ms-fasta 0.4.0 → 0.4.1

data/VERSION

@@ -1 +1 @@
-0.4.0
+0.4.1

data/lib/ms/fasta.rb

@@ -1,4 +1,5 @@
 require 'ms/fasta/archive'
+require 'ms/fasta/header'
 
 module Ms
   module Fasta
@@ -20,61 +21,7 @@ module Ms
       end
     end
 
-    # returns :ipi, :ncbi, or nil if can't be determined
-    def self.filetype(file_or_io)
-      ft = nil
-      io = 
-        if file_or_io.is_a?(String)
-          File.open(file_or_io)
-        else
-          init_pos = file_or_io.pos
-          file_or_io.rewind
-          file_or_io
-        end
-      io.each_line do |line|
-        if line =~ /^>/
-          ft = header_to_filetype(line[1..-1])
-          break
-        end
-      end
-
-      if file_or_io.is_a?(String)
-        io.close
-      else
-        io.pos = init_pos
-      end
-      ft
-    end
-
-    # takes the header line (no leading >) and returns the kind of file
-    def self.header_to_filetype(line)
-      if line =~ /^IPI\:/
-        :ipi
-      elsif line =~ /^gi\|/
-        :ncbi
-      else
-        nil
-      end
-    end
-
-    # kind is :ipi or :ncbi or a String (the header)
-    # gives the regular expression for parsing the header (no leading >)
-    def self.id_regexp(kind)
-      sym = 
-        if kind.is_a?(String)
-          header_to_filetype(kind)
-        else ; kind
-        end
-      case sym
-      when :ipi
-        /^IPI:(.*?)\|/o
-      when :ncbi
-        /^gi\|(.*?)\|/o
-      else
-        nil
-      end
-    end
-
+    extend Ms::Fasta::Header
   end
 end
 

data/lib/ms/fasta/header.rb

@@ -0,0 +1,66 @@
+
+module Ms
+  module Fasta
+    module Header
+      # scans for a header and returns the results of header_to_filetype
+      def filetype(file_or_io)
+        ft = nil
+        io = 
+          if file_or_io.is_a?(String)
+            File.open(file_or_io)
+          else
+            init_pos = file_or_io.pos
+            file_or_io.rewind
+            file_or_io
+          end
+        io.each_line do |line|
+          if line =~ /^>/
+            ft = header_to_filetype(line[1..-1])
+            break
+          end
+        end
+
+        if file_or_io.is_a?(String)
+          io.close
+        else
+          io.pos = init_pos
+        end
+        ft
+      end
+
+      # takes the header line (no leading >) and returns the kind of file
+      def header_to_filetype(line)
+        if line =~ /^sp|tr\|/
+          :uniprot
+        elsif line =~ /^IPI\:/
+          :ipi
+        elsif line =~ /^gi\|/
+          :ncbi
+        else
+          nil
+        end
+      end
+
+      # kind is :uniprot, :ipi, :ncbi or a String (the header)
+      # gives the regular expression for parsing the header (no leading >)
+      def id_regexp(kind)
+        sym = 
+          if kind.is_a?(String)
+            header_to_filetype(kind)
+          else ; kind
+          end
+        case sym
+        when :uniprot
+          /^[st][pr]\|(.*?)\|/o
+        when :ipi
+          /^IPI:(.*?)\|/o
+        when :ncbi
+          /^gi\|(.*?)\|/o
+        else
+          nil
+        end
+      end
+      extend self
+    end
+  end
+end

data/spec/ms/fasta/archive_spec.rb

@@ -2,7 +2,7 @@ require File.join(File.dirname(__FILE__), '../../spec_helper.rb')
 require 'ms/fasta/archive'
 
 class FastaAchiveSpec
-  include Ms::Fasta
+  include 
 
   describe 'fasta archive operations' do
 
@@ -19,7 +19,7 @@ PROTEIN
     it 'reindexes' do
       strio = StringIO.new(FASTA_0 + FASTA_1)
       begin
-        a = Archive.new(strio)
+        a = Ms::Fasta::Archive.new(strio)
 
         a.length.is 0
         a.reindex
@@ -35,10 +35,10 @@ PROTEIN
 
     it 'properly converts the fasta string to an entry object' do
       begin
-        a = Archive.new
+        a = Ms::Fasta::Archive.new
         e = a.str_to_entry(FASTA_0)
 
