[BioRuby-cvs] bioruby/lib/bio/appl/iprscan report.rb,1.3,1.4

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/appl/iprscan
In directory dev.open-bio.org:/tmp/cvs-serv15976/lib/bio/appl/iprscan

Modified Files:
	report.rb 
Log Message:
* Added list_of_interpro method.


Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/iprscan/report.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** report.rb	22 Feb 2007 08:44:34 -0000	1.3
--- report.rb	22 Feb 2007 10:15:01 -0000	1.4
***************
*** 120,129 ****
        end
  
!       # Splits entry stream.
        # 
        # == Usage
        #  Bio::Iprscan::Report.reports_in_txt(File.open("merged.txt")) do |report|
!       #    report
        #  end
        def self.reports_in_txt(io)
          io.each("\n\nSequence") do |entry|
--- 120,131 ----
        end
  
!       # Splits the entry stream.
        # 
        # == Usage
+       #
        #  Bio::Iprscan::Report.reports_in_txt(File.open("merged.txt")) do |report|
!       #    report.class #=> Bio::Iprscan::Report
        #  end
+       #
        def self.reports_in_txt(io)
          io.each("\n\nSequence") do |entry|
***************
*** 145,149 ****
        def self.parse_in_txt(str)
          unless str =~ /^Sequence /
!           raise Exception, "Invalid format: \n\n#{str}"
          end
          header, *matches = str.split(/\n\n/)
--- 147,151 ----
        def self.parse_in_txt(str)
          unless str =~ /^Sequence /
!           raise ArgumentError, "Invalid format:  \n\n#{str}"
          end
          header, *matches = str.split(/\n\n/)
***************
*** 172,175 ****
--- 174,178 ----
                                              :description => match[2], 
                                              :evalue      => pos_score[3],
+                                             :status      => pos_score[0],
                                              :match_start => pos_score[1].to_i,
                                              :match_end   => pos_score[2].to_i,
***************
*** 246,250 ****
        end
        
!       def to_ebihtml
          NotImplementedError        
        end
--- 249,253 ----
        end
        
!       def to_ebixml
          NotImplementedError        
        end
***************
*** 255,259 ****
        
        def to_raw
!         NotImplementedError        
        end
        
--- 258,278 ----
        
        def to_raw
!         @matches.map { |match|
!           [self.query_id,
!                 self.crc64,
!                 self.query_length,
!                 match.method,
!                 match.accession,
!                 match.description,
!                 match.match_start,
!                 match.match_end,
!                 match.evalue,
!                 match.status,
!                 match.date,
!                 match.ipr_id,
!                 match.ipr_description,
!                 match.go_terms.map {|x| x[0] + ': ' + x[1] + ' (' + x[2] + ')' }.join(', ')
!           ].join("\t")
!         }.join("\n")
        end
        
***************
*** 262,273 ****
        end
  
!       # == DESCRIPTION
        # Container class for InterProScan matches.
        #
!       # == USAGE
        #  match = Match.new(:query_id => ...)
        #
        #  match.ipr_id = 'IPR001234'
!       #  match.ipr_id #=> 'IPR1234'
        #
        class Match
--- 281,313 ----
        end
  
! 
!       # Returns a Hash (key as an interpro id and value as index key for 
!       # matches (Array).
!       #
!       #   report.list_of_interpro.each do |ipr_id, indexes|
!       #     indexes.each do |index|
!       #       report.matches[index].ipr_id == ipr_id #=> true
!       #     end
!       #   end
!       #
!       def list_of_interpro
!         @ipr_ids = {} unless @ipr_ids
!         @matches.each_with_index do |match, i|
!           @ipr_ids[match.ipr_id] = [] unless @ipr_ids[match.ipr_id]
!           @ipr_ids[match.ipr_id] << i
!         end
!         @ipr_ids
!       end
! 
! 
! 
!       # == Description
        # Container class for InterProScan matches.
        #
!       # == Usage
        #  match = Match.new(:query_id => ...)
        #
        #  match.ipr_id = 'IPR001234'
!       #  match.ipr_id #=> 'IPR001234'
        #
        class Match
***************
*** 306,310 ****
          def match_start;     @data[:match_start];     end
          # the descriotion of the InterPro entry.
!         def ipr_description; @data[:ipr_description]; end
  
          def method_missing(name, arg = nil)
--- 346,350 ----
          def match_start;     @data[:match_start];     end
          # the descriotion of the InterPro entry.
!         def ipr_odescription; @data[:ipr_description]; end
  
          def method_missing(name, arg = nil)