ms-fasta 0.2.0 → 0.2.3

data/History

@@ -1,3 +1,18 @@
+== 0.2.3 / 2009-06-17
+
+* added Ms::Fasta.new and Ms::Fasta.open methods and specs
+* Ms::Fasta::Archive parsing can handle fasta files with "\r\n"
+
+== 0.2.2
+
+* transfered tests into specs
+* version determined by Ms::Fasta::VERSION
+
+== 0.2.1
+
+* reworked load/fasta to load fasta off a stream
+* refactored the previous load/fasta to select/fasta
+
 == 0.2.0 / 2009-05-06
 
 * updated to use tap-0.17.0
@@ -6,4 +21,4 @@
 == 0.1.0 / 2009-03-24
 
 Initial release with tasks to load entries
-from a FASTA file.
+from a FASTA file.

data/lib/ms/fasta.rb

@@ -0,0 +1,16 @@
+require 'ms/fasta/archive'
+
+module Ms
+  module Fasta
+    VERSION = '0.2.3'
+
+    def self.new(*args, &block)
+      Ms::Fasta::Archive.new(*args, &block).reindex
+    end
+
+    def self.open(*args, &block)
+      Ms::Fasta::Archive.open(*args, &block)
+    end
+
+  end
+end

data/lib/ms/fasta/archive.rb

@@ -18,4 +18,4 @@ module Ms
 
     end
   end
-end
+end

data/lib/ms/fasta/entry.rb

@@ -25,7 +25,7 @@ module Ms
             raise "input should begin with '>'"
           end
 
-          seq_begin = str.index("\n")
+          seq_begin = str.index(/\r?\n/)
           Entry.new(str[1, seq_begin-1], str[seq_begin, str.length - seq_begin].gsub(/\r?\n/, ""))
         end
       end
@@ -72,4 +72,4 @@ module Ms
       end
     end
   end
-end
+end

data/lib/ms/load/fasta.rb

@@ -1,29 +1,44 @@
-require 'ms/fasta/archive'
+require 'tap/tasks/load'
+require 'ms/fasta/entry'
 
 module Ms
   module Load
     # :startdoc::task loads entries in a fasta file
     #
-    # Loads entries from a fasta file.  Entries are returned as an array and
-    # by default as Ms::Fasta::Entry objects.
+    # Loads entries from a fasta file.
     #
-    class Fasta < Tap::Task
+    class Fasta < Tap::Tasks::Load
+      Entry = Ms::Fasta::Entry
       
-      config :range, 0..10, &c.range     # the range of entries to select
-      config :fasta, false, &c.switch    # returns entries as fasta strings
+      config :header, true, &c.switch
+      config :sequence, true, &c.switch
+      
+      def entry_break?(io)
+        if c = io.getc
+          io.ungetc(c)
+          c == ?>
+        else
+          true
+        end
+      end
+      
+      def load(io)
+        header = io.readline
+        sequence = []
+        while !entry_break?(io)
+          sequence << io.readline
+        end
         
-      def process(fasta_file)
-        Ms::Fasta::Archive.open(fasta_file) do |archive|
-          entries = archive[range]
-          
-          # totally wasteful... ExternalArchive needs
-          # a way to read a selection of string without
-          # conversion to entries.
-          # watch (http://bahuvrihi.lighthouseapp.com/projects/10590-external/tickets/7-for-strings)
-          entries.collect! {|entry| entry.to_s } if fasta
-          entries
+        case
+        when !self.header
+          sequence.join('')
+        when !self.sequence
+          header
+        else
+          "#{header}#{sequence.join('')}"
         end
       end
+      
     end 
   end
 end

data/lib/ms/random/fasta.rb

@@ -9,9 +9,9 @@ module Ms
     #
     class Fasta < Tap::Task
   
-      config :n, 1, &c.integer           # the number of fasta to select
-      config :fasta, false, &c.switch    # returns entries as fasta strings
-      config :distinct, true, &c.switch  # requires entries to be unique by sequence
+      config :n, 1, &c.integer           # The number of fasta to select
+      config :fasta, false, &c.switch    # Returns entries as fasta strings
+      config :distinct, true, &c.switch  # Requires entries to be unique by sequence
     
       def process(fasta_file)
         entries = []

data/lib/ms/select/fasta.rb

@@ -0,0 +1,29 @@
+require 'ms/fasta/archive'
+
+module Ms
+  module Select
+    # :startdoc::task selects entries from a fasta file
+    #
+    # Load the selected entries from a fasta file.  Entries are returned as an
+    # array and by default as Ms::Fasta::Entry objects.
+    #
+    class Fasta < Tap::Task
+      
+      config :range, 0..10, &c.range     # The range of entries to select
+      config :fasta, false, &c.switch    # Returns entries as fasta strings
+        
+      def process(fasta_file)
+        Ms::Fasta::Archive.open(fasta_file) do |archive|
+          entries = archive[range]
+          
+          # totally wasteful... ExternalArchive needs
+          # a way to read a selection of string without
+          # conversion to entries.
+          # watch (http://bahuvrihi.lighthouseapp.com/projects/10590-external/tickets/7-for-strings)
+          entries.collect! {|entry| entry.to_s } if fasta
+          entries
+        end
+      end
+    end 
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ms-fasta
 version: !ruby/object:Gem::Version 
-  version: 0.2.0
+  version: 0.2.3
 platform: ruby
 authors: 
 - Simon Chiang
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-05-06 00:00:00 -06:00
+date: 2009-06-17 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -20,7 +20,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.17.0
+        version: 0.17.1
     version: 
 - !ruby/object:Gem::Dependency 
   name: tap-test
@@ -50,23 +50,25 @@ extensions: []
 
 extra_rdoc_files: 
 - History
-- README
+- README.rdoc
 - MIT-LICENSE
 files: 
+- lib/ms/fasta.rb
 - lib/ms/fasta/archive.rb
 - lib/ms/fasta/entry.rb
 - lib/ms/load/fasta.rb
 - lib/ms/random/fasta.rb
+- lib/ms/select/fasta.rb
 - tap.yml
 - History
-- README
+- README.rdoc
 - MIT-LICENSE
 has_rdoc: true
 homepage: http://mspire.rubyforge.org/projects/ms-fasta
 post_install_message: 
 rdoc_options: 
 - --main
-- README
+- README.rdoc
 - -S
 - -N
 - --title