class Bio::Sim4::Report::SegmentPair
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.)
Attributes
Returns directions of mapping. Maybe one of “->”, “<-”, “==” or “” or nil. This would be a Bio::Sim4 specific method.
Returns the “midline” of the segment pair. Returns nil if no alignment data are available.
Returns percent identity of the segment pair.
Returns segment informations of ‘seq1’. Returns a Bio::Sim4::Report::Segment object. These would be Bio::Sim4 specific methods.
Returns segment informations of ‘seq2’. Returns a Bio::Sim4::Report::Segment object. These would be Bio::Sim4 specific methods.
Public Class Methods
Source
# File lib/bio/appl/sim4/report.rb 206 def self.both_intron(prev_e, e, aln) 207 self.new(Segment.new(prev_e.seq1.to+1, e.seq1.from-1, aln[0]), 208 Segment.new(prev_e.seq2.to+1, e.seq2.from-1, aln[2]), 209 aln[1]) 210 end
Parses part of sim4 result text and creates a new SegmentPair object for regions which can not be aligned correctly. It is designed to be called internally from Bio::Sim4::Report::Hit class. Users shall not use it directly.
Source
# File lib/bio/appl/sim4/report.rb 139 def initialize(seq1, seq2, midline = nil, 140 percent_identity = nil, direction = nil) 141 @seq1 = seq1 142 @seq2 = seq2 143 @midline = midline 144 @percent_identity = percent_identity 145 @direction = direction 146 end
Creates a new SegmentPair object. It is designed to be called internally from Bio::Sim4::Report::Hit object. Users shall not use it directly.
Source
# File lib/bio/appl/sim4/report.rb 172 def self.parse(str, aln) 173 /^(\d+)\-(\d+)\s*\((\d+)\-(\d+)\)\s*([\d\.]+)\%\s*([\-\<\>\=]*)/ =~ str 174 self.new(Segment.new($1, $2, aln[0]), 175 Segment.new($3, $4, aln[2]), 176 aln[1], $5, $6) 177 end
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.
Source
# File lib/bio/appl/sim4/report.rb 184 def self.seq1_intron(prev_e, e, aln) 185 self.new(Segment.new(prev_e.seq1.to+1, e.seq1.from-1, aln[0]), 186 Segment.new(nil, nil, aln[2]), 187 aln[1]) 188 end
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.
Source
# File lib/bio/appl/sim4/report.rb 195 def self.seq2_intron(prev_e, e, aln) 196 self.new(Segment.new(nil, nil, aln[0]), 197 Segment.new(prev_e.seq2.to+1, e.seq2.from-1, aln[2]), 198 aln[1]) 199 end
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.
Public Instance Methods
Source
# File lib/bio/appl/sim4/report.rb 238 def align_len 239 (@midline and @seq1.seq and @seq2.seq) ? @midline.length : nil 240 end
Returns alignment length of the segment pair. Returns nil if no alignment data are available.
Source
# File lib/bio/appl/sim4/report.rb 227 def hit_from; @seq2.from; end
start position of the hit(target) (the first position is 1)
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# File lib/bio/appl/sim4/report.rb 230 def hit_to; @seq2.to; end
end position of the hit(target) (including its position)
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# File lib/bio/appl/sim4/report.rb 234 def hseq; @seq2.seq; end
hit(target) sequence (with gaps) of the alignment of the segment pair.
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# File lib/bio/appl/sim4/report.rb 224 def qseq; @seq1.seq; end
query sequence (with gaps) of the alignment of the segment pair.
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# File lib/bio/appl/sim4/report.rb 218 def query_from; @seq1.from; end
start position of the query (the first position is 1)
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# File lib/bio/appl/sim4/report.rb 221 def query_to; @seq1.to; end
end position of the query (including its position)