Class: Bio::Blat::Report::Hit

new(str)

Creates a new Hit object from a piece of BLAT result text. It is designed to be called internally from Bio::Blat::Report object. Users shall not use it directly.

[Source]

     # File lib/bio/appl/blat/report.rb, line 293
293:         def initialize(str)
294:           @data = str.chomp.split(/\t/)
295:         end

block_count()

Number of blocks(exons, segment pairs).

[Source]

     # File lib/bio/appl/blat/report.rb, line 350
350:         def block_count; @data[17].to_i; end

block_sizes()

Sizes of all blocks(exons, segment pairs). Returns an array of numbers.

[Source]

     # File lib/bio/appl/blat/report.rb, line 354
354:         def block_sizes
355:           unless defined?(@block_sizes) then
356:             @block_sizes = split_comma(@data[18]).collect { |x| x.to_i }
357:           end
358:           @block_sizes
359:         end

blocks()

Returns blocks(exons, segment pairs) of the hit. Returns an array of Bio::Blat::Report::SegmentPair objects.

[Source]

     # File lib/bio/appl/blat/report.rb, line 363
363:         def blocks
364:           unless defined?(@blocks)
365:             bs    = block_sizes
366:             qst   = query.starts
367:             tst   = target.starts
368:             qseqs = query.seqs
369:             tseqs = target.seqs
370:             pflag = self.protein?
371:             @blocks = (0...block_count).collect do |i|
372:               SegmentPair.new(query.size, target.size, strand, bs[i],
373:                               qst[i], tst[i], qseqs[i], tseqs[i],
374:                               pflag)
375:             end
376:           end
377:           @blocks
378:         end

definition()

Alias for target_def

each() {|segmentpair| ...}

Iterates over each block(exon, segment pair) of the hit.

 Yields a Bio::Blat::Report::SegmentPair object.

[Source]

     # File lib/bio/appl/blat/report.rb, line 404
404:         def each(&x) #:yields: segmentpair
405:           exons.each(&x)
406:         end

exons()

Alias for blocks

hsps()

Alias for blocks

len()

Alias for target_len

match()

Match nucleotides.

[Source]

     # File lib/bio/appl/blat/report.rb, line 332
332:         def match;       @data[0].to_i;  end

milli_bad()

Calculates the pslCalcMilliBad value defined in the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

The algorithm is taken from the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

[Source]

     # File lib/bio/appl/blat/report.rb, line 418
418:         def milli_bad
419:           w = (self.protein? ? 3 : 1)
420:           qalen = w * (self.query.end - self.query.start)
421:           talen = self.target.end - self.target.start
422:           alen = (if qalen < talen then qalen; else talen; end)
423:           return 0 if alen <= 0
424:           d = qalen - talen
425:           d = 0 if d < 0
426:           total = w * (self.match + self.rep_match + self.mismatch)
427:           return 0 if total == 0
428:           return (1000 * (self.mismatch * w + self.query.gap_count +
429:                             (3 * Math.log(1 + d)).round) / total)
430:         end

mismatch()

Mismatch nucleotides.

[Source]

     # File lib/bio/appl/blat/report.rb, line 334
334:         def mismatch;    @data[1].to_i;  end

n_s()

"N‘s". Number of ‘N’ bases.

[Source]

     # File lib/bio/appl/blat/report.rb, line 342
342:         def n_s;         @data[3].to_i;  end

percent_identity()

Calculates the percent identity compatible with the BLAT web server as described in the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

The algorithm is taken from the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

[Source]

     # File lib/bio/appl/blat/report.rb, line 438
438:         def percent_identity
439:           100.0 - self.milli_bad * 0.1
440:         end

protein?()

When the output data comes from the protein query, returns true. Otherwise (nucleotide query), returns false. It returns nil if this cannot be determined.

The algorithm is taken from the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

Note: It seems that it returns true only when protein query with nucleotide database (blat options: -q=prot -t=dnax).

[Source]

     # File lib/bio/appl/blat/report.rb, line 451
451:         def protein?
452:           return nil if self.block_sizes.empty?
453:           case self.strand[1,1]
454:           when '+'
455:             if self.target.end == self.target.starts[-1] +
456:                 3 * self.block_sizes[-1] then
457:               true
458:             else
459:               false
460:             end
461:           when '-'
462:             if self.target.start == self.target.size -
463:                 self.target.starts[-1] - 3 * self.block_sizes[-1] then
464:               true
465:             else
466:               false
467:             end
468:           else
469:             nil
470:           end
471:         end

query()

Returns sequence informations of the query. Returns a Bio::Blat::Report::SeqDesc object. This would be Bio::Blat specific method.

[Source]

     # File lib/bio/appl/blat/report.rb, line 310
310:         def query
311:           unless defined?(@query)
312:             d = @data
313:             @query = SeqDesc.new(d[4], d[5], d[9], d[10], d[11], d[12],
314:                                  split_comma(d[19]), split_comma(d[21]))
315:           end
316:           @query
317:         end

query_def()

Returns the name of query sequence.

[Source]

     # File lib/bio/appl/blat/report.rb, line 390
390:         def query_def;  query.name;  end

query_id()

Alias for query_def

query_len()

Returns the length of query sequence.

[Source]

     # File lib/bio/appl/blat/report.rb, line 387
387:         def query_len;  query.size;  end

rep_match()

"rep. match". Number of bases that match but are part of repeats. Note that current version of BLAT always set 0.

[Source]

     # File lib/bio/appl/blat/report.rb, line 339
339:         def rep_match;   @data[2].to_i;  end

score()

Calculates the score compatible with the BLAT web server as described in the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

The algorithm is taken from the BLAT FAQ (genome.ucsc.edu/FAQ/FAQblat#blat4).

[Source]

     # File lib/bio/appl/blat/report.rb, line 479
479:         def score
480:           w = (self.protein? ? 3 : 1)
481:           w * (self.match + (self.rep_match >> 1)) -
482:             w * self.mismatch - self.query.gap_count - self.target.gap_count
483:         end

strand()

Returns strand information of the hit. Returns ’+’ or ’-’. This would be a Bio::Blat specific method.

[Source]

     # File lib/bio/appl/blat/report.rb, line 347
347:         def strand;      @data[8];       end

target()

Returns sequence informations of the target(hit). Returns a Bio::Blat::Report::SeqDesc object. This would be Bio::Blat specific method.

[Source]

     # File lib/bio/appl/blat/report.rb, line 322
322:         def target
323:           unless defined?(@target)
324:             d = @data
325:             @target = SeqDesc.new(d[6], d[7], d[13], d[14], d[15], d[16],
326:                                   split_comma(d[20]), split_comma(d[22]))
327:           end
328:           @target
329:         end

target_def()

Returns the name of the target(subject) sequence.

[Source]

     # File lib/bio/appl/blat/report.rb, line 398
398:         def target_def; target.name; end

target_id()

Alias for target_def

target_len()

Returns the length of the target(subject) sequence.

[Source]

     # File lib/bio/appl/blat/report.rb, line 394
394:         def target_len; target.size; end

Methods

Attributes

Public Class methods

Public Instance methods