unipept 0.7.1 → 0.8.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 2c9ac26e6bcc27b4bc9c5f7a31ef8c4dba1682a4
+  metadata.gz: 2079ea0c1b40f957d73ba24d167f5ec468f71c5e
+  data.tar.gz: c9a508bdc4a5293d5801e8bfba74dc8c52d641a8
 SHA512:
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+  data.tar.gz: c411d49dc862f28bbde1edafe74f7b2275c0b9735cea484d3fb75f43ecaf4f3d2e51141a409db7ea35b8d9864178f233986731fa1b2e64817be104aefee1afb2

data/.rubocop.yml

@@ -0,0 +1,26 @@
+AllCops:
+  Include:
+    -
+  Exclude:
+    - 'unipept.gemspec'
+    - 'vendor/**/*'
+
+Style/ClassAndModuleChildren:
+  EnforcedStyle: compact
+  Enabled: false
+
+# disable for now
+Style/ClassVars:
+  Enabled: false
+Style/Documentation:
+  Enabled: false
+Style/RescueModifier:
+  Enabled: false
+Metrics/AbcSize:
+  Enabled: false
+Metrics/ClassLength:
+  Enabled: false
+Metrics/LineLength:
+  Enabled: false
+Metrics/MethodLength:
+  Enabled: false

data/.travis.yml

@@ -0,0 +1,7 @@
+language: ruby
+rvm:
+  - 2.2.2
+  - 2.1.6
+  - 2.0.0
+  - 1.9.3
+  - jruby-19mode

data/Gemfile

@@ -1,17 +1,15 @@
-source "http://rubygems.org"
+source 'http://rubygems.org'
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
 
-gem "cri", "~> 2.7"
-gem "typhoeus", "~> 0.6"
+gem 'cri', '~> 2.7'
+gem 'typhoeus', '~> 0.6'
 
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "shoulda", "~> 3.5"
-  gem "rdoc", "~> 3.12"
-  gem "bundler", "~> 1.0"
-  gem "jeweler", "~> 2.0"
-  gem "simplecov", "~> 0.8"
+  gem 'rake'
+  gem 'minitest'
+  gem 'rubocop'
+  gem 'jeweler'
+  gem 'coveralls', require: false
 end

data/Gemfile.lock

@@ -1,15 +1,18 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activesupport (4.2.1)
-      i18n (~> 0.7)
-      json (~> 1.7, >= 1.7.7)
-      minitest (~> 5.1)
-      thread_safe (~> 0.3, >= 0.3.4)
-      tzinfo (~> 1.1)
     addressable (2.3.8)
+    ast (2.0.0)
+    astrolabe (1.3.0)
+      parser (>= 2.2.0.pre.3, < 3.0)
     builder (3.2.2)
     colored (1.2)
+    coveralls (0.7.1)
+      multi_json (~> 1.3)
+      rest-client
+      simplecov (>= 0.7)
+      term-ansicolor
+      thor
     cri (2.7.0)
       colored (~> 1.2)
     descendants_tracker (0.0.4)
@@ -31,7 +34,6 @@ GEM
       oauth2
     hashie (3.4.1)
     highline (1.7.2)
-    i18n (0.7.0)
     jeweler (2.0.1)
       builder
       bundler (>= 1.0)
@@ -43,11 +45,13 @@ GEM
       rdoc
     json (1.8.2)
     jwt (1.4.1)
+    mime-types (2.4.3)
     mini_portile (0.6.2)
     minitest (5.6.1)
     multi_json (1.11.0)
     multi_xml (0.5.5)
     multipart-post (2.0.0)
+    netrc (0.9.0)
     nokogiri (1.6.6.2)
       mini_portile (~> 0.6.0)
     oauth2 (1.0.0)
@@ -56,35 +60,45 @@ GEM
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (~> 1.2)
+    parser (2.2.0.2)
+      ast (>= 1.1, < 3.0)
+    powerpack (0.0.9)
     rack (1.6.0)
+    rainbow (2.0.0)
     rake (10.4.2)
-    rdoc (3.12.2)
+    rdoc (4.2.0)
       json (~> 1.4)
-    shoulda (3.5.0)
-      shoulda-context (~> 1.0, >= 1.0.1)
-      shoulda-matchers (>= 1.4.1, < 3.0)
-    shoulda-context (1.2.1)
-    shoulda-matchers (2.8.0)
-      activesupport (>= 3.0.0)
+    rest-client (1.7.2)
+      mime-types (>= 1.16, < 3.0)
+      netrc (~> 0.7)
+    rubocop (0.28.0)
+      astrolabe (~> 1.3)
+      parser (>= 2.2.0.pre.7, < 3.0)
+      powerpack (~> 0.0.6)
+      rainbow (>= 1.99.1, < 3.0)
+      ruby-progressbar (~> 1.4)
+    ruby-progressbar (1.7.1)
     simplecov (0.10.0)
       docile (~> 1.1.0)
       json (~> 1.8)
       simplecov-html (~> 0.10.0)
     simplecov-html (0.10.0)
+    term-ansicolor (1.3.0)
+      tins (~> 1.0)
+    thor (0.19.1)
     thread_safe (0.3.5)
+    tins (1.3.3)
     typhoeus (0.7.1)
       ethon (>= 0.7.1)
-    tzinfo (1.2.2)
-      thread_safe (~> 0.1)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  bundler (~> 1.0)
+  coveralls
   cri (~> 2.7)
-  jeweler (~> 2.0)
-  rdoc (~> 3.12)
-  shoulda (~> 3.5)
-  simplecov (~> 0.8)
+  jeweler
+  minitest
+  rake
+  rubocop
   typhoeus (~> 0.6)