-        e.isa Entry
+        e.isa Ms::Fasta::Entry
         e.header.is "gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]"
         e.sequence.is("LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV" + "GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX" + "IENY")
       ensure

data/spec/ms/fasta/entry_spec.rb

@@ -2,7 +2,6 @@ require File.join(File.dirname(__FILE__), '../../spec_helper.rb')
 require 'ms/fasta/entry'
 
 class FastaEntryTest
-  include Ms::Fasta
   
   describe 'basic Entry operations' do
     # Abbreviated FASTA entry from wikipedia (http://en.wikipedia.org/wiki/FASTA_format)
@@ -17,7 +16,7 @@ IENY
     #
 
     it 'parses an entry as per docs' do
-      entry = Entry.parse %q{
+      entry = Ms::Fasta::Entry.parse %q{
 >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
 LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
 EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
@@ -35,7 +34,7 @@ IENY
     #
 
     it 'parses header and sequence' do
-      e = Entry.parse(FASTA_0)
+      e = Ms::Fasta::Entry.parse(FASTA_0)
       e.header.is "gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]"
       e.sequence.is(
         "LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV" +
@@ -44,7 +43,7 @@ IENY
 
     it 'raises error for entries that do not start with gt' do
       
-      lambda { Entry.parse "\n#{FASTA_0}" }.should.raise(RuntimeError).message.should.equal("input should begin with '>'")
+      lambda { Ms::Fasta::Entry.parse "\n#{FASTA_0}" }.should.raise(RuntimeError).message.should.equal("input should begin with '>'")
     end
 
     #
@@ -52,11 +51,11 @@ IENY
     #
 
     def test_entry_initialization
-      e = Entry.new
+      e = Ms::Fasta::Entry.new
       assert_equal("", e.header)
       assert_equal("", e.sequence)
 
-      e = Entry.new "head", "SEQ"
+      e = Ms::Fasta::Entry.new "head", "SEQ"
       assert_equal("head", e.header)
       assert_equal("SEQ", e.sequence)
     end
@@ -66,20 +65,20 @@ IENY
     #
 
     def test_dump_formats_a_fasta_entry
-      e = Entry.new
+      e = Ms::Fasta::Entry.new
       assert_equal(">\n", e.dump)
 
-      e = Entry.new "head", "SEQ"
+      e = Ms::Fasta::Entry.new "head", "SEQ"
       assert_equal(">head\nSEQ\n", e.dump)
     end
 
     def test_dump_formats_output_with_desired_line_length
-      e = Entry.new "header", "ABCDEFGH"
+      e = Ms::Fasta::Entry.new "header", "ABCDEFGH"
       assert_equal(">header\nABC\nDEF\nGH\n", e.dump("", :line_length => 3))
     end
 
     def test_dump_line_length_less_than_1_raises_error
-      e = Entry.new
+      e = Ms::Fasta::Entry.new
       assert_raise(ArgumentError) { e.dump("", :line_length => 0) }
     end
   end

data/spec/ms/fasta/header_spec.rb

@@ -0,0 +1,63 @@
+require File.join(File.dirname(__FILE__), '../../spec_helper.rb') 
+
+require 'ms/fasta'
+require 'ms/fasta/header'
+
+shared 'determining filetype based on the header' do
+
+  before do
+    @header_lines = {
+      :ipi => ['IPI:IPI00000005.1|SWISS-PROT:P01111|TREMBL:Q5U091|ENSEMBL:ENSP00000358548;ENSP00000385392|REFSEQ:NP_002515|VEGA:OTTHUMP00000013879 Tax_Id=9606 Gene_Symbol=NRAS GTPase NRas'],
+      :uniprot => ['sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3', 'tr|D3DSH8|D3DSH8_HUMAN HCG2036819, isoform CRA_a OS=Homo sapiens GN=hCG_2036819 PE=4 SV=1'],
+      :ncbi => ['gi|16127999|ref|NP_414546.1| hypothetical protein b0005 [Escherichia coli K12]'],
+    }
+  end
+
+  xit 'can return the filetype given a file or io object' do
+    # need to write this
+  end
+
+  it 'returns a filetype or nil given a header line' do
+    @header_lines.each do |k,array|
+      array.each do |v|
+        @klass.header_to_filetype(v).is k
+      end
+    end
+  end
+
+  it 'returns a regular expression that retrieves the ID from a header' do
+    # A basic example:
+    header = "tr|D3DSH8|D3DSH8_HUMAN HCG2036819, iso ..."
+    regexp1 = @klass.id_regexp(:uniprot)
+    regexp2 = @klass.id_regexp(header)
+    regexp1.is regexp2
+    header.match(regexp1)[1].is "D3DSH8"
+
+    # exhaustively test:
+    {:ipi => %w(IPI00000005.1), :uniprot => %w(P31946 D3DSH8), :ncbi => %w(16127999)}.each do |symbol,v|
+      @header_lines[symbol].each do |header|
+        to_equal = v.shift
+        # takes either a header line (no >)
+        [symbol, header].each do |query|
+          regexp = @klass.id_regexp(query)
+          header.match(regexp)[1].is to_equal
+        end
+      end
+    end
+  end
+
+end
+
+describe 'Ms::Fasta::Header' do
+  before do
+    @klass = Ms::Fasta::Header
+  end
+  behaves_like 'determining filetype based on the header'
+end
+
+describe 'Ms::Fasta' do
+  before do
+    @klass = Ms::Fasta
+  end
+  behaves_like 'determining filetype based on the header'
+end

data/spec/ms/fasta/ipi_spec.rb

@@ -2,33 +2,29 @@ require File.dirname(__FILE__) + '/../../spec_helper'
 
 require 'ms/fasta/ipi'
 
