ms-fasta 0.1.0

data/History

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+== 0.1.0 / 2009-03-24
+
+Initial release with tasks to load entries
+from a FASTA file.

data/MIT-LICENSE

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+Copyright (c) 2009, Regents of the University of Colorado.
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use,
+copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.

data/README

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+= {Ms-Fasta}[http://mspire.rubyforge.org/projects/ms-fasta]
+
+An {Mspire}[http://mspire.rubyforge.org] library for working with {FASTA}[http://en.wikipedia.org/wiki/Fasta_format] files.
+
+== Description
+
+* Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/16692-mspire/tickets]
+* Github[http://github.com/bahuvrihi/ms-fasta/tree/master]
+* {Google Group}[http://groups.google.com/group/mspire-forum]
+
+== Installation
+
+Ms-Fasta is available as a gem on RubyForge[http://rubyforge.org/projects/mspire].  Use:
+
+  % gem install ms-fasta
+
+== Info 
+
+Copyright (c) 2009, Regents of the University of Colorado.
+Developer:: {Simon Chiang}[http://bahuvrihi.wordpress.com], {Biomolecular Structure Program}[http://biomol.uchsc.edu/], {Hansen Lab}[http://hsc-proteomics.uchsc.edu/hansenlab/] 
+Support:: CU Denver School of Medicine Deans Academic Enrichment Fund
+Licence:: {MIT-Style}[link:files/MIT-LICENSE.html]

data/lib/ms/fasta/archive.rb

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+require 'external'
+require 'ms/fasta/entry'
+
+module Ms
+  module Fasta
+    # Provides access to a FASTA file as an ExternalArchive.
+    class Archive < ExternalArchive
+
+      # Reindexes self to each FASTA entry in io
+      def reindex(&block)
+        reindex_by_sep(nil, :sep_regexp => /\n>/, :sep_length => 1, :entry_follows_sep => true, &block)
+      end
+
+      # Returns a Fasta::Entry initialized using str
+      def str_to_entry(str)
+        Entry.parse(str)
+      end
+
+    end
+  end
+end

data/lib/ms/fasta/entry.rb

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+module Ms
+  module Fasta
+
+    # Entry represents a FASTA formatted entry. 
+    #
+    #   entry = Entry.parse %q{
+    #   >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
+    #   LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
+    #   EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
+    #   LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
+    #   GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
+    #   IENY
+    #   }.strip
+    #
+    #   entry.header[0,30]       # => 'gi|5524211|gb|AAD44166.1| cyto'
+    #   entry.sequence[0,30]     # => 'LCLYTHIGRNIYYGSYLYSETWNTGIMLLL'
+    #
+    class Entry
+      class << self
+
+        # Parses the entry string into a Fasta::Entry.  The entry string must
+        # be well-formatted, ie begin with '>'.
+        def parse(str)
+          unless str[0] == ?>
+            raise "input should begin with '>'"
+          end
+
+          seq_begin = str.index("\n")
+          Entry.new(str[1, seq_begin-1], str[seq_begin, str.length - seq_begin].gsub(/\r?\n/, ""))
+        end
+      end
+      
+      # The header for self
+      attr_accessor :header
+      
+      # The sequence of self
+      attr_accessor :sequence
+
+      def initialize(header="", sequence="")
+        @header = header
+        @sequence = sequence
+      end
+
+      # Returns the header and sequence formated into lines of line_length
+      # or less.  The '>' delimiter is added to the header line.
+      def lines(line_length=70)
+        raise ArgumentError.new("line length must be greater than 0") unless line_length > 0
+
+        lines = [">#{header}"]
+        current = 0
+        while current < sequence.length
+          lines << sequence[current, line_length]
+          current += line_length
+        end
+
+        lines
+      end
+
+      # Formats and dumps self to the target.  Use the options to modify the output:
+      #
+      # line_length:: the length of each output line (default 70)
+      def dump(target="", options={})
+        line_length = options.has_key?(:line_length) ? options[:line_length ] : 70
+        target << self.lines(line_length).join("\n")
+        target << "\n"
+        target
+      end
+
+      # Returns self formatted as a string
+      def to_s
+        dump
+      end
+    end
+  end
+end

data/lib/ms/load/fasta.rb

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+require 'ms/fasta/archive'
+
+module Ms
+  module Load
+    # :startdoc::manifest 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.
+    #
+    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

data/lib/ms/load/random_fasta.rb

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+require 'ms/fasta/archive'
+
+module Ms
+  module Load
+    # :startdoc::manifest selects n random fasta entries
+    #
+    # Selects random fasta entries from a fasta file. Entries are returned as
+    # an array, and by default as Ms::Fasta::Entry objects.
+    #
+    class RandomFasta < 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
+    
+      def process(fasta_file)
+        entries = []
+      
+        log :index, fasta_file unless File.exist?("#{fasta_file}.index")
+        Ms::Fasta::Archive.open(fasta_file) do |archive|
+          total_entries = archive.length
+          log :select, "#{n} entries"
+        
+          # pick entries, filtering by sequence
+          while entries.length < n
+            entry = archive[rand(total_entries)]
+            next if distinct && entries.find {|existing| existing.sequence == entry.sequence }
+          
+            entries << entry
+          end
+        end
+      
+        entries.collect! do |entry|
+          entry.to_s
+        end if fasta
+      
+        entries
+      end
+    end
+  end 
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: ms-fasta
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Simon Chiang
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-03-24 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: tap
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.12.4
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: external
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.3.0
+    version: 
+description: 
+email: simon.a.chiang@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History
+- README
+- MIT-LICENSE
+files: 
+- lib/ms/fasta/archive.rb
+- lib/ms/fasta/entry.rb
+- lib/ms/load/fasta.rb
+- lib/ms/load/random_fasta.rb
+- tap.yml
+- History
+- README
+- MIT-LICENSE
+has_rdoc: true
+homepage: http://mspire.rubyforge.org/projects/ms-fasta
+post_install_message: 
+rdoc_options: 
+- --main
+- README
+- -S
+- -N
+- --title
+- Ms-Fasta
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: mspire
+rubygems_version: 1.3.1
+signing_key: 
+specification_version: 2
+summary: ms-fasta
+test_files: []
+