unipept 2.1.1 → 2.2.2
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/.github/dependabot.yml +9 -0
- data/.github/workflows/ci.yml +6 -27
- data/.rakeTasks +7 -0
- data/.rubocop.yml +2 -0
- data/.ruby-version +1 -1
- data/CITATION.cff +30 -0
- data/Gemfile +2 -2
- data/Gemfile.lock +60 -41
- data/README.md +2 -2
- data/Rakefile +4 -4
- data/VERSION +1 -1
- data/lib/batch_iterator.rb +16 -0
- data/lib/commands/prot2pept.rb +1 -2
- data/lib/commands/unipept/api_runner.rb +10 -12
- data/lib/commands/unipept/config.rb +1 -1
- data/lib/commands/unipept/pept2taxa.rb +1 -5
- data/lib/commands/unipept/taxa2tree.rb +74 -0
- data/lib/commands/unipept.rb +25 -1
- data/lib/commands/uniprot.rb +4 -5
- data/lib/configuration.rb +6 -7
- data/lib/formatters.rb +108 -36
- data/lib/server_message.rb +2 -4
- data/test/commands/unipept/test_api_runner.rb +8 -7
- data/test/commands/unipept/test_config.rb +1 -1
- data/test/commands/unipept/test_pept2ec.rb +11 -11
- data/test/commands/unipept/test_pept2funct.rb +15 -15
- data/test/commands/unipept/test_pept2go.rb +10 -10
- data/test/commands/unipept/test_pept2interpro.rb +26 -26
- data/test/commands/unipept/test_pept2lca.rb +2 -2
- data/test/commands/unipept/test_pept2prot.rb +2 -2
- data/test/commands/unipept/test_pept2taxa.rb +2 -4
- data/test/commands/unipept/test_peptinfo.rb +16 -16
- data/test/commands/unipept/test_taxa2lca.rb +2 -2
- data/test/commands/unipept/test_taxa2tree.rb +68 -0
- data/test/commands/unipept/test_taxonomy.rb +2 -2
- data/test/helper.rb +10 -0
- data/test/support/api_stub.rb +60 -0
- data/test/support/resources/pept2ec.json +55 -0
- data/test/support/resources/pept2funct.json +73 -0
- data/test/support/resources/pept2go.json +43 -0
- data/test/support/resources/pept2interpro.json +43 -0
- data/test/support/resources/pept2lca.json +14 -0
- data/test/support/resources/pept2prot.json +422 -0
- data/test/support/resources/pept2taxa.json +194 -0
- data/test/support/resources/peptinfo.json +70 -0
- data/test/support/resources/taxa2tree.json +194 -0
- data/test/support/resources/taxonomy.json +22 -0
- data/test/test_configuration.rb +1 -1
- data/test/test_formatters.rb +5 -5
- data/test/test_output_writer.rb +1 -1
- data/test/test_server_message.rb +2 -2
- data/test.taxa +4 -0
- data/unipept.gemspec +32 -21
- metadata +26 -9
data/unipept.gemspec
CHANGED
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@@ -1,17 +1,17 @@
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-
# Generated by
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# Generated by juwelier
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit
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# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: unipept 2.
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# stub: unipept 2.2.2 ruby lib
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Gem::Specification.new do |s|
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s.name = "unipept".freeze
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s.version = "2.
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s.version = "2.2.2"
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s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
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s.require_paths = ["lib".freeze]
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s.authors = ["Bart Mesuere".freeze, "Pieter Verschaffelt".freeze, "Toon Willems".freeze, "Tom Naessens".freeze]
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s.date = "
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s.date = "2022-04-13"
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s.description = " Command line interface to the Unipept (http://unipept.ugent.be) web services\n (pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility\n commands for handling proteins using the command line.\n".freeze
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s.email = "unipept@ugent.be".freeze
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s.executables = ["unipept".freeze, "prot2pept".freeze, "peptfilter".freeze, "uniprot".freeze]
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]
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s.files = [
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".document",
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".github/dependabot.yml",
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".github/workflows/ci.yml",
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".rakeTasks",
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".rubocop.yml",
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".ruby-version",
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"CITATION.cff",
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"Gemfile",
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"Gemfile.lock",
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"LICENSE.txt",
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@@ -51,6 +54,7 @@ Gem::Specification.new do |s|
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"lib/commands/unipept/pept2taxa.rb",
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"lib/commands/unipept/peptinfo.rb",
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"lib/commands/unipept/taxa2lca.rb",
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"lib/commands/unipept/taxa2tree.rb",
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"lib/commands/unipept/taxonomy.rb",
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"lib/commands/uniprot.rb",
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"lib/configuration.rb",
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"lib/retryable_typhoeus.rb",
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"lib/server_message.rb",
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"lib/version.rb",
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"test.taxa",
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"test/commands/test_peptfilter.rb",
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"test/commands/test_prot2pept.rb",
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"test/commands/test_unipept.rb",
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"test/commands/unipept/test_pept2taxa.rb",
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"test/commands/unipept/test_peptinfo.rb",
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"test/commands/unipept/test_taxa2lca.rb",
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"test/commands/unipept/test_taxa2tree.rb",
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"test/commands/unipept/test_taxonomy.rb",
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"test/helper.rb",
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"test/support/api_stub.rb",
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"test/support/resources/pept2ec.json",
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"test/support/resources/pept2funct.json",
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"test/support/resources/pept2go.json",
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"test/support/resources/pept2interpro.json",
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"test/support/resources/pept2lca.json",
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"test/support/resources/pept2prot.json",
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"test/support/resources/pept2taxa.json",
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"test/support/resources/peptinfo.json",
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"test/support/resources/taxa2tree.json",
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"test/support/resources/taxonomy.json",
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"test/test_batch_iterator.rb",
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"test/test_batch_order.rb",
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"test/test_configuration.rb",
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]
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s.homepage = "http://unipept.ugent.be".freeze
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s.licenses = ["MIT".freeze]
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s.required_ruby_version = Gem::Requirement.new(">= 2.