-class IpiSpec
-  include Ms::Fasta
+describe 'basic IPI operations' do
 
-  describe 'basic IPI operations' do
+  before do
+    @headers = ['IPI:IPI00000001.2|SWISS-PROT:O95793-1|TREMBL:A8K622;Q59F99|ENSEMBL:ENSP00000360922;ENSP00000379466|REFSEQ:NP_059347|H-INV:HIT000329496|VEGA:OTTHUMP00000031233 Tax_Id=9606 Gene_Symbol=STAU1 Isoform Long of Double-stranded RNA-binding protein Staufen homolog 1',
+      'IPI:IPI00000005.1|SWISS-PROT:P01111|TREMBL:Q5U091|ENSEMBL:ENSP00000358548;ENSP00000385392|REFSEQ:NP_002515|VEGA:OTTHUMP00000013879 Tax_Id=9606 Gene_Symbol=NRAS GTPase NRas']
 
-    before do
-      @headers = ['IPI:IPI00000001.2|SWISS-PROT:O95793-1|TREMBL:A8K622;Q59F99|ENSEMBL:ENSP00000360922;ENSP00000379466|REFSEQ:NP_059347|H-INV:HIT000329496|VEGA:OTTHUMP00000031233 Tax_Id=9606 Gene_Symbol=STAU1 Isoform Long of Double-stranded RNA-binding protein Staufen homolog 1',
-        'IPI:IPI00000005.1|SWISS-PROT:P01111|TREMBL:Q5U091|ENSEMBL:ENSP00000358548;ENSP00000385392|REFSEQ:NP_002515|VEGA:OTTHUMP00000013879 Tax_Id=9606 Gene_Symbol=NRAS GTPase NRas']
-
-      @answers = [{"Gene_Symbol"=>"STAU1", "VEGA"=>"OTTHUMP00000031233", "IPI"=>"IPI00000001.2", "H-INV"=>"HIT000329496", "REFSEQ"=>"NP_059347", "Tax_Id"=>"9606", "SWISS-PROT"=>"O95793-1", "ENSEMBL"=>"ENSP00000360922;ENSP00000379466", "TREMBL"=>"A8K622;Q59F99", "description"=>"Isoform Long of Double-stranded RNA-binding protein Staufen homolog 1"},
-        {"Gene_Symbol"=>"NRAS", "VEGA"=>"OTTHUMP00000013879", "IPI"=>"IPI00000005.1", "REFSEQ"=>"NP_002515", "Tax_Id"=>"9606", "SWISS-PROT"=>"P01111", "ENSEMBL"=>"ENSP00000358548;ENSP00000385392", "TREMBL"=>"Q5U091", "description"=>"GTPase NRas"}]
-    end
+    @answers = [{"Gene_Symbol"=>"STAU1", "VEGA"=>"OTTHUMP00000031233", "IPI"=>"IPI00000001.2", "H-INV"=>"HIT000329496", "REFSEQ"=>"NP_059347", "Tax_Id"=>"9606", "SWISS-PROT"=>"O95793-1", "ENSEMBL"=>"ENSP00000360922;ENSP00000379466", "TREMBL"=>"A8K622;Q59F99", "description"=>"Isoform Long of Double-stranded RNA-binding protein Staufen homolog 1"},
+      {"Gene_Symbol"=>"NRAS", "VEGA"=>"OTTHUMP00000013879", "IPI"=>"IPI00000005.1", "REFSEQ"=>"NP_002515", "Tax_Id"=>"9606", "SWISS-PROT"=>"P01111", "ENSEMBL"=>"ENSP00000358548;ENSP00000385392", "TREMBL"=>"Q5U091", "description"=>"GTPase NRas"}]
+  end
 
-    it 'parses IPI headers' do
-      # assumes that the leading '>' has been removed
-      @headers.zip(@answers) do |header, answ|
-        Ipi.parse(header).is answ
-      end
+  it 'parses IPI headers' do
+    # assumes that the leading '>' has been removed
+    @headers.zip(@answers) do |header, answ|
+      Ms::Fasta::Ipi.parse(header).is answ
     end
+  end
 
-    it 'can retrive the IPI ID' do
-      answers = ["IPI00000001.2", "IPI00000005.1"]
+  it 'can retrive the IPI ID' do
+    answers = ["IPI00000001.2", "IPI00000005.1"]
 
