ms-uniprot 0.1.0

data/History

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+== 0.1.0 / 2009-03-30
+
+Initial release with a task to retrieve fasta
+entries.

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-Uniprot}[http://mspire.rubyforge.org/projects/ms-uniprot]
+
+An {Mspire}[http://mspire.rubyforge.org] library for working with {UniProt}[http://www.uniprot.org/].
+
+== Description
+
+* Lighthouse[http://bahuvrihi.lighthouseapp.com/projects/16692-mspire/tickets]
+* Github[http://github.com/bahuvrihi/ms-uniprot/tree/master]
+* {Google Group}[http://groups.google.com/group/mspire-forum]
+
+== Installation
+
+Ms-Uniprot is available as a gem on RubyForge[http://rubyforge.org/projects/mspire].  Use:
+
+  % gem install ms-uniprot
+
+== 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/uniprot/entry.rb

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+require 'net/http'
+
+module Ms
+  module Uniprot
+    
+    # :startdoc::manifest gets a UniProt entry
+    #
+    # Retrieves the UniProt entry for the specified accession number by making
+    # an HTTP get request to the UniProt website.  The format obviously
+    # specifies the result format; different formats typically contain
+    # different information.  These are the available formats (02/2009):
+    #
+    #   * fasta
+    #   * txt
+    #   * xml
+    #   * rdf
+    #   * gff
+    #
+    # Examples:
+    #
+    #   % rap uniprot/entry P08246 --: dump
+    #   % rap uniprot/entry P08246 --format xml --: dump
+    #
+    class Entry < Tap::Task
+      FORMATS = %w{fasta txt xml rdf gff}
+      
+      config :uniprot_url, "http://www.uniprot.org/"  # The url of UniProt
+      config :format, 'fasta', &c.select(*FORMATS)    # The entry format
+      
+      def uri(accession)
+        File.join(uniprot_url, "uniprot", "#{accession}.#{format}")
+      end
+      
+      def process(accession)
+        Net::HTTP.get URI.parse(uri(accession))
+      end
+    end
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: ms-uniprot
+version: !ruby/object:Gem::Version 
+  version: 0.1.0
+platform: ruby
+authors: 
+- Simon Chiang
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-03-30 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: configurable
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.4.2
+    version: 
+- !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: 
+description: 
+email: simon.a.chiang@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History
+- README
+- MIT-LICENSE
+files: 
+- lib/ms/uniprot/entry.rb
+- tap.yml
+- History
+- README
+- MIT-LICENSE
+has_rdoc: true
+homepage: http://rubyforge.org/projects/ms-uniprot/
+post_install_message: 
+rdoc_options: 
+- --main
+- README
+- -S
+- -N
+- --title
+- Ms-Uniprot
+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-uniprot
+test_files: []
+