bio-assembly 0.0.0 → 0.0.1

data/README.rdoc

@@ -1,6 +1,15 @@
 = bio-assembly
 
-Description goes here.
+BioRuby plugin for parsing, writing, and maniuplating assembly data
+
+== Install
+
+gem install bio-assembly
+
+== Usage
+
+Examples on my blog:
+http://chasemiller4.blogspot.com/2010/10/bioruby-ace-parser-example.html
 
 == Contributing to bio-assembly
  

data/VERSION

@@ -1 +1 @@
-0.0.0
+0.0.1

data/bio-assembly.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-assembly}
-  s.version = "0.0.0"
+  s.version = "0.0.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Chase Miller"]
@@ -27,9 +27,9 @@ Gem::Specification.new do |s|
     "bio-assembly.gemspec",
     "data/example1.ace",
     "lib/bio-assembly.rb",
+    "lib/bio-assembly/ace.rb",
     "lib/bio-assembly/contig.rb",
     "lib/bio-assembly/read.rb",
-    "lib/bio-assembly/read/ace.rb",
     "test/helper.rb",
     "test/test_bio-assembly.rb"
   ]

data/lib/bio-assembly.rb

@@ -1,169 +1,55 @@
-
-require 'bio/sequence'
+require 'bio/sequence' 
 require 'bio-assembly/contig'
 require 'bio-assembly/read'
 
 module Bio
 
-  class Assembly
-    attr_accessor :contigs
-  
-    def initialize(path)
-      @file = File.new(path, 'r') 
-      @contigs = Array.new
-      parse_as
-    end
-    
-    def contigs
-      # use each_contig to stream large files
-      parse_whole_file if @contigs.empty?
-      @contigs
-    end
-  
-    def each_contig
-      # check if file is already parsed
-      if @total_num_contigs.to_i == @contigs.size
-        @contigs.each{ |contig| yield contig }
-      else
-        each_identifier do |identifier, attrs|
-          next unless identifier == 'CO'
-          contig = parse_contig(attrs)
-          @contigs.push contig
-          yield(contig)   
-        end
+   class Assembly
+      attr_accessor :contigs
+      
+      @@formats = { }
+    
+      def self.create(path, format)
+         streamer = @@formats[format]
+         if streamer
+            streamer.new(path)
+         else
+            raise "Format type '#{format}' is not supported"
+         end
       end
-    end
-    
-    def to_ace
-      ace = ""
-      ace += "AS " + num_contigs.to_s + " " + num_reads.to_s + "\n\n"
-      each_contig { |contig| ace += contig.to_ace + "\n" }
-      ace
-    end
-  
-    private
-  
-    def parse_contig(attrs)
-      contig = Bio::Assembly::Contig.new
-      contig.name, base_num, @num_reads, base_segments_num, contig.orientation = attrs.split(" ")
-      # keep track of the number of RD identifiers parsed
-      @num_rds_parsed = 0
       
-      # get sequence
-      seq = @file.gets("\n\n").tr(" \r\n", "")
-      contig.seq = seq
-    
-      # loop through identifiers (e.g AF, RD, etc)
-      each_identifier do |identifier, attrs|    
-        case identifier
-          when "BQ" then parse_bq(contig)
-          when "AF" then parse_af(contig, attrs)
-          when "BS" then parse_bs(contig, attrs)
-          when "RD" then parse_rd(contig, attrs); break if @num_rds_parsed == @num_reads.to_i
-          when "WR" then parse_wr(contig, attrs)
-          when "RT" then parse_rt(contig, attrs)
-          when "CT" then parse_ct(contig, attrs)
-          when "WA" then parse_wa(contig, attrs)
-        end
+      def self.register_parser name
+         @@formats[name] = self
       end
-     
-     contig
-    end
-  
-    # Finds the next_identifier
-    def each_identifier
-      @file.each do |line|
-        next if line !~ /^[ABCDQRW][ADFOQRST][\s\n].*/
-        yield(line[0..1], line[3..-1])
+      
+      def contigs
+        # use each_contig to stream large files
+        parse_whole_file if @contigs.empty?
+        @contigs
       end
-    end
-    
-    # parse assembly meta data
-    def parse_as
-      line = @file.gets
-      identifier, @total_num_contigs, total_num_reads = line.split(" ")
-    end
-  
-    # parse contig sequence quality data
-    def parse_bq(contig)
-      contig.quality = @file.gets("\n\n").tr("\r\n", "").gsub(/^\s/, "").split(' ')
-    end
-  
-    # parse read meta data
-    def parse_af(contig, attrs)
-      read = Bio::Assembly::Read.new
-      read.name , read.orientation, read.from = attrs.split(" ")
-      contig.add_read read
-    end
-  
-    # parse base sequence data
-    def parse_bs(contig, attrs)
-      from, to, read_name = attrs.split(" ")
-      read = contig.find_read_by_name( read_name )
-      read.add_base_sequence(from, to, read_name)
-    end
-  
-    # parse read sequence and position data
-    def parse_rd(contig, attrs)
-      # increment counter
-      @num_rds_parsed += 1
       
