viral_seq 0.3.0

data/lib/viral_seq/version.rb

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+# lib/version.rb
+# version info and histroy
+
+module ViralSeq
+  VERSION = "0.3.0"
+end

data/lib/viral_seq.rb

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+# Copyright (c) 2019 Shuntai Zhou (shuntai.zhou@gmail.com)
+#
+# 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.
+
+# viral_seq main
+module ViralSeq; end
+
+# load all modules
+
+require "viral_seq/version"
+require "viral_seq/sequence"
+require "viral_seq/math"
+require "viral_seq/fasta"
+require "viral_seq/misc"
+require "viral_seq/refseq"
+require "viral_seq/locator"
+require "viral_seq/muscle"
+require "viral_seq/tcs_core.rb"
+require "viral_seq/poisson_cutoff"
+require "viral_seq/a3g"
+require "viral_seq/sdrm_core"
+require "viral_seq/hcv_dr"
+require "viral_seq/nt_variation"
+
+require "muscle_bio"

data/viral_seq.gemspec

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+
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "viral_seq/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "viral_seq"
+  spec.version       = ViralSeq::VERSION
+  spec.authors       = ["Shuntai Zhou", "Michael Clark"]
+  spec.email         = ["shuntai.zhou@gmail.com", "clarkmu@gmail.com"]
+
+  spec.summary       = %q{A Ruby Gem containing bioinformatics tools for processing viral NGS data.}
+  spec.description   = %q{Specifically for Primer-ID sequencing and HIV drug resistance analysis.}
+  spec.homepage      = "https://github.com/ViralSeq/viral_seq"
+  spec.license       = "MIT"
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files         = Dir.chdir(File.expand_path('..', __FILE__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  end
+  spec.bindir        = "exe"
+  # spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }\
+  spec.require_paths = ["lib"]
+  spec.post_install_message = "Thanks for installing!"
+
+  spec.add_development_dependency "bundler", "~> 2.0"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+
+  # muscle_bio gem required
+  spec.add_runtime_dependency "muscle_bio", "~> 0.4"
+
+
+  spec.requirements << 'MUSCLE (http://www.drive5.com/muscle) required for some functions'
+  spec.requirements << 'R required for some functions'
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: viral_seq
+version: !ruby/object:Gem::Version
+  version: 0.3.0
+platform: ruby
+authors:
+- Shuntai Zhou
+- Michael Clark
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2019-06-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+- !ruby/object:Gem::Dependency
+  name: muscle_bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.4'
+description: Specifically for Primer-ID sequencing and HIV drug resistance analysis.
+email:
+- shuntai.zhou@gmail.com
+- clarkmu@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/viral_seq.rb
+- lib/viral_seq/a3g.rb
+- lib/viral_seq/fasta.rb
+- lib/viral_seq/hcv_dr.rb
+- lib/viral_seq/locator.rb
+- lib/viral_seq/math.rb
+- lib/viral_seq/misc.rb
+- lib/viral_seq/muscle.rb
+- lib/viral_seq/nt_variation.rb
+- lib/viral_seq/poisson_cutoff.rb
+- lib/viral_seq/refseq.rb
+- lib/viral_seq/sdrm_core.rb
+- lib/viral_seq/sequence.rb
+- lib/viral_seq/tcs_core.rb
+- lib/viral_seq/version.rb
+- viral_seq.gemspec
+homepage: https://github.com/ViralSeq/viral_seq
+licenses:
+- MIT
+metadata: {}
+post_install_message: Thanks for installing!
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements:
+- MUSCLE (http://www.drive5.com/muscle) required for some functions
+- R required for some functions
+rubygems_version: 3.0.3
+signing_key: 
+specification_version: 4
+summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.
+test_files: []