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
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.
# File lib/bio/appl/sim4/report.rb, line 206 def self.both_intron(prev_e, e, aln) self.new(Segment.new(prev_e.seq1.to+1, e.seq1.from-1, aln[0]), Segment.new(prev_e.seq2.to+1, e.seq2.from-1, aln[2]), aln[1]) 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.
# 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
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.
# 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
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.
# 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
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.
# 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
Public Instance Methods
Returns alignment length of the segment pair. Returns nil if no alignment data are available.
# File lib/bio/appl/sim4/report.rb, line 238 def align_len (@midline and @seq1.seq and @seq2.seq) ? @midline.length : nil end
start position of the hit(target) (the first position is 1)
# File lib/bio/appl/sim4/report.rb, line 227 def hit_from; @seq2.from; end
end position of the hit(target) (including its position)
# File lib/bio/appl/sim4/report.rb, line 230 def hit_to; @seq2.to; end
hit(target) sequence (with gaps) of the alignment of the segment pair.
# File lib/bio/appl/sim4/report.rb, line 234 def hseq; @seq2.seq; end
query sequence (with gaps) of the alignment of the segment pair.
# File lib/bio/appl/sim4/report.rb, line 224 def qseq; @seq1.seq; end
start position of the query (the first position is 1)
# File lib/bio/appl/sim4/report.rb, line 218 def query_from; @seq1.from; end
end position of the query (including its position)
# File lib/bio/appl/sim4/report.rb, line 221 def query_to; @seq1.to; end