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.

Methods

each   each_hit   mrna   new   num_hits   query_def   query_id   query_len  

Classes and Modules

Class Bio::Spidey::Report::Hit
Class Bio::Spidey::Report::Segment
Class Bio::Spidey::Report::SegmentPair
Class Bio::Spidey::Report::SeqDesc

Constants

DELIMITER = RS = "\n--SPIDEY "   Delimiter of each entry. Bio::FlatFile uses it.
DELIMITER_OVERRUN = 9   (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

Creates a new Bio::Spidey::Report object from String. You can use Bio::FlatFile to read a file.

[Source]

    # 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

Public Instance methods

each()

Alias for each_hit

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

[Source]

     # 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.

[Source]

     # File lib/bio/appl/spidey/report.rb, line 563
563:       def mrna; @hit.mrna; end

Returns number of hits. Same as hits.size.

[Source]

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

Returns definition of the mRNA (query) sequence.

[Source]

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

Returns identifier of the mRNA (query) sequence.

[Source]

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

Returns the length of the mRNA (query) sequence.

[Source]

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

[Validate]