class Bio::Blast::Default::Report::Iteration
Bio::Blast::Default::Report::Iteration stores information about a iteration. It may contain some Bio::Blast::Default::Report::Hit objects. Note that a PSI-BLAST (blastpgp command) result usually contain multiple iterations in it, and a normal BLAST (blastall command) result usually contain one iteration in it.
Attributes
name (title or filename) of the database
number of sequences in database
number of letters in database
effective length of the database
entropy of the database
e-value threshold specified when BLAST was executed
gapped entropy of the database
gapped kappa of the database
gapped lambda of the database
kappa of the database
lambda of the database
(PSI-BLAST) Messages of the iteration.
(PSI-BLAST) Iteration round number.
(PHI-BLAST) Number of occurrences of pattern in the database.
posted date of the database
Public Class Methods
Creates a new Iteration object. It is designed to be called only internally from the Bio::Blast::Default::Report class. Users shall not use the method directly.
# File lib/bio/appl/blast/format0.rb 492 def initialize(data) 493 @f0stat = [] 494 @f0dbstat = AlwaysNil.instance 495 @f0hitlist = [] 496 @hits = [] 497 @num = 1 498 r = data.shift 499 @f0message = [ r ] 500 r.gsub!(/^Results from round (\d+).*\z/) { |x| 501 @num = $1.to_i 502 @f0message << x 503 '' 504 } 505 r = data.shift 506 while /^Number of occurrences of pattern in the database is +(\d+)/ =~ r 507 # PHI-BLAST 508 @pattern_in_database = $1.to_i 509 @f0message << r 510 r = data.shift 511 end 512 if /^Results from round (\d+)/ =~ r then 513 @num = $1.to_i 514 @f0message << r 515 r = data.shift 516 end 517 if r and !(/\*{5} No hits found \*{5}/ =~ r) then 518 @f0hitlist << r 519 begin 520 @f0hitlist << data.shift 521 end until r = data[0] and /^\>/ =~ r 522 if r and /^CONVERGED\!/ =~ r then 523 r.sub!(/(.*\n)*^CONVERGED\!.*\n/) { |x| @f0hitlist << x; '' } 524 end 525 if defined?(@pattern_in_database) and r = data.first then 526 #PHI-BLAST 527 while /^\>/ =~ r 528 @hits << Hit.new(data) 529 r = data.first 530 break unless r 531 while /^Significant alignments for pattern/ =~ r 532 data.shift 533 r = data.first 534 end 535 end 536 else 537 #not PHI-BLAST 538 while r = data[0] and /^\>/ =~ r 539 @hits << Hit.new(data) 540 end 541 end 542 end 543 if /^CONVERGED\!\s*$/ =~ @f0hitlist[-1].to_s then 544 @message = 'CONVERGED!' 545 @flag_converged = true 546 end 547 end
Public Instance Methods
(PSI-BLAST) Returns true if the iteration is converged. Otherwise, returns false.
# File lib/bio/appl/blast/format0.rb 573 def converged? 574 @flag_converged 575 end
Iterates over each hit of the iteration. Yields a Bio::Blast::Default::Report::Hit object.
# File lib/bio/appl/blast/format0.rb 565 def each 566 hits.each do |x| 567 yield x 568 end 569 end
Returns the hits of the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.
# File lib/bio/appl/blast/format0.rb 558 def hits 559 parse_hitlist 560 @hits 561 end
(PHI-BLAST) Returns hits for pattern. ????
# File lib/bio/appl/blast/format0.rb 625 def hits_for_pattern 626 parse_hitlist 627 @hits_for_pattern 628 end
(PSI-BLAST) Returns hits which have been found again in the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.
# File lib/bio/appl/blast/format0.rb 611 def hits_found_again 612 parse_hitlist 613 @hits_found_again 614 end
(PSI-BLAST) Returns hits which have been newly found in the iteration. It returns an array of Bio::Blast::Default::Report::Hit objects.
# File lib/bio/appl/blast/format0.rb 619 def hits_newly_found 620 parse_hitlist 621 @hits_newly_found 622 end
(PHI-BLAST) Returns pattern string. Returns nil if it is not a PHI-BLAST result.
# File lib/bio/appl/blast/format0.rb 579 def pattern 580 #PHI-BLAST 581 if defined? @pattern 582 @pattern 583 elsif defined? @pattern_in_database then 584 @pattern = nil 585 @pattern_positions = [] 586 @f0message.each do |r| 587 sc = StringScanner.new(r) 588 if sc.skip_until(/^ *pattern +([^\s]+)/) then 589 @pattern = sc[1] unless @pattern 590 sc.skip_until(/(?:^ *| +)at position +(\d+) +of +query +sequence/) 591 @pattern_positions << sc[1].to_i 592 end 593 end 594 @pattern 595 else 596 nil 597 end 598 end
(PHI-BLAST) Returns pattern positions. Returns nil if it is not a PHI-BLAST result.
# File lib/bio/appl/blast/format0.rb 602 def pattern_positions 603 #PHI-BLAST 604 pattern 605 @pattern_positions 606 end