-      # parse read
-      read_name, num_padded_bases, num_read_infos, num_read_tags = attrs.split(" ") 
-      seq = @file.gets("\n\n").tr( " \r\n", "")
-    
-      # get read with matching name
-      read = contig.find_read_by_name( read_name )
-      read.seq = seq
-      read.to = read.from.to_i + read.seq.length
-      # set read.to to contig length if read runs off contig
-      read.to = contig.seq.length if read.to > contig.seq.length
-    
-      # if present parse QA and DS associated with this read
-      each_identifier do |identifier, attrs|
-        case identifier
-          when "QA" then parse_qa(read, attrs)
-          when "DS" then parse_ds(read, attrs); break
-        end
+      def each_contig
+         # implemented by each format subclass
+      end
+      
+      private
+      
+      def num_contigs
+        contigs.size
       end
-   
-    end
-  
-    # parse a read's clear ranges (the part of the read that contributes to the contig)
-    def parse_qa(read, attrs)
-      start, stop, clear_range_from, clear_range_to = attrs.split(" ")
-      read.clear_range_from = clear_range_from
-      read.clear_range_to = clear_range_to
-    end
-  
-    # parse file data - ignored
-    def parse_ds(read, attrs)
-    end
-  
-    # parse run meta data - ignored
-    def parse_wa(contig, attrs)
-    end
-    
-    # parse run meta data - ignored
-    def parse_ct(contig, attrs)
-    end
-    
-    def num_contigs
-      contigs.size
-    end
-    
-    def num_reads
-      read_num = 0
-      each_contig { |contig| read_num += contig.num_reads }
-      read_num
-    end
-    
-    def parse_whole_file
-      each_contig { |x| 1 }
-    end
-  
-  end
 
-end
+      def num_reads
+        read_num = 0
+        each_contig { |contig| read_num += contig.num_reads }
+        read_num
+      end
 
+      def parse_whole_file
+        each_contig { |x| 1 }
+      end
+    
+   end
+   
+end
 
+require 'bio-assembly/ace'

