Class: Bio::Blat::Report

Inherits:
Object show all
Defined in:
lib/bio/appl/blat/report.rb

Overview

Bio::Blat::Report is a BLAT report parser class. Its object may contain some Bio::Blat::Report::Hits objects.

In BLAT results, the start position of a sequnece is numbered as 0. On the other hand, in many other homology search programs, the start position of a sequence is numbered as 1. To keep compatibility, the BLAT parser adds 1 to every position number except Bio::Blat::Report::Seqdesc and some Bio::Blat specific methods.

Note that Bio::Blat::Report#query_def, #query_id, #query_len methods simply return first hit’s query_*. If multiple query sequences are given, these values will be incorrect.

Defined Under Namespace

Classes: Hit, SegmentPair, SeqDesc

Constant Summary collapse

DELIMITER =

Delimiter of each entry. Bio::FlatFile uses it. In Bio::Blat::Report, it it nil (1 entry 1 file).

RS = nil

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(text) ⇒ Report

Creates a new Bio::Blat::Report object from BLAT result text (String). You can use Bio::FlatFile to read a file. Currently, results created with options -out=psl (default) or -out=pslx are supported.



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# File 'lib/bio/appl/blat/report.rb', line 53

def initialize(text)
  flag = false
  head = []
  @hits = []
  text.each do |line|
    if flag then
      @hits << Hit.new(line)
    else
      # for headerless data
      if /^\d/ =~ line then
        flag = true
        redo
      end
      line = line.chomp
      if /\A\-+\s*\z/ =~ line
        flag = true
      else
        head << line
      end
    end
  end
  @columns = parse_header(head)
end

Instance Attribute Details

#columns ⇒ Object (readonly)

Returns descriptions of columns. Returns an Array. This would be a Bio::Blat specific method.



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# File 'lib/bio/appl/blat/report.rb', line 84

def columns
  @columns
end

#hits ⇒ Object (readonly)

hits of the result. Returns an Array of Bio::Blat::Report::Hit objects.



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# File 'lib/bio/appl/blat/report.rb', line 79

def hits
  @hits
end

#psl_version ⇒ Object (readonly)

version of the psl format (String or nil).



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# File 'lib/bio/appl/blat/report.rb', line 111

def psl_version
  @psl_version
end

Instance Method Details

#each_hit(&x) ⇒ Object Also known as: each

Iterates over each Bio::Blat::Report::Hit object. Same as hits.each.



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# File 'lib/bio/appl/blat/report.rb', line 455

def each_hit(&x) #:yields: hit
  @hits.each(&x)
end

#num_hits ⇒ Object

Returns number of hits. Same as hits.size.



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# File 'lib/bio/appl/blat/report.rb', line 451

def num_hits;     @hits.size;     end

#query_def ⇒ Object Also known as: query_id

Returns the name of query sequence. CAUTION: query_* methods simply return first hit’s query_*. If multiple query sequences are given, these values will be incorrect.



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# File 'lib/bio/appl/blat/report.rb', line 464

def query_def; (x = @hits.first) ? x.query_def : nil; end

#query_len ⇒ Object

Returns the length of query sequence. CAUTION: query_* methods simply return first hit’s query_*. If multiple query sequences are given, these values will be incorrect.



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# File 'lib/bio/appl/blat/report.rb', line 470

def query_len; (x = @hits.first) ? x.query_len : nil; end