class Bio::Spidey::Report::SegmentPair
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.)
Attributes
Returns amino acide sequence in alignment. Returns String, because white spaces is also important. Returns nil if no alignment data are available.
Returns alignment length of the segment pair. Returns nil if no alignment data are available.
Returns gaps.
Returns segment informations of the ‘Genomic’. Returns a Bio::Spidey::Report::Segment object. This would be a Bio::Spidey specific method.
Returns the middle line of the alignment of the segment pair. Returns nil if no alignment data are available.
Returns mismatches.
Returns mismatches.
Returns segment informations of the ‘mRNA’. Returns a Bio::Spidey::Report::Segment object. This would be a Bio::Spidey specific method.
Returns percent identity of the segment pair.
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.
Public Class Methods
Source
# File lib/bio/appl/spidey/report.rb 125 def initialize(genomic, mrna, midline, aaseqline, 126 percent_identity, mismatches, gaps, splice_site, 127 align_len) 128 @genomic = genomic 129 @mrna = mrna 130 @midline = midline 131 @aaseqline = aaseqline 132 @percent_identity = percent_identity 133 @mismaches = mismatches 134 @gaps = gaps 135 @splice_site = splice_site 136 @align_len = align_len 137 end
Creates a new SegmentPair object. It is designed to be called from Bio::Spidey::Report::* classes. Users shall not call it directly.
Source
# File lib/bio/appl/spidey/report.rb 182 def self.new_intron(from, to, strand, aln) 183 genomic = Segment.new(from, to, strand, aln[0]) 184 mrna = Segment.new(nil, nil, nil, aln[2]) 185 midline = aln[1] 186 aaseqline = aln[3] 187 self.new(genomic, mrna, midline, aaseqline, 188 nil, nil, nil, nil, nil) 189 end
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.
Source
# File lib/bio/appl/spidey/report.rb 196 def self.parse(str, strand, complement, aln) 197 /\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 198 if strand == 'minus' then 199 genomic = Segment.new($3, $2, strand, aln[0]) 200 else 201 genomic = Segment.new($2, $3, 'plus', aln[0]) 202 end 203 if complement then 204 mrna = Segment.new($4, $5, 'minus', aln[2]) 205 else 206 mrna = Segment.new($4, $5, 'plus', aln[2]) 207 end 208 percent_identity = $6 209 mismatches = ($7 ? $7.to_i : nil) 210 gaps = ($8 ? $8.to_i : nil) 211 splice_site = { 212 :d => ($9 ? $9.to_i : nil), 213 :a => ($10 ? $10.to_i : nil) 214 } 215 midline = aln[1] 216 aaseqline = aln[3] 217 self.new(genomic, mrna, midline, aaseqline, 218 percent_identity, mismatches, gaps, splice_site, 219 (midline ? midline.length : nil)) 220 end
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.
Public Instance Methods
Source
# File lib/bio/appl/spidey/report.rb 243 def hit_from; @genomic.from; end
Returns start position of the genomic (target, hit) (the first position is 1).
Source
# File lib/bio/appl/spidey/report.rb 254 def hit_strand; @genomic.strand; end
Returns strand information of the genomic (target, hit). Returns ‘plus’, ‘minus’, or nil.
Source
# File lib/bio/appl/spidey/report.rb 247 def hit_to; @genomic.to; end
Returns end position (including its position) of the genomic (target, hit).
Source
# File lib/bio/appl/spidey/report.rb 250 def hseq; @genomic.seq; end
Returns the sequence (with gaps) of the genomic (target, hit).
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# File lib/bio/appl/spidey/report.rb 235 def qseq; @mrna.seq; end
Returns the sequence (with gaps) of the mRNA (query).
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# File lib/bio/appl/spidey/report.rb 229 def query_from; @mrna.from; end
Returns start position of the mRNA (query) (the first position is 1).
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# File lib/bio/appl/spidey/report.rb 239 def query_strand; @mrna.strand; end
Returns strand information of the mRNA (query). Returns ‘plus’, ‘minus’, or nil.
Source
# File lib/bio/appl/spidey/report.rb 232 def query_to; @mrna.to; end
Returns end position (including its position) of the mRNA (query).