also aliased as: each

mrna() click to toggle source

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
563 def mrna; @hit.mrna; end

num_hits() click to toggle source

Returns number of hits. Same as hits.size.

    # File lib/bio/appl/spidey/report.rb
571 def num_hits;     @hits.size;     end

query_def() click to toggle source

Returns definition of the mRNA (query) sequence.

    # File lib/bio/appl/spidey/report.rb
582 def query_def; @hit.mrna.definition; end

query_id() click to toggle source

Returns identifier of the mRNA (query) sequence.

    # File lib/bio/appl/spidey/report.rb
585 def query_id;  @hit.mrna.entry_id;   end

query_len() click to toggle source

Returns the length of the mRNA (query) sequence.

    # File lib/bio/appl/spidey/report.rb
588 def query_len; @hit.mrna.len;        end