ms-core 0.0.13 → 0.0.14

data/VERSION

@@ -1 +1 @@
-0.0.13
+0.0.14

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 13
-  version: 0.0.13
+  - 14
+  version: 0.0.14
 platform: ruby
 authors: 
 - John T. Prince
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-28 00:00:00 -07:00
+date: 2011-03-09 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -118,9 +118,6 @@ files:
 - lib/ms/data/transposed.rb
 - lib/ms/fasta.rb
 - lib/ms/format/format_error.rb
-- lib/ms/id/peptide.rb
-- lib/ms/id/protein.rb
-- lib/ms/id/search.rb
 - lib/ms/mass.rb
 - lib/ms/mass/aa.rb
 - lib/ms/spectrum.rb
@@ -146,7 +143,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -1109965199117656197
+      hash: 1895205922860773162
       segments: 
       - 0
       version: "0"

data/lib/ms/id/peptide.rb

@@ -1,76 +0,0 @@
-
-module Ms ; end
-module Ms::Id ; end
-
-# A 'sequence' is a notation of a peptide that includes the leading and
-# trailing amino acid after cleavage (e.g., K.PEPTIDER.E or -.STARTK.L )
-# and may contain post-translational modification information.
-#
-# 'aaseq' is the amino acid sequence of just the peptide with no leading or
-# trailing notation (e.g., PEPTIDER or LAKKLY)
-module Ms::Id::Peptide
-  Nonstandard_AA_re = /[^A-Z\.\-]/
-  
-  class << self
-
-    def sequence_to_aaseq(sequence)
-      after_removed = remove_non_amino_acids(sequence)
-      pieces = after_removed.split('.') 
-      case pieces.size
-      when 3
-        pieces[1]
-      when 2
-        if pieces[0].size > 1  ## N termini
-          pieces[0]
-        else  ## C termini
-          pieces[1]
-        end
-      when 1  ## this must be a parse error!
-        pieces[0] ## which is the peptide itself  
-      else
-        abort "bad peptide sequence: #{sequence.inspect}"
-      end
-    end
-
-    # removes non standard amino acids specified by Nonstandard_AA_re
-    def remove_non_amino_acids(sequence)
-      sequence.gsub(Nonstandard_AA_re, '')
-    end
-
-    # remove non amino acids and split the sequence
-    def prepare_sequence(sequence)
-      nv = remove_non_amino_acids(sequence)
-      split_sequence(nv)
-    end
-
-    # Returns prev, peptide, next from sequence.  Parse errors return
-    # nil,nil,nil
-    #   R.PEPTIDE.A  # -> R, PEPTIDE, A
-    #   R.PEPTIDE.-  # -> R, PEPTIDE, -
-    #   PEPTIDE.A    # -> -, PEPTIDE, A
-    #   A.PEPTIDE    # -> A, PEPTIDE, -
-    #   PEPTIDE      # -> nil,nil,nil
-    def split_sequence(sequence)
-      peptide_prev_aa = ""; peptide = ""; peptide_next_aa = ""
-      pieces = sequence.split('.') 
-      case pieces.size
-      when 3
-        peptide_prev_aa, peptide, peptide_next_aa = *pieces
-      when 2
-        if pieces[0].size > 1  ## N termini
-          peptide_prev_aa, peptide, peptide_next_aa = '-', pieces[0], pieces[1]
-        else  ## C termini
-          peptide_prev_aa, peptide, peptide_next_aa = pieces[0], pieces[1], '-'
-        end
-      when 1  ## this must be a parse error!
-        peptide_prev_aa, peptide, peptide_next_aa = nil,nil,nil
-      when 0
-        peptide_prev_aa, peptide, peptide_next_aa = nil,nil,nil
-      end
-      return peptide_prev_aa, peptide, peptide_next_aa
-    end
-
-  end
-
-
-end

data/lib/ms/id/protein.rb

@@ -1,17 +0,0 @@
-
-module Ms ; end
-module Ms::Id ; end
-
-module Ms::Id::Protein
-  
-  class << self
-  end
-
-  # gives the information up until the first space or carriage return.
-  # Assumes the protein can respond_to? :reference
-  def first_entry
-    reference.split(/[\s\r]/)[0]
-  end
-
-end
-

data/lib/ms/id/search.rb

@@ -1,110 +0,0 @@
-
-module Ms
-  module Id
-
-    module Search
-      attr_accessor :prots
-      attr_accessor :peps
-
-      def protein_class
-        self.const_get("Prot")
-      end
-
-
-      # returns an array of peptide_hits and protein_hits that are linked to
-      # one another.  NOTE: this will update peptide and protein
-      # hits :prots and :peps attributes respectively).  Assumes that each search
-      # responds to :peps, each peptide responds to :prots and each protein to
-      # :peps.  Can be done on a single file to restore protein/peptide
-      # linkages to their original single-file state.
-      # Assumes the protein is initialized with (reference, peptide_ar)
-      #
-      # yields the protein that will become the template for a new protein
-      # and expects a new protein hit
-      def merge!(ar_of_peptide_hit_arrays)
-        all_peptide_hits = []
-        reference_hash = {}
-        ar_of_peptide_hit_arrays.each do |peptide_hits|
-          all_peptide_hits.push(*peptide_hits)
-          peptide_hits.each do |pep|
-            pep.prots.each do |prot|
-              ref = prot.reference
-              if reference_hash.key? ref
-                reference_hash[ref].peps << pep
-                reference_hash[ref]
-              else
-                reference_hash[ref] = yield(prot, [pep])
-              end
-            end
-          end
-        end
-        [all_peptide_hits, reference_hash.values]
-      end
-
-    end
-
-
-    module SearchGroup 
-      include Search
-
-      # an array of search objects
-      attr_accessor :searches
-      
-      # the group's file extension (with no leading period)
-      def extension
-        'grp'
-      end
-
-      def search_class
-        Search
-      end
-
-      # a simple formatted file with paths to the search files
-      def to_paths(file)
-        IO.readlines(file).grep(/\w/).reject {|v| v =~ /^#/}.map {|v| v.chomp }
-      end
-
-      def from_file(file)
-        from_filenames(to_paths(file))
-      end
-
-
-      def from_filenames(filenames)
-        filenames.each do |file|
-          if !File.exist? file
-            message = "File: #{file} does not exist!\n"
-            message << "perhaps you need to modify the file with file paths"
-            abort message
-          end
-          @searches << search_class.new(file)
-        end
-      end
-
-
-      # takes an array of filenames or a single search filename (with
-      # extension defined by 'extendsion') or an array of objects passes any
-      # arguments to the initializer for each search
-      # the optional block yields the object for further processing
-      def initialize(arg=nil, opts={})
-        @peps = []
-        @reference_hash = {}
-        @searches = []
-
-        if arg
-          if arg.is_a?(String) && arg =~ /\.#{Regexp.escap(extension)}$/
-            from_file(arg)
-          elsif arg.is_a?(Array) && arg.first.is_a?(String)
-            from_filenames(arg)
-          elsif arg.is_a?(Array)
-            @searches = array
-          else
-            raise ArgumentError, "must be file, array of filenames, or array of objs"
-          end
-          @searches << search_class.new(file, opts)
-        end
-        yield(self) if block_given?
-      end
-
-    end
-  end
-end