data/lib/bio-assembly/ace.rb

@@ -0,0 +1,258 @@
+
+module Bio
+class Assembly
+
+   class Ace < Bio::Assembly
+
+      # register parser with superclass
+      register_parser :ace
+
+      def initialize(path)
+         @file = File.new(path, 'r') 
+         @contigs = Array.new
+         parse_as
+       end
+
+      def each_contig
+        # check if file is already parsed
+        if @total_num_contigs.to_i == @contigs.size
+          @contigs.each{ |contig| yield contig }
+        else
+          each_identifier do |identifier, attrs|
+            next unless identifier == 'CO'
+            contig = parse_contig(attrs)
+            @contigs.push contig
+            yield(contig)   
+          end
+        end
+      end
+
+      def to_ace
+        ace = ""
+        ace += "AS " + num_contigs.to_s + " " + num_reads.to_s + "\n\n"
+        each_contig { |contig| ace += contig.to_ace + "\n" }
+        ace
+      end
+
+      private
+      def parse_contig(attrs)
+        contig = Bio::Assembly::Contig.new
+        contig.name, base_num, @num_reads, base_segments_num, contig.orientation = attrs.split(" ")
+        # keep track of the number of RD identifiers parsed
+        @num_rds_parsed = 0
+
+        # get sequence
+        seq = @file.gets("\n\n").tr(" \r\n", "")
+        contig.seq = seq
+
+        # loop through identifiers (e.g AF, RD, etc)
+        each_identifier do |identifier, attrs|    
+          case identifier
+            when "BQ" then parse_bq(contig)
+            when "AF" then parse_af(contig, attrs)
+            when "BS" then parse_bs(contig, attrs)
+            when "RD" then parse_rd(contig, attrs); break if @num_rds_parsed == @num_reads.to_i
+            when "WR" then parse_wr(contig, attrs)
+            when "RT" then parse_rt(contig, attrs)
+            when "CT" then parse_ct(contig, attrs)
+            when "WA" then parse_wa(contig, attrs)
+          end
+        end
+
+       contig
+      end
+
+      # Finds the next_identifier
+      def each_identifier
+        @file.each do |line|
+          next if line !~ /^[ABCDQRW][ADFOQRST][\s\n].*/
+          yield(line[0..1], line[3..-1])
+        end
+      end
+
+      # parse assembly meta data
+      def parse_as
+        line = @file.gets
+        identifier, @total_num_contigs, total_num_reads = line.split(" ")
+      end
+
+      # parse contig sequence quality data
+      def parse_bq(contig)
+        contig.quality = @file.gets("\n\n").tr("\r\n", "").gsub(/^\s/, "").split(' ')
+      end
+
+      # parse read meta data
+      def parse_af(contig, attrs)
+        read = Bio::Assembly::Read.new
+        read.name , read.orientation, read.from = attrs.split(" ")
+        contig.add_read read
+      end
+
+      # parse base sequence data
+      def parse_bs(contig, attrs)
+        from, to, read_name = attrs.split(" ")
+        read = contig.find_read_by_name( read_name )
+        read.add_base_sequence(from, to, read_name)
+      end
+
+      # parse read sequence and position data
+      def parse_rd(contig, attrs)
+        # increment counter
+        @num_rds_parsed += 1
+
+        # parse read
+        read_name, num_padded_bases, num_read_infos, num_read_tags = attrs.split(" ") 
+        seq = @file.gets("\n\n").tr( " \r\n", "")
+
+        # get read with matching name
+        read = contig.find_read_by_name( read_name )
+        read.seq = seq
+        read.to = read.from.to_i + read.seq.length
+        # set read.to to contig length if read runs off contig
+        read.to = contig.seq.length if read.to > contig.seq.length
+
+        # if present parse QA and DS associated with this read
+        each_identifier do |identifier, attrs|
+          case identifier
+            when "QA" then parse_qa(read, attrs)
+            when "DS" then parse_ds(read, attrs); break
+          end
+        end
+
+      end
+
+      # parse a read's clear ranges (the part of the read that contributes to the contig)
+      def parse_qa(read, attrs)
+        start, stop, clear_range_from, clear_range_to = attrs.split(" ")
+        read.clear_range_from = clear_range_from
+        read.clear_range_to = clear_range_to
+      end
+
+      # parse file data - ignored
+      def parse_ds(read, attrs)
+      end
+
+      # parse run meta data - ignored
+      def parse_wa(contig, attrs)
+      end
+
+      # parse run meta data - ignored
+      def parse_ct(contig, attrs)
+      end
+
+   end # => end class Ace
+   
+   # open contig class and write ace specific methods for contig objects         
+   class Contig
+
+      def to_ace
+        ace = ""
+        ace += ['CO', name, num_bases, num_reads, num_base_segments, orientation].join(' ') + "\n"
+        ace += seq.to_s.gsub(Regexp.new(".{1,50}"), "\\0\n") + "\n"
+        ace += "BQ\n"
+        last_stop = quality.size - 1
+        (quality.size/50+1).times do |i|
+          start = i * 50
+          stop = (i+1) * 50 - 1
+          stop = last_stop if stop > last_stop
+          ace += ' ' + quality[start..stop].join(' ')  + "\n"
+        end
+        ace += "\n"
+
+        # holds BS data for reads
+        bs_str = ""
+        # holds RD, QA, and DS data for reads 
+        rest_str = ""
+        @reads.values.sort.each do |read|
+          ace += read.to_ace_af
+          bs_str += read.to_ace_bs
+          rest_str += read.to_ace_rest
+        end
+
+        # compile data in correct order
+        ace += bs_str
+        ace += "\n"
+        ace += rest_str
+        ace
+      end
+         
+   end # => end Contig class
+   
+   # open Read class to add ace specific methods for read objects
+   class Read
+
+     attr_accessor :base_sequences
+  
+     def to_ace
+       ace += ""
+       # holds BS data for reads
+       bs_str = ""
+       # holds RD, QA, and DS data for reads 
+       rest_str = ""
+       ace += to_ace_af
+       bs_str += to_ace_bs
+       rest_str = to_ace_rest
+
+       # compile data in correct order
+       ace += bs_str
+       ace += "\n"
+       ace += rest_str
+       ace
+     end
+
+     def to_ace_bs
+       bs_str = ""
+       unless base_sequences.nil?
+         base_sequences.each do |bs|
+           bs_str += ['BS', bs.from, bs.to, bs.read_name].join(' ') + "\n"
+         end
+       end
+       bs_str
+     end
+
+     def to_ace_af
+       ['AF', name, orientation, from].join(' ') + "\n"
+     end
+
+     def to_ace_rest
+       rest_str = ""
+       rest_str += ['RD', name, num_bases, 0, 0].join(' ') + "\n"
+       rest_str += seq.to_s.gsub(Regexp.new(".{1,50}"), "\\0\n")  + "\n"
+       rest_str += ['QA', clear_range_from, clear_range_to, clear_range_from, clear_range_to].join(' ') + "\n"
+       rest_str += ['DS', 'CHROMAT_FILE:', name, 'PHD_FILE:', "#{name}.phd.1", 'TIME:', Time.now].join(' ') + "\n"
+       rest_str
+     end
+  
+     def add_base_sequence(from, to, read_name)
+       @base_sequences = Array.new if @base_sequences.nil?
+       @base_sequences.push BaseSequence.new(from, to, read_name)
+     end
+  
+     class BaseSequence
+        attr_accessor :from, :to, :read_name
+    
+        def initialize(from, to, read_name)
+           @from = from
+           @to = to
+           @read_name = read_name
+        end
+    
+        def <=>(other)
+           unless other.kind_of?(Bio::Assembly::Read::BaseSequence)
+              raise "[Error] markers are not comparable"
+           end
+           if self.from == other.from
+              # sort by to if froms are identical
+              return self.to.<=>(other.to)
+           else
+              return self.from.<=>(other.from)
+           end
+        end    
+  
+      end # => end BaseSequence Class
+
+   end # => end Read Class
+   
+
+end # => end class Assembly
+end # => end module Bio