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s.rubygems_version = "3.
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s.required_ruby_version = Gem::Requirement.new(">= 2.6.0".freeze)
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s.rubygems_version = "3.1.4".freeze
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s.summary = "Command line interface to Unipept web services.".freeze
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if s.respond_to? :specification_version then
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s.specification_version = 4
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end
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else
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s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
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s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
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s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
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s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
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s.add_dependency(%q<rubocop>.freeze, ["~> 0.79.0"])
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end
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if s.respond_to? :add_runtime_dependency then
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s.add_runtime_dependency(%q<cri>.freeze, ["~> 2.15.10"])
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s.add_runtime_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
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s.add_development_dependency(%q<minitest>.freeze, ["~> 5.14"])
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s.add_development_dependency(%q<rake>.freeze, ["~> 13.0.1"])
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s.add_development_dependency(%q<rubocop>.freeze, ["~> 1.11"])
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else
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s.add_dependency(%q<cri>.freeze, ["~> 2.15.10"])
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s.add_dependency(%q<typhoeus>.freeze, ["~> 1.3.1"])
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s.add_dependency(%q<minitest>.freeze, ["~> 5.14"])
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s.add_dependency(%q<rake>.freeze, ["~> 13.0.1"])
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s.add_dependency(%q<rubocop>.freeze, ["~>
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s.add_dependency(%q<rubocop>.freeze, ["~> 1.11"])
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end
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end
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: unipept
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version: !ruby/object:Gem::Version
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version: 2.
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version: 2.2.2
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platform: ruby
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authors:
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- Bart Mesuere
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- Pieter Verschaffelt
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- Toon Willems
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- Tom Naessens
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autorequire:
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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: 2022-04-13 00:00:00.000000000 Z
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dependencies:
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name: cri
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requirements:
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version:
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version: '1.11'
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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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version:
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version: '1.11'
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description: |2
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Command line interface to the Unipept (http://unipept.ugent.be) web services
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(pept2lca, taxa2lca, pept2taxa, pept2prot and taxonomy) and some utility
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- README.md
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files:
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- ".document"
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- ".github/dependabot.yml"
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- ".github/workflows/ci.yml"
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- ".rakeTasks"
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- ".rubocop.yml"
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- ".ruby-version"
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- CITATION.cff
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- Gemfile
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- Gemfile.lock
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- LICENSE.txt
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- lib/commands/unipept/pept2taxa.rb
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- lib/commands/unipept/peptinfo.rb
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- lib/commands/unipept/taxa2lca.rb
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- lib/commands/unipept/taxa2tree.rb
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- lib/commands/unipept/taxonomy.rb
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- lib/commands/uniprot.rb
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- lib/configuration.rb
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- lib/retryable_typhoeus.rb
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- lib/server_message.rb
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- lib/version.rb
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- test.taxa
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- test/commands/test_peptfilter.rb
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- test/commands/test_prot2pept.rb
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- test/commands/test_unipept.rb
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- test/commands/unipept/test_peptinfo.rb
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- test/commands/unipept/test_taxa2lca.rb
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- test/commands/unipept/test_taxa2tree.rb
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- test/commands/unipept/test_taxonomy.rb
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- test/helper.rb
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- test/support/api_stub.rb
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- test/support/resources/pept2ec.json
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- test/support/resources/pept2funct.json
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- test/support/resources/pept2go.json
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- test/support/resources/pept2interpro.json
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- test/support/resources/pept2lca.json
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- test/support/resources/pept2prot.json
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- test/support/resources/pept2taxa.json
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- test/support/resources/peptinfo.json
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- test/support/resources/taxonomy.json
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licenses:
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- MIT
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metadata: {}
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post_install_message:
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post_install_message:
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rdoc_options: []
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require_paths:
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requirements:
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version: 2.
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version: 2.6.0
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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version: '0'
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requirements: []
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rubygems_version: 3.
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signing_key:
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rubygems_version: 3.1.4
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signing_key:
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specification_version: 4
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summary: Command line interface to Unipept web services.
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test_files: []
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