viral_seq 1.0.6 → 1.0.11
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile.lock +6 -4
- data/README.md +116 -45
- data/bin/locator +31 -9
- data/bin/tcs +454 -0
- data/lib/viral_seq.rb +4 -1
- data/lib/viral_seq/constant.rb +5 -1
- data/lib/viral_seq/hash.rb +1 -1
- data/lib/viral_seq/hivdr.rb +1 -1
- data/lib/viral_seq/muscle.rb +2 -2
- data/lib/viral_seq/sdrm.rb +43 -0
- data/lib/viral_seq/seq_hash.rb +173 -42
- data/lib/viral_seq/seq_hash_pair.rb +16 -6
- data/lib/viral_seq/tcs_core.rb +305 -0
- data/lib/viral_seq/tcs_json.rb +178 -0
- data/lib/viral_seq/version.rb +2 -1
- data/viral_seq.gemspec +5 -1
- metadata +24 -5
data/lib/viral_seq/version.rb
CHANGED
data/viral_seq.gemspec
CHANGED
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@@ -26,10 +26,14 @@ Gem::Specification.new do |spec|
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spec.post_install_message = "Thanks for installing!"
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spec.add_development_dependency "bundler", "~> 2.0"
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-
spec.add_development_dependency "rake", "~>
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+
spec.add_development_dependency "rake", "~> 13.0"
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spec.add_development_dependency "rspec", "~> 3.0"
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# muscle_bio gem required
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spec.add_runtime_dependency "muscle_bio", "~> 0.4"
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+
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# colorize gem required
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spec.add_runtime_dependency "colorize", "~> 0.1"
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+
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spec.requirements << 'R required for some functions'
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end
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
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--- !ruby/object:Gem::Specification
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name: viral_seq
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version: !ruby/object:Gem::Version
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-
version: 1.0.
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4
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version: 1.0.11
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platform: ruby
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authors:
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- Shuntai Zhou
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2021-03-02 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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@@ -31,14 +31,14 @@ dependencies:
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '
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version: '13.0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '
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version: '13.0'
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement: !ruby/object:Gem::Requirement
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@@ -67,6 +67,20 @@ dependencies:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.4'
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- !ruby/object:Gem::Dependency
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name: colorize
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.1'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '0.1'
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description: |-
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A Ruby Gem with bioinformatics tools for processing viral NGS data.
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Specifically for Primer-ID sequencing and HIV drug resistance analysis.
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@@ -75,6 +89,7 @@ email:
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- clarkmu@gmail.com
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executables:
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- locator
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- tcs
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extensions: []
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extra_rdoc_files: []
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files:
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@@ -88,6 +103,7 @@ files:
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- README.md
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- Rakefile
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- bin/locator
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- bin/tcs
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- lib/viral_seq.rb
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- lib/viral_seq/constant.rb
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- lib/viral_seq/enumerable.rb
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@@ -98,10 +114,13 @@ files:
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- lib/viral_seq/pid.rb
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- lib/viral_seq/ref_seq.rb
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- lib/viral_seq/rubystats.rb
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- lib/viral_seq/sdrm.rb
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- lib/viral_seq/seq_hash.rb
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- lib/viral_seq/seq_hash_pair.rb
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- lib/viral_seq/sequence.rb
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- lib/viral_seq/string.rb
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- lib/viral_seq/tcs_core.rb
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- lib/viral_seq/tcs_json.rb
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- lib/viral_seq/version.rb
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- viral_seq.gemspec
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homepage: https://github.com/ViralSeq/viral_seq
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@@ -124,7 +143,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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version: '0'
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requirements:
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- R required for some functions
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rubygems_version: 3.
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rubygems_version: 3.2.2
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signing_key:
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specification_version: 4
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summary: A Ruby Gem containing bioinformatics tools for processing viral NGS data.
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