data/lib/bio-assembly/contig.rb

@@ -1,3 +1,5 @@
+#require 'bio-assembly/contig/ace'
+
 module Bio
   class Assembly
     
@@ -59,39 +61,9 @@ module Bio
         end
         num_base_sequences
       end
-      
-      def to_ace
-        ace = ""
-        ace += ['CO', name, num_bases, num_reads, num_base_segments, orientation].join(' ') + "\n"
-        ace += seq.to_s.gsub(Regexp.new(".{1,50}"), "\\0\n") + "\n"
-        ace += "BQ\n"
-        last_stop = quality.size - 1
-        (quality.size/50+1).times do |i|
-          start = i * 50
-          stop = (i+1) * 50 - 1
-          stop = last_stop if stop > last_stop
-          ace += ' ' + quality[start..stop].join(' ')  + "\n"
-        end
-        ace += "\n"
-        
-        # holds BS data for reads
-        bs_str = ""
-        # holds RD, QA, and DS data for reads 
-        rest_str = ""
-        @reads.values.sort.each do |read|
-          ace += read.to_ace_af
-          bs_str += read.to_ace_bs
-          rest_str += read.to_ace_rest
-        end
-        
-        # compile data in correct order
-        ace += bs_str
-        ace += "\n"
-        ace += rest_str
-        ace
-      end
 
     end
     
   end
-end
+end
+

data/lib/bio-assembly/read.rb

@@ -1,10 +1,9 @@
 
-require 'bio-assembly/read/ace'
+#require 'bio-assembly/read/ace'
 
