ms-core 0.0.10 → 0.0.11

data/Gemfile

@@ -2,6 +2,7 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
+gem 'bio', '>= 1.4.1'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/Gemfile.lock

@@ -2,6 +2,7 @@ GEM
   remote: http://rubygems.org/
   specs:
     bacon (1.1.0)
+    bio (1.4.1)
     git (1.2.5)
     jeweler (1.5.2)
       bundler (~> 1.0.0)
@@ -16,6 +17,7 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
+  bio (>= 1.4.1)
   bundler (~> 1.0.0)
   jeweler (~> 1.5.2)
   rcov

data/VERSION

@@ -1 +1 @@
-0.0.10
+0.0.11

data/lib/ms/fasta.rb

@@ -0,0 +1,59 @@
+require 'bio'
+
+class Bio::FlatFile
+  include Enumerable
+end
+
+class Bio::FastaFormat
+  alias_method :header, :definition
+  alias_method :sequence, :seq
+end
+
+module Ms
+  # A convenience class for working with fasta formatted sequence databases.
+  # the file which includes this class also includes Enumerable with
+  # Bio::FlatFile so you can do things like this:
+  #
+  #     accessions = Ms::Fasta.open("file.fasta") do |fasta| 
+  #       fasta.map(&:accession)
+  #     end
+  # 
+  # A few aliases are added to Bio::FastaFormat
+  #
+  #     entry.header == entry.definition
+  #     entry.sequence == entry.seq
+  #
+  # Ms::Fasta.new accepts both an IO object or a String (a fasta formatted
+  # string itself)
+  #
+  #     # taking an io object:
+  #     File.open("file.fasta") do |io| 
+  #       fasta = Ms::Fasta.new(io)
+  #       ... do something with it
+  #     end
+  #     # taking a string
+  #     string = ">id1 a simple header\nAAASDDEEEDDD\n>id2 header again\nPPPPPPWWWWWWTTTTYY\n"
+  #     fasta = Ms::Fasta.new(string)
+  #     (simple, not_simple) = fasta.partition {|entry| entry.header =~ /simple/ }
+  module Fasta
+
+    # opens the flatfile and yields a Bio::FlatFile object
+    def self.open(file, &block)
+      Bio::FlatFile.open(Bio::FastaFormat, file, &block)
+    end
+
+    # yields each Bio::FastaFormat object in turn
+    def self.foreach(file, &block)
+      Bio::FlatFile.open(Bio::FastaFormat, file) do |fasta|
+        fasta.each(&block)
+      end
+    end
+
+    # takes an IO object or a string that is the fasta data itself
+    def self.new(io)
+      io = StringIO.new(io) if io.is_a?(String)
+      Bio::FlatFile.new(Bio::FastaFormat, io)
+    end
+
+  end
+end

