unipept 0.5.7 → 0.6.1

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data/LICENSE.txt CHANGED
@@ -1,20 +1,21 @@
1
- Copyright (c) 2014 Toon Willems
1
+ The MIT License (MIT)
2
2
 
3
- Permission is hereby granted, free of charge, to any person obtaining
4
- a copy of this software and associated documentation files (the
5
- "Software"), to deal in the Software without restriction, including
6
- without limitation the rights to use, copy, modify, merge, publish,
7
- distribute, sublicense, and/or sell copies of the Software, and to
8
- permit persons to whom the Software is furnished to do so, subject to
9
- the following conditions:
3
+ Copyright (c) 2010-2014 Universiteit Gent <unipept@ugent.be>
10
4
 
11
- The above copyright notice and this permission notice shall be
12
- included in all copies or substantial portions of the Software.
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
13
11
 
14
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
15
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
16
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
17
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
18
- LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
19
- OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
20
- WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
12
+ The above copyright notice and this permission notice shall be included in all
13
+ copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
+ SOFTWARE.
data/README.md ADDED
@@ -0,0 +1,37 @@
1
+ # unipept-cli
2
+
3
+ [![Code Climate](https://codeclimate.com/github/unipept/unipept-cli/badges/gpa.svg)](https://codeclimate.com/github/unipept/unipept-cli)
4
+
5
+ Unipept-cli offers a command line interface to the [Unipept](http://unipept.ugent.be) web service.
6
+ Documentation about the web service can be found at [http://unipept.ugent.be/apidocs](http://unipept.ugent.be/apidocs).
7
+
8
+ ## Installation
9
+
10
+ To use the Unipept CLI, Ruby version 1.9.3 or higher needs to be installed. You can check this by running `ruby -v` on the commandline:
11
+
12
+ ```
13
+ $ ruby -v
14
+ ruby 2.1.1p76 (2014-02-24 revision 45161) [x86_64-darwin12.0]
15
+ ```
16
+
17
+ More information on installing Ruby can be found at https://www.ruby-lang.org/en/installation/
18
+
19
+ The Unipept CLI is available as a *gem*. This means it can easily be installed with the following command:
20
+
21
+ ```bash
22
+ $ gem install unipept
23
+ Successfully installed unipept-0.6.0
24
+ Parsing documentation for unipept-0.6.0
25
+ Done installing documentation for unipept after 0 seconds
26
+ 1 gem installed
27
+ ```
28
+
29
+ After successful installation, the unipept command should be available:
30
+
31
+ ```bash
32
+ $ unipept -v
33
+ 0.6.0
34
+ ```
35
+
36
+ The help can be accessed by running `unipept -h`.
37
+
data/Rakefile CHANGED
@@ -16,12 +16,13 @@ Jeweler::Tasks.new do |gem|
16
16
  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
17
17
  gem.name = "unipept"
18
18
  gem.executables = ['unipept', 'prot2pept', 'peptfilter', 'uniprot']
19
- gem.homepage = "http://github.ugent.be/bmesuere/unipept/"
19
+ gem.homepage = "https://github.com/unipept/unipept/"
20
20
  gem.license = "MIT"
21
- gem.summary = %Q{CLI interface to unipept}
22
- gem.description = %Q{CLI interface to unipept}
23
- gem.email = "willemstoon@gmail.com"
24
- gem.authors = ["Toon Willems"]
21
+ gem.summary = %Q{Command line interface to Unipept web services.}
22
+ gem.description = %Q{Command line interface to Unipept web services.}
23
+ gem.email = "unipept@ugent.be"
24
+ gem.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
25
+ gem.required_ruby_version = '>= 1.9.3'
25
26
  # dependencies defined in Gemfile
26
27
  gem.add_dependency 'typhoeus', '~> 0.6'
27
28
  gem.add_dependency 'cri', '~> 2.6'
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.5.7
1
+ 0.6.1
data/bin/unipept CHANGED
@@ -8,55 +8,10 @@ require 'fileutils'
8
8
 
9
9
  require_relative '../lib/unipept'
10
10
 
11
+ # Prevent broken pipe errors
11
12
  Signal.trap("PIPE", "EXIT")
12
13
  Signal.trap("INT", "EXIT")
13
14
 