 module Bio
   class Assembly
     class Read 
-      include Bio::Assembly::Read::Ace
       
       attr_accessor :seq, :name, :orientation, :from, :to, :clear_range_from, :clear_range_to
       def initialize(str="")
@@ -34,24 +33,7 @@ module Bio
       def clear_range_to=(new_clear_range_to)
         @clear_range_to = new_clear_range_to.to_i
       end
-      
-      def to_ace
-        ace += ""
-        # holds BS data for reads
-        bs_str = ""
-        # holds RD, QA, and DS data for reads 
-        rest_str = ""
-        ace += to_ace_af
-        bs_str += to_ace_bs
-        rest_str = to_ace_rest
-        
-        # compile data in correct order
-        ace += bs_str
-        ace += "\n"
-        ace += rest_str
-        ace
-      end
-      
+            
       def <=>(other)
         unless other.kind_of?(Bio::Assembly::Read)
           raise "[Error] markers are not comparable"
@@ -64,29 +46,6 @@ module Bio
         end
       end
       
-      def to_ace_bs
-        bs_str = ""
-        unless base_sequences.nil?
-          base_sequences.each do |bs|
-            bs_str += ['BS', bs.from, bs.to, bs.read_name].join(' ') + "\n"
-          end
-        end
-        bs_str
-      end
-      
-      def to_ace_af
-        ['AF', name, orientation, from].join(' ') + "\n"
-      end
-      
-      def to_ace_rest
-        rest_str = ""
-        rest_str += ['RD', name, num_bases, 0, 0].join(' ') + "\n"
-        rest_str += seq.to_s.gsub(Regexp.new(".{1,50}"), "\\0\n")  + "\n"
-        rest_str += ['QA', clear_range_from, clear_range_to, clear_range_from, clear_range_to].join(' ') + "\n"
-        rest_str += ['DS', 'CHROMAT_FILE:', name, 'PHD_FILE:', "#{name}.phd.1", 'TIME:', Time.now].join(' ') + "\n"
-        rest_str
-      end
-      
     end
     
   end

data/test/test_bio-assembly.rb

@@ -4,7 +4,7 @@ class TestBioAssembly < Test::Unit::TestCase
 
      def setup
        ace_filename = File.join('data', 'example1.ace')
-       @obj = Bio::Assembly.new(ace_filename)
+       @obj = Bio::Assembly.create(ace_filename, :ace)
 
        # pick a contig to do in depth tests on
        @contig = nil

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: bio-assembly
 version: !ruby/object:Gem::Version 
-  hash: 31
+  hash: 29
   prerelease: false
   segments: 
   - 0
   - 0
-  - 0
-  version: 0.0.0
+  - 1
+  version: 0.0.1
 platform: ruby
 authors: 
 - Chase Miller
@@ -114,9 +114,9 @@ files:
 - bio-assembly.gemspec
 - data/example1.ace
 - lib/bio-assembly.rb
+- lib/bio-assembly/ace.rb
 - lib/bio-assembly/contig.rb
 - lib/bio-assembly/read.rb
-- lib/bio-assembly/read/ace.rb
 - test/helper.rb
 - test/test_bio-assembly.rb
 has_rdoc: true

data/lib/bio-assembly/read/ace.rb

@@ -1,39 +0,0 @@
-module Bio
-  class Assembly
-    class Read
-      
-      module Ace 
-        attr_accessor :base_sequences
-        
-        def add_base_sequence(from, to, read_name)
-          @base_sequences = Array.new if @base_sequences.nil?
-          @base_sequences.push BaseSequence.new(from, to, read_name)
-        end
-        
-        class BaseSequence
-          attr_accessor :from, :to, :read_name
-          
-          def initialize(from, to, read_name)
-            @from = from
-            @to = to
-            @read_name = read_name
-          end
-          
-          def <=>(other)
-            unless other.kind_of?(Bio::Assembly::Read::BaseSequence)
-              raise "[Error] markers are not comparable"
-            end
-            if self.from == other.from
-              # sort by to if froms are identical
-              return self.to.<=>(other.to)
-            else
-              return self.from.<=>(other.from)
-            end
-          end
-          
-        end
-        
-      end
-    end
-  end
-end