Class: Bio::Spidey::Report::SegmentPair

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

Overview

Sequence segment pair of Spidey result. Similar to Bio::Blast::Report::Hsp but lacks many methods. For mRNA-genome mapping programs, unlike other homology search programs, the class is used not only for exons but also for introns. (Note that intron data would not be available according to run-time options of the program.)

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(genomic, mrna, midline, aaseqline, percent_identity, mismatches, gaps, splice_site, align_len) ⇒ SegmentPair

Creates a new SegmentPair object. It is designed to be called from Bio::Spidey::Report::* classes. Users shall not call it directly.



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# File 'lib/bio/appl/spidey/report.rb', line 125

def initialize(genomic, mrna, midline, aaseqline,
               percent_identity, mismatches, gaps, splice_site,
               align_len)
  @genomic   = genomic
  @mrna      = mrna
  @midline   = midline
  @aaseqline = aaseqline
  @percent_identity = percent_identity
  @mismaches        = mismatches
  @gaps             = gaps
  @splice_site      = splice_site
  @align_len        = align_len
end

Instance Attribute Details

#aaseqline ⇒ Object (readonly)

Returns amino acide sequence in alignment. Returns String, because white spaces is also important. Returns nil if no alignment data are available.



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# File 'lib/bio/appl/spidey/report.rb', line 156

def aaseqline
  @aaseqline
end

#align_len ⇒ Object (readonly)

Returns alignment length of the segment pair. Returns nil if no alignment data are available.



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# File 'lib/bio/appl/spidey/report.rb', line 176

def align_len
  @align_len
end

#gaps ⇒ Object (readonly)

Returns gaps.



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# File 'lib/bio/appl/spidey/report.rb', line 166

def gaps
  @gaps
end

#genomic ⇒ Object (readonly)

Returns segment informations of the ‘Genomic’. Returns a Bio::Spidey::Report::Segment object. This would be a Bio::Spidey specific method.



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# File 'lib/bio/appl/spidey/report.rb', line 142

def genomic
  @genomic
end

#midline ⇒ Object (readonly)

Returns the middle line of the alignment of the segment pair. Returns nil if no alignment data are available.



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# File 'lib/bio/appl/spidey/report.rb', line 151

def midline
  @midline
end

#mismatches ⇒ Object (readonly) Also known as: mismatch_count

Returns mismatches.



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# File 'lib/bio/appl/spidey/report.rb', line 162

def mismatches
  @mismatches
end

#mrna ⇒ Object (readonly)

Returns segment informations of the ‘mRNA’. Returns a Bio::Spidey::Report::Segment object. This would be a Bio::Spidey specific method.



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# File 'lib/bio/appl/spidey/report.rb', line 147

def mrna
  @mrna
end

#percent_identity ⇒ Object (readonly)

Returns percent identity of the segment pair.



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# File 'lib/bio/appl/spidey/report.rb', line 159

def percent_identity
  @percent_identity
end

#splice_site ⇒ Object (readonly)

Returns splice site information. Returns a hash which contains :d and :a for keys and 0, 1, or nil for values. This would be a Bio::Spidey specific methods.



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# File 'lib/bio/appl/spidey/report.rb', line 172

def splice_site
  @splice_site
end

Class Method Details

.new_intron(from, to, strand, aln) ⇒ Object

Creates a new SegmentPair object when the segment pair is an intron. It is designed to be called internally from Bio::Spidey::Report::* classes. Users shall not call it directly.



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# File 'lib/bio/appl/spidey/report.rb', line 182

def self.new_intron(from, to, strand, aln)
  genomic   = Segment.new(from, to, strand, aln[0])
  mrna      = Segment.new(nil, nil, nil,    aln[2])
  midline   = aln[1]
  aaseqline = aln[3]
  self.new(genomic, mrna, midline, aaseqline,
           nil, nil, nil, nil, nil)
end

.parse(str, strand, complement, aln) ⇒ Object

Parses a piece of Spidey result text and creates a new SegmentPair object. It is designed to be called internally from Bio::Spidey::Report::* classes. Users shall not call it directly.



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# File 'lib/bio/appl/spidey/report.rb', line 196

def self.parse(str, strand, complement, aln)
  /\AExon\s*\d+(\(\-\))?\:\s*(\d+)\-(\d+)\s*\(gen\)\s+(\d+)\-(\d+)\s*\(mRNA\)\s+id\s*([\d\.]+)\s*\%\s+mismatches\s+(\d+)\s+gaps\s+(\d+)\s+splice site\s*\(d +a\)\s*\:\s*(\d+)\s+(\d+)/ =~ str
  if strand == 'minus' then
    genomic = Segment.new($3, $2, strand, aln[0])
  else
    genomic = Segment.new($2, $3, 'plus', aln[0])
  end
  if complement then
    mrna    = Segment.new($4, $5, 'minus', aln[2])
  else
    mrna    = Segment.new($4, $5, 'plus',  aln[2])
  end
  percent_identity = $6
  mismatches = ($7 ? $7.to_i : nil)
  gaps = ($8 ? $8.to_i : nil)
  splice_site = {
    :d => ($9  ? $9.to_i  : nil),
    :a => ($10 ? $10.to_i : nil)
  }
  midline   = aln[1]
  aaseqline = aln[3]
  self.new(genomic, mrna, midline, aaseqline,
           percent_identity, mismatches, gaps, splice_site,
           (midline ? midline.length : nil))
end

Instance Method Details

#hit_from ⇒ Object

Returns start position of the genomic (target, hit) (the first position is 1).



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# File 'lib/bio/appl/spidey/report.rb', line 243

def hit_from;     @genomic.from;    end

#hit_strand ⇒ Object

Returns strand information of the genomic (target, hit). Returns ‘plus’, ‘minus’, or nil.



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# File 'lib/bio/appl/spidey/report.rb', line 254

def hit_strand;   @genomic.strand;  end

#hit_to ⇒ Object

Returns end position (including its position) of the genomic (target, hit).



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# File 'lib/bio/appl/spidey/report.rb', line 247

def hit_to;       @genomic.to;      end

#hseq ⇒ Object

Returns the sequence (with gaps) of the genomic (target, hit).



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# File 'lib/bio/appl/spidey/report.rb', line 250

def hseq;         @genomic.seq;     end

#qseq ⇒ Object

Returns the sequence (with gaps) of the mRNA (query).



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# File 'lib/bio/appl/spidey/report.rb', line 235

def qseq;         @mrna.seq;        end

#query_from ⇒ Object

Returns start position of the mRNA (query) (the first position is 1).



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# File 'lib/bio/appl/spidey/report.rb', line 229

def query_from;   @mrna.from;       end

#query_strand ⇒ Object

Returns strand information of the mRNA (query). Returns ‘plus’, ‘minus’, or nil.



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# File 'lib/bio/appl/spidey/report.rb', line 239

def query_strand; @mrna.strand;     end

#query_to ⇒ Object

Returns end position (including its position) of the mRNA (query).



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# File 'lib/bio/appl/spidey/report.rb', line 232

def query_to;     @mrna.to;         end