14
- module Unipept
15
- class Taxa2lca < ApiRunner
16
-
17
- def mapping
18
- {"taxa2lca" => "taxa2lca"}
19
- end
20
-
21
- def peptide_iterator(peptides, &block)
22
- block.call(peptides.to_a, 0)
23
- end
24
-
25
- def batch_size
26
- raise "NOT NEEDED FOR TAXA2LCA"
27
- end
28
-
29
- end
30
-
31
- class Pept2prot < ApiRunner
32
-
33
- def mapping
34
- {"pept2prot" => "pept2prot"}
35
- end
36
-
37
- def download_xml(result)
38
- if options[:xml]
39
- FileUtils.mkdir_p(options[:xml])
40
- result.first.each do |prot|
41
- File.open(options[:xml] + "/#{prot['uniprot_id']}.xml", "wb") do |f|
42
- f.write Typhoeus.get("http://www.uniprot.org/uniprot/#{prot['uniprot_id']}.xml").response_body
43
- end
44
- end
45
- end
46
- end
47
-
48
- def batch_size
49
- 10
50
- end
51
- end
52
-
53
- class Taxonomy < ApiRunner
54
- def mapping
55
- {"taxonomy" => "taxonomy"}
56
- end
57
- end
58
- end
59
-
60
15
  root_cmd = Cri::Command.new_basic_root.modify do
61
16
  name 'unipept'
62
17
  flag :v, :version, "print version"
@@ -101,7 +56,7 @@ root_cmd.define_command('pept2taxa') do
101
56
  option :a, :extra, "Show full lineage"
102
57
  option :x, :xml, "Download taxonomy from NCBI as xml (specify output filename)", :argument => :required
103
58
 
104
- runner Unipept::ApiRunner
59
+ runner Unipept::Commands::Pept2taxa
105
60
  end
106
61
 
107
62
  root_cmd.define_command('pept2lca') do
@@ -114,7 +69,7 @@ root_cmd.define_command('pept2lca') do
114
69
  option :s, :select, "select the attributes", :argument => :required, :multiple => true
115
70
  option :a, :extra, "Show full lineage"
116
71
 
117
- runner Unipept::ApiRunner
72
+ runner Unipept::Commands::Pept2lca
118
73
  end
119
74
 
120
75
  root_cmd.define_command('taxa2lca') do
@@ -126,7 +81,7 @@ root_cmd.define_command('taxa2lca') do
126
81
  option :s, :select, "select the attributes", :argument => :required, :multiple => true
127
82
  option :a, :extra, "Show full lineage"
128
83
 
129
- runner Unipept::Taxa2lca
84
+ runner Unipept::Commands::Taxa2lca
130
85
  end
131
86
 
132
87
  root_cmd.define_command('pept2prot') do
@@ -140,7 +95,7 @@ root_cmd.define_command('pept2prot') do
140
95
  option :x, :xml, "download uniprot record in specified directory", :argument => :required
141
96
  flag :a, :extra, "include all information. WARNING: will take much longer!"
142
97
 
143
- runner Unipept::Pept2prot
98
+ runner Unipept::Commands::Pept2prot
144
99
  end
145
100
 
146
101
  root_cmd.define_command('taxonomy') do
@@ -152,7 +107,7 @@ root_cmd.define_command('taxonomy') do
152
107
  option :s, :select, "select the attributes", :argument => :required, :multiple => true
153
108
  flag :a, :extra, "include all information. WARNING: will take much longer!"
154
109
 
155
- runner Unipept::Taxonomy
110
+ runner Unipept::Commands::Taxonomy
156
111
  end
157
112
 
158
113
  root_cmd.run(ARGV)
@@ -1,4 +1,6 @@
1
- module Unipept
1
+ require 'set'
2
+
3
+ module Unipept::Commands
2
4
  class ApiRunner < Cri::CommandRunner
3
5
 
4
6
  def initialize(args, opts, cmd)
@@ -7,7 +9,7 @@ module Unipept
7
9
 
8
10
  set_configuration
9
11
 
10
- @url = "#{@host}/api/v1/#{mapping[cmd.name]}.json"
12
+ @url = "#{@host}/api/v1/#{cmd.name}.json"
11
13
  @message_url = "#{@host}/api/v1/messages.json"
12
14
  end
13
15
 
@@ -31,10 +33,6 @@ module Unipept
31
33
  @host = host
32
34
  end
33
35
 
34
- def mapping
35
- {'pept2taxa' => 'pept2taxa', 'pept2lca' => 'pept2lca'}
36
- end
37
-
38
36
  def input_iterator
39
37
  # Argument over file input over stdin
40
38
  if !arguments.empty?
@@ -71,7 +69,7 @@ module Unipept
71
69
  return unless STDOUT.tty?
72
70
  last_fetched = @configuration['last_fetch_date']
73
71
  if last_fetched.nil? || (last_fetched + 60 * 60 * 24) < Time.now
74
- version = File.read(File.join(File.dirname(__FILE__), "..", "..", "VERSION"))
72
+ version = Unipept::VERSION
75
73
  resp = Typhoeus.get(@message_url, params: {version: version})
76
74
  puts resp.body unless resp.body.chomp.empty?
77
75
  @configuration['last_fetch_date'] = Time.now
@@ -97,7 +95,7 @@ module Unipept
97
95
  hydra = Typhoeus::Hydra.new(max_concurrency: 10)
98
96
  num_req = 0
99
97
 