data/spec/ms/fasta_spec.rb

@@ -0,0 +1,96 @@
+require 'spec_helper'
+
+require 'ms/fasta'
+
+describe 'basic fasta operations' do
+  before do
+    @headers = [">gi|5524211 [hello]", ">another B", ">again C"]
+    @entries = ["LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV\nGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX\nIENY", "ABCDEF\nGHIJK", "ABCD"]
+    @sequences = @entries.map {|v| v.gsub("\n", '') }
+    @data = {}
+    @data['newlines'] = @headers.zip(@entries).map do |header, data|
+      header + "\n" + data
+    end.join("\n")
+    @data['carriage_returns_and_newlines'] = @data['newlines'].gsub("\n", "\r\n")
+    file_key_to_filename_pairs = @data.map do |k,v|
+      file_key = k + '_file'
+      filename = k + '.tmp'
+      File.open(filename, 'w') {|out| out.print v }
+      [file_key, filename]
+    end
+    file_key_to_filename_pairs.each {|k,v| @data[k] = v }
+  end
+
+  after do
+    @data.select {|k,v| k =~ /_file$/ }.each do |k,filename|
+      index = filename.sub('.tmp', '.index')
+      [filename, index].each do |fn|
+        File.unlink(fn) if File.exist? fn
+      end
+    end
+  end
+
+  def fasta_correct?(fasta)
+    entries = fasta.map
+    @headers.size.times.zip(entries) do |i,entry|
+      header, sequence, entry = @headers[i], @sequences[i], entry
+      entry.header.isnt nil
+      entry.sequence.isnt nil
+      entry.header.is header[1..-1]
+      entry.sequence.is sequence
+    end
+  end
+
+  it 'can read a file' do
+    %w(newlines_file carriage_returns_and_newlines_file).each do |file|
+      Ms::Fasta.open(@data[file]) do |fasta|
+        fasta_correct? fasta
+      end
+    end
+  end
+
+  it 'can read an IO object' do
+    %w(newlines_file carriage_returns_and_newlines_file).each do |file|
+      File.open(@data[file]) do |io|
+        fasta = Ms::Fasta.new(io)
+        fasta_correct? fasta
+      end
+    end
+  end
+
+  it 'can read a string' do
+    %w(newlines carriage_returns_and_newlines).each do |key|
+      fasta = Ms::Fasta.new @data[key]
+      fasta_correct? fasta
+    end
+  end
+
+  it 'iterates entries with foreach' do
+    %w(newlines_file carriage_returns_and_newlines_file).each do |file|
+      Ms::Fasta.foreach(@data[file]) do |entry|
+        entry.isa Bio::FastaFormat
+      end
+    end
+  end
+
+  it 'runs the documentation' do
+    fasta_file = @data['newlines_file']
+    ids = Ms::Fasta.open(fasta_file) do |fasta| 
+      fasta.map(&:entry_id)
+    end
+    ids.is_a?(Array)
+    ids.enums %w(gi|5524211 another again)
+   
+    # this code is already tested above
+    # File.open(fasta_file) do |io| 
+    #   fasta = Ms::Fasta.new(io)
+    # end
+
+    # taking a string
+    string = ">id1 a simple header\nAAASDDEEEDDD\n>id2 header again\nPPPPPPWWWWWWTTTTYY\n"
+    fasta = Ms::Fasta.new(string)
+    (simple, not_simple) = fasta.partition {|entry| entry.header =~ /simple/ }
+    simple.first.header.include?("simple").is true
+    not_simple.first.header.include?("simple").is false
+  end
+end

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 10
-  version: 0.0.10
+  - 11
+  version: 0.0.11
 platform: ruby
 authors: 
 - John T. Prince
@@ -19,8 +19,23 @@ date: 2011-02-24 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: spec-more
+  name: bio
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 4
+        - 1
+        version: 1.4.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: spec-more
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -30,10 +45,10 @@ dependencies:
         version: "0"
   type: :development
   prerelease: false
-  version_requirements: *id001
+  version_requirements: *id002
 - !ruby/object:Gem::Dependency 
   name: bundler
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -45,10 +60,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *id002
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: jeweler
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -60,10 +75,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *id003
+  version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: rcov
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -73,7 +88,7 @@ dependencies:
         version: "0"
   type: :development
   prerelease: false
-  version_requirements: *id004
+  version_requirements: *id005
 description: basic, shared functionality for mspire libraries
 email: jtprince@gmail.com
 executables: []
@@ -101,6 +116,7 @@ files:
 - lib/ms/data/lazy_string.rb
 - lib/ms/data/simple.rb
 - 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
@@ -112,6 +128,7 @@ files:
 - lib/openany.rb
 - spec/ms/calc_spec.rb
 - spec/ms/data_spec.rb
+- spec/ms/fasta_spec.rb
 - spec/ms/mass/aa_spec.rb
 - spec/ms/support/binary_search_spec.rb
 - spec/spec_helper.rb
@@ -129,7 +146,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -2752488455848385314
+      hash: -4553226932043159578
       segments: 
       - 0
       version: "0"
@@ -151,6 +168,7 @@ summary: basic, shared functionality for mspire libraries
 test_files: 
 - spec/ms/calc_spec.rb
 - spec/ms/data_spec.rb
+- spec/ms/fasta_spec.rb
 - spec/ms/mass/aa_spec.rb
 - spec/ms/support/binary_search_spec.rb
 - spec/spec_helper.rb