Class: Bio::Sim4::Report::SegmentPair

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/sim4/report.rb

Overview

Sequence segment pair of the sim4 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(seq1, seq2, midline = nil, percent_identity = nil, direction = nil) ⇒ SegmentPair

Creates a new SegmentPair object. It is designed to be called internally from Bio::Sim4::Report::Hit object. Users shall not use it directly.



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# File 'lib/bio/appl/sim4/report.rb', line 139

def initialize(seq1, seq2, midline = nil,
               percent_identity = nil, direction = nil)
  @seq1 = seq1
  @seq2 = seq2
  @midline = midline
  @percent_identity = percent_identity
  @direction = direction
end

Instance Attribute Details

#direction ⇒ Object (readonly)

Returns directions of mapping. Maybe one of “->”, “<-” or “” or nil. This would be a Bio::Sim4 specific method.



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# File 'lib/bio/appl/sim4/report.rb', line 166

def direction
  @direction
end

#midline ⇒ Object (readonly)

Returns the “midline” of the segment pair. Returns nil if no alignment data are available.



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# File 'lib/bio/appl/sim4/report.rb', line 158

def midline
  @midline
end

#percent_identity ⇒ Object (readonly)

Returns percent identity of the segment pair.



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# File 'lib/bio/appl/sim4/report.rb', line 161

def percent_identity
  @percent_identity
end

#seq1 ⇒ Object (readonly)

Returns segment informations of ‘seq1’. Returns a Bio::Sim4::Report::Segment object. These would be Bio::Sim4 specific methods.



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# File 'lib/bio/appl/sim4/report.rb', line 150

def seq1
  @seq1
end

#seq2 ⇒ Object (readonly)

Returns segment informations of ‘seq2’. Returns a Bio::Sim4::Report::Segment object. These would be Bio::Sim4 specific methods.



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# File 'lib/bio/appl/sim4/report.rb', line 154

def seq2
  @seq2
end

Class Method Details

.parse(str, aln) ⇒ Object

Parses part of sim4 result text and creates a new SegmentPair object. It is designed to be called internally from Bio::Sim4::Report::Hit class. Users shall not use it directly.



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# File 'lib/bio/appl/sim4/report.rb', line 172

def self.parse(str, aln)
  /^(\d+)\-(\d+)\s*\((\d+)\-(\d+)\)\s*([\d\.]+)\%\s*([\-\<\>]*)/ =~ str
  self.new(Segment.new($1, $2, aln[0]),
           Segment.new($3, $4, aln[2]),
           aln[1], $5, $6)
end

.seq1_intron(prev_e, e, aln) ⇒ Object

Parses part of sim4 result text and creates a new SegmentPair object when the seq1 is a intron. It is designed to be called internally from Bio::Sim4::Report::Hit class. Users shall not use it directly.



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# File 'lib/bio/appl/sim4/report.rb', line 184

def self.seq1_intron(prev_e, e, aln)
  self.new(Segment.new(prev_e.seq1.to+1, e.seq1.from-1, aln[0]),
           Segment.new(nil, nil, aln[2]),
           aln[1])
end

.seq2_intron(prev_e, e, aln) ⇒ Object

Parses part of sim4 result text and creates a new SegmentPair object when seq2 is a intron. It is designed to be called internally from Bio::Sim4::Report::Hit class. Users shall not use it directly.



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# File 'lib/bio/appl/sim4/report.rb', line 195

def self.seq2_intron(prev_e, e, aln)
  self.new(Segment.new(nil, nil, aln[0]),
           Segment.new(prev_e.seq2.to+1, e.seq2.from-1, aln[2]),
           aln[1])
end

Instance Method Details

#align_len ⇒ Object

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



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# File 'lib/bio/appl/sim4/report.rb', line 227

def align_len
  (@midline and @seq1.seq and @seq2.seq) ? @midline.length : nil
end

#hit_from ⇒ Object

start position of the hit(target) (the first position is 1)



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# File 'lib/bio/appl/sim4/report.rb', line 216

def hit_from;   @seq2.from; end

#hit_to ⇒ Object

end position of the hit(target) (including its position)



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# File 'lib/bio/appl/sim4/report.rb', line 219

def hit_to;     @seq2.to;   end

#hseq ⇒ Object

hit(target) sequence (with gaps) of the alignment of the segment pair.



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# File 'lib/bio/appl/sim4/report.rb', line 223

def hseq;       @seq2.seq;  end

#qseq ⇒ Object

query sequence (with gaps) of the alignment of the segment pair.



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# File 'lib/bio/appl/sim4/report.rb', line 213

def qseq;       @seq1.seq;  end

#query_from ⇒ Object

start position of the query (the first position is 1)



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# File 'lib/bio/appl/sim4/report.rb', line 207

def query_from; @seq1.from; end

#query_to ⇒ Object

end position of the query (including its position)



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# File 'lib/bio/appl/sim4/report.rb', line 210

def query_to;   @seq1.to;   end