Class Bio::Spidey::Report::SegmentPair
In: lib/bio/appl/spidey/report.rb
Parent: Object

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.)

Methods

hit_from   hit_strand   hit_to   hseq   new   new_intron   parse   qseq   query_from   query_strand   query_to  

External Aliases

mismatches -> mismatch_count

Attributes

aaseqline  [R]  Returns amino acide sequence in alignment. Returns String, because white spaces is also important. Returns nil if no alignment data are available.
align_len  [R]  Returns alignment length of the segment pair. Returns nil if no alignment data are available.
gaps  [R]  Returns gaps.
genomic  [R]  Returns segment informations of the ‘Genomic’. Returns a Bio::Spidey::Report::Segment object. This would be a Bio::Spidey specific method.
midline  [R]  Returns the middle line of the alignment of the segment pair. Returns nil if no alignment data are available.
mismatches  [R]  Returns mismatches.
mrna  [R]  Returns segment informations of the ‘mRNA’. Returns a Bio::Spidey::Report::Segment object. This would be a Bio::Spidey specific method.
percent_identity  [R]  Returns percent identity of the segment pair.
splice_site  [R]  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

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, line 125
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 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, line 182
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

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.

[Source]

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

Public Instance methods

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

[Source]

     # File lib/bio/appl/spidey/report.rb, line 243
243:         def hit_from;     @genomic.from;    end

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

[Source]

     # File lib/bio/appl/spidey/report.rb, line 254
254:         def hit_strand;   @genomic.strand;  end

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

[Source]

     # File lib/bio/appl/spidey/report.rb, line 247
247:         def hit_to;       @genomic.to;      end

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

[Source]

     # File lib/bio/appl/spidey/report.rb, line 250
250:         def hseq;         @genomic.seq;     end

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

[Source]

     # File lib/bio/appl/spidey/report.rb, line 235
235:         def qseq;         @mrna.seq;        end

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

[Source]

     # File lib/bio/appl/spidey/report.rb, line 229
229:         def query_from;   @mrna.from;       end

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

[Source]

     # File lib/bio/appl/spidey/report.rb, line 239
239:         def query_strand; @mrna.strand;     end

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

[Source]

     # File lib/bio/appl/spidey/report.rb, line 232
232:         def query_to;     @mrna.to;         end

[Validate]