data/README.md

@@ -1,7 +1,9 @@
 # unipept-cli
 
-[![Code Climate](https://codeclimate.com/github/unipept/unipept-cli/badges/gpa.svg)](https://codeclimate.com/github/unipept/unipept-cli)
 [![Gem Version](https://badge.fury.io/rb/unipept.svg)](http://badge.fury.io/rb/unipept)
+[![Build Status](https://api.travis-ci.org/unipept/unipept-cli.svg)](https://travis-ci.org/unipept/unipept-cli)
+[![Coverage Status](https://coveralls.io/repos/unipept/unipept-cli/badge.svg)](https://coveralls.io/r/unipept/unipept-cli)
+[![Code Climate](https://codeclimate.com/github/unipept/unipept-cli/badges/gpa.svg)](https://codeclimate.com/github/unipept/unipept-cli)
 
 Unipept-cli offers a command line interface to the [Unipept](http://unipept.ugent.be) web service.
 Documentation about the web service can be found at [http://unipept.ugent.be/apidocs](http://unipept.ugent.be/apidocs).
@@ -21,8 +23,8 @@ The Unipept CLI is available as a *gem*. This means it can easily be installed w
 
 ```bash
 $ gem install unipept
-Successfully installed unipept-0.7.1
-Parsing documentation for unipept-0.7.1
+Successfully installed unipept-0.8.0
+Parsing documentation for unipept-0.8.0
 Done installing documentation for unipept after 0 seconds
 1 gem installed
 ```
@@ -31,7 +33,7 @@ After successful installation, the unipept command should be available:
 
 ```bash
 $ unipept -v
-0.7.1
+0.8.0
 ```
 
 The help can be accessed by running `unipept -h`.

data/Rakefile

@@ -10,6 +10,8 @@ rescue Bundler::BundlerError => e
   exit e.status_code
 end
 require 'rake'
+require 'rake/testtask'
+require 'rubocop/rake_task'
 
 require 'jeweler'
 Jeweler::Tasks.new do |gem|
@@ -30,19 +32,18 @@ Jeweler::Tasks.new do |gem|
 end
 Jeweler::RubygemsDotOrgTasks.new
 
-require 'rake/testtask'
-Rake::TestTask.new(:test) do |test|
-  test.libs << 'lib' << 'test'
-  test.pattern = 'test/**/test_*.rb'
-  test.verbose = true
-end
+task :test_unit do
+  require './test/helper.rb'
 