-      @headers.zip(answers) do |header, answ|
-        Ipi.ipi(header).is answ
-      end
+    @headers.zip(answers) do |header, answ|
+      Ms::Fasta::Ipi.ipi(header).is answ
     end
-
   end
+
 end

data/spec/ms/fasta_spec.rb

@@ -13,16 +13,17 @@ describe 'basic fasta operations' do
       header + "\n" + data
     end.join("\n")
     @data['carriage_returns_and_newlines'] = @data['newlines'].gsub("\n", "\r\n")
+    @files = {}
     @data.each do |k,v|
       file_key = k + '_file'
       filename = k + '.tmp'
-      @data[file_key] = filename
+      @files[file_key] = filename
       File.open(filename, 'w') {|out| out.print v }
     end
   end
 
   after do
-    @data.select {|k,v| k =~ /_file$/ }.each do |k,filename|
+    @files.select {|k,v| k =~ /_file$/ }.each do |k,filename|
       index = filename.sub('.tmp', '.index')
       [filename, index].each do |fn|
         File.unlink(fn) if File.exist? fn
@@ -43,7 +44,7 @@ describe 'basic fasta operations' do
 
   it 'can read a file' do
     %w(newlines_file carriage_returns_and_newlines_file).each do |file|
-      Ms::Fasta.open(@data[file]) do |fasta|
+      Ms::Fasta.open(@files[file]) do |fasta|
         fasta_correct? fasta
       end
     end
@@ -51,7 +52,7 @@ describe 'basic fasta operations' do
 
   it 'can read an IO object' do
     %w(newlines_file carriage_returns_and_newlines_file).each do |file|
-      File.open(@data[file]) do |io|
+      File.open(@files[file]) do |io|
         fasta = Ms::Fasta.new(io)
         fasta_correct? fasta
       end
@@ -67,7 +68,7 @@ describe 'basic fasta operations' do
 
   it 'iterates entries with foreach' do
     %w(newlines_file carriage_returns_and_newlines_file).each do |file|
-      Ms::Fasta.foreach(@data[file]) do |entry|
+      Ms::Fasta.foreach(@files[file]) do |entry|
         entry.isa Ms::Fasta::Entry 
       end
     end

metadata

@@ -1,7 +1,12 @@
 --- !ruby/object:Gem::Specification 
 name: ms-fasta
 version: !ruby/object:Gem::Version 
-  version: 0.4.0
+  prerelease: false
+  segments: 
+  - 0
+  - 4
+  - 1
+  version: 0.4.1
 platform: ruby
 authors: 
 - John T. Prince
@@ -9,19 +14,23 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-12-09 00:00:00 -07:00
+date: 2010-06-28 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: spec-more
-  type: :development
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 1
+        - 0
         version: 1.1.0
-    version: 
+  type: :development
+  version_requirements: *id001
 description: provides programmatic access to fasta files
 email: jtprince@gmail.com
 executables: []
@@ -41,6 +50,7 @@ files:
 - lib/ms/fasta.rb
 - lib/ms/fasta/archive.rb
 - lib/ms/fasta/entry.rb
+- lib/ms/fasta/header.rb
 - lib/ms/fasta/ipi.rb
 - lib/ms/fasta/ipi/dat.rb
 - lib/ms/load/fasta.rb
@@ -48,7 +58,7 @@ files:
 - lib/ms/select/fasta.rb
 - spec/ms/fasta/archive_spec.rb
 - spec/ms/fasta/entry_spec.rb
-- spec/ms/fasta/ipi/dat_spec.rb
+- spec/ms/fasta/header_spec.rb
 - spec/ms/fasta/ipi_spec.rb
 - spec/ms/fasta_spec.rb
 - spec/spec_helper.rb
@@ -66,25 +76,27 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
-  version: 
 required_rubygems_version: !ruby/object:Gem::Requirement 
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      segments: 
+      - 0
       version: "0"
-  version: 
 requirements: []
 
 rubyforge_project: mspire
-rubygems_version: 1.3.5
+rubygems_version: 1.3.6
 signing_key: 
 specification_version: 3
 summary: An mspire library for working with fasta formatted files
 test_files: 
 - spec/ms/fasta/archive_spec.rb
 - spec/ms/fasta/ipi_spec.rb
-- spec/ms/fasta/ipi/dat_spec.rb
+- spec/ms/fasta/header_spec.rb
 - spec/ms/fasta/entry_spec.rb
 - spec/ms/fasta_spec.rb
 - spec/spec_helper.rb

data/spec/ms/fasta/ipi/dat_spec.rb

@@ -1,7 +0,0 @@
-require File.dirname(__FILE__) + '/../../../spec_helper'
-
-require 'ms/fasta/ipi/dat'
-
-class IpiDatSpec
-  
-end