Class: Bio::Spidey::Report

Inherits:
Object show all
Defined in:
lib/bio/appl/spidey/report.rb

Overview

Spidey report parser class. Please see bio/appl/spidey/report.rb for details.

Its object may contain some Bio::Spidey::Report::Hit objects.

Defined Under Namespace

Classes: Hit, Segment, SegmentPair, SeqDesc

Constant Summary

DELIMITER =

Delimiter of each entry. Bio::FlatFile uses it.

RS = "\n--SPIDEY "
DELIMITER_OVERRUN =

(Integer) excess read size included in DELIMITER.

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Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (Report) initialize(str)

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



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# 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

Instance Attribute Details

- (Object) all_hits (readonly)

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.



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# File 'lib/bio/appl/spidey/report.rb', line 73

def all_hits
  @all_hits
end

- (Object) entry_overrun (readonly)

piece of next entry. Bio::FlatFile uses it.



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# File 'lib/bio/appl/spidey/report.rb', line 62

def entry_overrun
  @entry_overrun
end

- (Object) hits (readonly)

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.



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# File 'lib/bio/appl/spidey/report.rb', line 67

def hits
  @hits
end

Instance Method Details

- (Object) each_hit(&x) Also known as: each

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



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# File 'lib/bio/appl/spidey/report.rb', line 576

def each_hit(&x) #:yields: hit
  @hits.each(&x)
end

- (Object) mrna

Returns sequence informationsof the mRNA. Returns a Bio::Spidey::Report::SeqDesc object. This would be a Bio::Spidey specific method.



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# File 'lib/bio/appl/spidey/report.rb', line 563

def mrna; @hit.mrna; end

- (Object) num_hits

Returns number of hits. Same as hits.size.



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# File 'lib/bio/appl/spidey/report.rb', line 571

def num_hits;     @hits.size;     end

- (Object) query_def

Returns definition of the mRNA (query) sequence.



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# File 'lib/bio/appl/spidey/report.rb', line 582

def query_def; @hit.mrna.definition; end

- (Object) query_id

Returns identifier of the mRNA (query) sequence.



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# File 'lib/bio/appl/spidey/report.rb', line 585

def query_id;  @hit.mrna.entry_id;   end

- (Object) query_len

Returns the length of the mRNA (query) sequence.



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# File 'lib/bio/appl/spidey/report.rb', line 588

def query_len; @hit.mrna.len;        end