-desc 'Code coverage detail'
-task :simplecov do
-  ENV['COVERAGE'] = 'true'
-  Rake::Task['test'].execute
+  FileList['./test/**/test_*.rb', './test/**/*_spec.rb'].each do |fn|
+    require fn
+  end
 end
 
+RuboCop::RakeTask.new(:test_style)
+
+task test: [:test_unit, :test_style]
+
 task default: :test
 
 require 'rdoc/task'

data/VERSION

@@ -1 +1 @@
-0.7.1
+0.8.0

data/bin/peptfilter

@@ -1,49 +1,7 @@
 #!/usr/bin/env ruby
-require 'cri'
+require_relative '../lib/commands'
 
 Signal.trap('PIPE', 'EXIT')
 Signal.trap('INT', 'EXIT')
-root_cmd = Cri::Command.new_basic_root.modify do
-  name 'peptfilter'
-  summary 'Filter peptides based on specific criteria.'
-  usage 'peptfilter [options]'
-  description <<-EOS
-  The peptfilter command filters a list of peptides according to specific criteria. The command expects a list of peptides that are passed
 
-  - as separate command line arguments
-
-  - in one or more text files that are passed as an argument to the -i option
-
-  - to standard input
-
-  The command will give priority to the first way peptides are passed, in the order as listed above. Text files and standard input should have one peptide per line. FASTA headers are preserved in the output, so that peptides remain bundled.
-  EOS
-  # flag :u, :unique, "filter duplicate peptides."
-  required nil, :minlen, 'only retain tryptic peptides that have at least min (default: 5) amino acids.'
-  required nil, :maxlen, 'only retain tryptic peptides that have at most max (default: 50) amino acids.'
-  required :l, :lacks, 'only retain tryptic peptides that lack all amino acids from the string of residues.'
-  required :c, :contains, 'only retain tryptic peptides that contain all amino acids from the string of residues.'
-  run do |opts, _args, _cmd|
-    minlen = opts.fetch(:minlen, '5').to_i
-    maxlen = opts.fetch(:maxlen, '50').to_i
-    lacks = opts.fetch(:lacks, '').chars.to_a
-    contains = opts.fetch(:contains, '').chars.to_a
-    $stdin.each_line do |pept|
-      # FASTA headers
-      if pept.start_with? '>'
-        puts pept
-        next
-      end
-      pept = pept.chomp
-      length_ok = pept.length >= minlen && pept.length <= maxlen
-      lacks_ok = (pept.chars.to_a & lacks).size == 0
-      contains_ok = (pept.chars.to_a & contains).size == contains.size
-
-      if length_ok && lacks_ok && contains_ok
-        puts pept
-      end
-    end
-  end
-end
-
-root_cmd.run(ARGV)
+Unipept::Commands::Peptfilter.run(ARGV)

data/bin/prot2pept

@@ -1,52 +1,7 @@
 #!/usr/bin/env ruby
-require 'cri'
+require_relative '../lib/commands'
 
-Signal.trap("PIPE", "EXIT")
-Signal.trap("INT", "EXIT")
-root_cmd = Cri::Command.new_basic_root.modify do
-  name        'prot2pept'
-  summary     'Split protein sequences into peptides.'
-  usage       'prot2pept [options]'
-  description <<-EOS
-  The prot2pept command splits each protein sequence into a list of peptides according to a given cleavage-pattern. The command expects a list of protein sequences that are passed
+Signal.trap('PIPE', 'EXIT')
+Signal.trap('INT', 'EXIT')
 
-  - as separate command line arguments
-
-  - in one or more text files that are passed as an argument to the -i option
-
-  - to standard input
-
-  The command will give priority to the first way protein sequences are passed, in the order as listed above. Text files and standard input should have either one protein sequence per line or contain a FASTA formatted list of protein sequences. FASTA headers are preserved in the output, so that peptides can be bundled per protein sequence.
-
-  EOS
-  required :p, :pattern, 'specify cleavage-pattern (regex) as the pattern after which the next peptide will be cleaved (default: ([KR])([^P]) for tryptic peptides).'
-  run do |opts, args, cmd|
-    pattern = opts.fetch(:pattern, "([KR])([^P])")
-    # decide if we have FASTA input
-    fasta_header = $stdin.gets
-    if fasta_header.start_with? '>'
-      # fasta input, need to join lines
-      while !$stdin.eof?
-        prot = ""
-        # Sometimes you just got to accept this weird and ugly code
-        until $stdin.eof? || (line = gets).start_with?('>')
-          prot += line.chomp
-        end
-        puts fasta_header
-        puts prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?)
-
-        fasta_header = line
-      end
-    else
-      # handle our already read line
-      puts fasta_header.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?)
-
-      # we no longer have to join lines as input is now more sane
-      $stdin.each_line do |prot|
-        puts prot.gsub(/#{pattern}/,"\\1\n\\2").gsub(/#{pattern}/, "\\1\n\\2").split("\n").reject(&:empty?)
-      end
-    end
-  end
-end
-
-root_cmd.run(ARGV)
+Unipept::Commands::Prot2pept.run(ARGV)

data/bin/unipept

@@ -1,203 +1,8 @@
 #!usr/bin/env ruby
-
-require 'cri'
-require 'typhoeus'
-require 'yaml'
-require 'json'
-require 'fileutils'
-
-require_relative '../lib/unipept'
+require_relative '../lib/commands'
 
 # Prevent broken pipe errors
 Signal.trap('PIPE', 'EXIT')
 Signal.trap('INT', 'EXIT')
 
-root_cmd = Cri::Command.new_basic_root.modify do
-  name 'unipept'
-  summary 'Command line interface to Unipept web services.'
-  usage 'unipept subcommand [options]'
-  description <<-EOS
-  The unipept subcommands are command line wrappers around the Unipept web services.
-
-  Subcommands that start with pept expect a list of tryptic peptides as input. Subcommands that start with tax expect a list of NCBI Taxonomy Identifiers as input. Input is passed
-
-  - as separate command line arguments
-
-  - in one or more text files that are passed as an argument to the -i option
-
-  - to standard input
-
-  The command will give priority to the first way the input is passed, in the order as listed above. Text files and standard input should have one tryptic peptide or one NCBI Taxonomy Identifier per line.
-  EOS
-  flag :v, :version, 'displays the version'
-  flag :q, :quiet, 'disable service messages'
-  option :i, :input, 'read input from file', argument: :required
-  option :o, :output, 'write output to file', argument: :required
-  option :f, :format, "define the output format (available: #{Unipept::Formatter.available.join ', ' }) (default: #{Unipept::Formatter.default})", argument: :required
-
-  # Configuration options
-  option nil, 'host', 'specify the server running the Unipept web service', argument: :required
-
-  run do |opts, _args, _cmd|
-    if opts[:version]
-      puts File.read(File.join(File.dirname(__FILE__), '..', 'VERSION'))
-    elsif
-      root_cmd.run(['help'])
-    end
-  end
-end
-
-root_cmd.define_command('config') do
-  summary 'Set configuration options.'
-  usage 'config option [value]'
-  description <<-EOS
-  Sets or shows the value for configuration options. All settings are stored in the .unipeptrc file in the home directory of the user.
-
-  Running the command with a value will set that value for the given option, running it without will show the current value.
-
-  These options are currently supported:
-
-  - host: Set the default host for api calls.
-
-  Example: "unipept config host http://api.unipept.ugent.be" will set the default host to the public unipept server.
-  EOS
-
-  run do |_opts, args, _cmd|
-    config = Unipept::Configuration.new
-    if args.size > 1
-      config[args.first] = args[1]
-      config.save
-    elsif args.size == 1
-      puts config[args.first]
-    elsif args.size == 0
-      root_cmd.run(['config', '-h'])
-    end
-  end
-end
-
-root_cmd.define_command('pept2taxa') do
-  usage 'pept2taxa [options]'
-  aliases :pt
-  summary 'Fetch taxa of Uniprot records that match tryptic peptides.'
-  description <<-EOS
-  For each tryptic peptide the unipept pept2taxa command retrieves from Unipept the set of taxa from all Uniprot records whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed
-
-  - as separate command line arguments
-
-  - in one or more text files that are passed as an argument to the -i option
-
-  - to standard input
-
-  The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.
-
-  The unipept pept2taxa subcommand yields NCBI Taxonomy records as output.
-  EOS
-
-  flag :e, :equate, 'equate isoleucine (I) and leucine (L) when matching peptides'
-  flag :a, :all, 'report all information fields of NCBI Taxonomy records available in Unipept. Note that this may have a performance penalty.'
-  option :s, :select, 'select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.', argument: :required, multiple: true
-  option :x, :xml, 'Download the matched records from the NCBI web service as an xml-formatted file (specify output filename)', argument: :required
-
-  runner Unipept::Commands::Pept2taxa
-end
-
-root_cmd.define_command('pept2lca') do
-  usage 'pept2lca [options]'
-  aliases :pl
-  summary 'Fetch taxonomic lowest common ancestor of Uniprot records that match tryptic peptides.'
-  description <<-EOS
-  For each tryptic peptide the unipept pept2lca command retrieves from Unipept the lowest common ancestor of the set of taxa from all Uniprot records whose protein sequence contains an exact matches to the tryptic peptide. The lowest common ancestor is based on the topology of the Unipept Taxonomy -- a cleaned up version of the NCBI Taxonomy -- and is itself a record from the NCBI Taxonomy. The command expects a list of tryptic peptides that are passed
-
-   - as separate command line arguments
-
-   - in one or more text files that are passed as an argument to the -i option
-
-   - to standard input
-
-  The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.
-
-  The unipept pept2lca subcommand yields an NCBI Taxonomy record as output.
-  EOS
-
-  flag :e, :equate, 'equate isoleucine (I) and leucine (L) when matching peptides'
-  flag :a, :all, 'report all information fields of NCBI Taxonomy records available in Unipept. Note that this may have a performance penalty.'
-  option :s, :select, 'select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.', argument: :required, multiple: true
-
-  runner Unipept::Commands::Pept2lca
-end
-
-root_cmd.define_command('taxa2lca') do
-  usage 'taxa2lca [options]'
-  aliases :tl
-  summary 'Compute taxonomic lowest common ancestor for given list of taxa.'
-  description <<-EOS
-  The unipept taxa2lca command computes the lowest common ancestor of a given list of NCBI Taxonomy Identifiers. The lowest common ancestor is based on the topology of the Unipept Taxonomy -- a cleaned up version of the NCBI Taxonomy -- and is itself a record from the NCBI Taxonomy. The command expects a list of NCBI Taxonomy Identifiers that are passed
-
-   - as separate command line arguments
-
-   - in one or more text files that are passed as an argument to the -i option
-
-   - to standard input
-
-  The command will give priority to the first way NCBI Taxonomy Identifiers are passed, in the order as listed above. Text files and standard input should have one NCBI Taxonomy Identifier per line.
-
-  The unipept taxonomy subcommand yields NCBI Taxonomy records as output.
-  EOS
-
-  flag :a, :all, 'report all information fields of NCBI Taxonomy records available in Unipept. Note that this may have a performance penalty.'
-  option :s, :select, 'select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.', argument: :required, multiple: true
-
-  runner Unipept::Commands::Taxa2lca
-end
-
-root_cmd.define_command('pept2prot') do
-  usage 'pept2prot [options]'
-  aliases :pp
-  summary 'Fetch Uniprot records that match tryptic peptides.'
-  description <<-EOS
-  For each tryptic peptide the unipept pept2prot command retrieves from Unipept all Uniprot records whose protein sequence contains an exact matches to the tryptic peptide. The command expects a list of tryptic peptides that are passed
-
-  - as separate command line arguments
-
-  - in one or more text files that are passed as an argument to the -i option
-
-  - to standard input
-
-  The command will give priority to the first way tryptic peptides are passed, in the order as listed above. Text files and standard input should have one tryptic peptide per line.
-
-  The unipept pept2prot subcommand yields Uniprot records as output.
-  EOS
-
-  flag :e, :equate, 'equate isoleucine (I) and leucine (L) when matching peptides'
-  flag :a, :all, 'report all information fields of Uniprot records available in Unipept. Note that this may have a performance penalty.'
-  option :s, :select, 'select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.', argument: :required, multiple: true
-  option :x, :xml, 'download XML-formatted Uniprot records into the specified download-directory. ', argument: :required
-
-  runner Unipept::Commands::Pept2prot
-end
-
-root_cmd.define_command('taxonomy') do
-  usage 'taxonomy [options]'
-  aliases :tax
-  summary 'Fetch taxonomic information from Unipept Taxonomy.'
-  description <<-EOS
-  The unipept taxonomy command yields information from the Unipept Taxonomy records for a given list of NCBI Taxonomy Identifiers. The Unipept Taxonomy is a cleaned up version of the NCBI Taxonomy, and its records are also records of the NCBI Taxonomy. The command expects a list of NCBI Taxonomy Identifiers that are passed
-
-  - as separate command line arguments
-
-  - in one or more text files that are passed as an argument to the -i option
-
-  - to standard input
-
-  The command will give priority to the first way NCBI Taxonomy Identifiers are passed, in the order as listed above. Text files and standard input should have one NCBI Taxonomy Identifier per line.
-
-  The unipept taxonomy subcommand yields NCBI Taxonomy records as output.
-  EOS
-
-  flag :a, :all, 'report all information fields of NCBI Taxonomy records available in Unipept. Note that this may have a performance penalty.'
-  option :s, :select, 'select the information fields to return. Selected fields are passed as a comma separated list of field names. Multiple -s (or --select) options may be used.', argument: :required, multiple: true
-
-  runner Unipept::Commands::Taxonomy
-end
-
-root_cmd.run(ARGV)
+Unipept::Commands::Unipept.run(ARGV)

data/bin/uniprot

@@ -1,56 +1,7 @@
 #!/usr/bin/env ruby
-require 'typhoeus'
-require 'cri'
+require_relative '../lib/commands'
 
-Signal.trap("PIPE", "EXIT")
-Signal.trap("INT", "EXIT")
+Signal.trap('PIPE', 'EXIT')
+Signal.trap('INT', 'EXIT')
 
-valid_formats = Set.new ["fasta", "txt", "xml", "rdf", "gff"]
-
-def get_uniprot_entry(arg, format)
-  if format.nil? || format.empty?
-    resp = Typhoeus.get("http://www.uniprot.org/uniprot/#{arg}.fasta")
-    if resp.success?
-      puts resp.response_body.lines.map(&:chomp)[1..-1].join("")
-    end
-  else
-    # other format has been specified, just download and output
-    resp = Typhoeus.get("http://www.uniprot.org/uniprot/#{arg}.#{format}")
-    if resp.success?
-      puts resp.response_body
-    end
-  end
-end
-
-root_cmd = Cri::Command.new_basic_root.modify do
-  name        'uniprot'
-  summary     'Command line interface to Uniprot web services.'
-  usage       'uniprot [options]'
-  description <<-EOS
-  The uniprot command is a command line wrapper around the Uniprot web services. The command expects a list of Uniprot Accession Numbers that are passed
-
-  - as separate command line arguments
-
-  - in one or more text files that are passed as an argument to the -i option
-
-  - to standard input
-
-  The command will give priority to the first way Uniprot Accession Numbers are passed, in the order as listed above. Text files and standard input should have one Uniprot Accession Number per line.
-
-  The uniprot command yields Uniprot records as output.
-  EOS
-  required :f, :format, "specify output format (available: " + valid_formats.to_a.join(", ") + ")"
-  run do |opts, args, cmd|
-    if !opts[:format].nil? and !valid_formats.include? opts[:format]
-      $stderr.puts opts[:format] + " is not a valid output format. Available formats are: " + valid_formats.to_a.join(", ")
-      exit 1
-    end
-    iterator = args.empty? ? $stdin.each_line : args
-    iterator.each do |pept|
-      get_uniprot_entry(pept.chomp, opts[:format])
-    end
-  end
-end
-
-# run_this runs this command without subcommands! Absolutely needed here
-root_cmd.run_this(ARGV)
+Unipept::Commands::Uniprot.run(ARGV)