100
- peptide_iterator(peptides) do |sub_division, i, fasta_mapper|
98
+ peptide_iterator(peptides) do |sub_division, i, fasta_input|
101
99
  request = Typhoeus::Request.new(
102
100
  @url,
103
101
  method: :post,
@@ -105,35 +103,54 @@ module Unipept
105
103
  accept_encoding: "gzip"
106
104
  )
107
105
  request.on_complete do |resp|
108
- if resp.timed_out?
109
- $stderr.puts "request timed out, continuing anyway, but results might be incomplete"
110
- else
111
- if resp.success?
112
- # if JSON parsing goes wrong
113
- sub_result = JSON[resp.response_body] rescue []
114
- sub_result = [sub_result] if not sub_result.kind_of? Array
115
106
 
116
- sub_result.map! {|r| r.select! {|k,v| filter_list.any? {|f| f.match k } } } if ! filter_list.empty?
107
+ if resp.success?
108
+ # if JSON parsing goes wrong
109
+ sub_result = JSON[resp.response_body] rescue []
110
+ sub_result = [sub_result] if not sub_result.kind_of? Array
117
111
 
118
- if options[:xml]
119
- result << sub_result
120
- end
112
+ sub_result.map! {|r| r.select! {|k,v| filter_list.any? {|f| f.match k } } } if ! filter_list.empty?
121
113
 
122
- # wait till it's our turn to write
123
- batch_order.wait(i) do
124
- if ! sub_result.empty?
125
- if ! printed_header
126
- write_to_output formatter.header(sub_result, fasta_mapper)
127
- printed_header = true
128
- end
129
- write_to_output formatter.format(sub_result, fasta_mapper)
114
+ if options[:xml]
115
+ result << sub_result
116
+ end
117
+
118
+ # wait till it's our turn to write
119
+ batch_order.wait(i) do
120
+ if ! sub_result.empty?
121
+ if ! printed_header
122
+ write_to_output formatter.header(sub_result, fasta_input)
123
+ printed_header = true
130
124
  end
125
+ write_to_output formatter.format(sub_result, fasta_input)
131
126
  end
132
- else
133
- save_error(resp.response_body)
134
127
  end
128
+
129
+ elsif resp.timed_out?
130
+
131
+ batch_order.wait(i) do
132
+ $stderr.puts "request timed out, continuing anyway, but results might be incomplete"
133
+ save_error("request timed out, continuing anyway, but results might be incomplete")
134
+ end
135
+
136
+ elsif resp.code == 0
137
+
138
+ batch_order.wait(i) do
139
+ $stderr.puts "could not get an http response, continuing anyway, but results might be incomplete"
140
+ save_error(resp.return_message)
141
+ end
142
+
143
+ else
144
+
145
+ batch_order.wait(i) do
146
+ $stderr.puts "received a non-successful http response #{resp.code.to_s}, continuing anyway, but results might be incomplete"
147
+ save_error("Got #{resp.code.to_s}: #{resp.response_body}")
148
+ end
149
+
135
150
  end
151
+
136
152
  end
153
+
137
154
  hydra.queue request
138
155
 
139
156
  num_req += 1
@@ -187,19 +204,24 @@ module Unipept
187
204
  # FASTA MODE ENGAGED
188
205
  fasta_header = first.chomp
189
206
  peptides.each_slice(batch_size).with_index do |sub,i|
190
- fasta_mapper = {}
191
- sub.map! {|s| s.chomp}
192
- j = 0
193
- while j < sub.size
194
- if sub[j].start_with? '>'
195
- fasta_header = sub[j]
207
+ fasta_input = []
208
+ # Use a set so we don't ask data twice
209
+ newsub = Set.new
210
+
211
+ # Iterate to find fasta headers
212
+ sub.each do |s|
213
+ s.chomp!
214
+ if s.start_with? '>'
215
+ # Save the FASTA header when found
216
+ fasta_header = s
196
217
  else
197
- fasta_mapper[sub[j]] = fasta_header
218
+ # Add the input pair to our input list
219
+ fasta_input << [fasta_header, s]
220
+ newsub << s
198
221
  end
199
- j += 1
200
222
  end
201
- sub -= fasta_mapper.values.uniq
202
- block.call(sub, i, fasta_mapper)
223
+
224
+ block.call(newsub.to_a, i, fasta_input)
203
225
  end
204
226
  else
205
227
  # shame we have to be this explicit, but it appears to be the only way
@@ -0,0 +1,6 @@
1
+ require_relative 'api_runner'
2
+ module Unipept::Commands
3
+ class Pept2lca < ApiRunner
4
+ end
5
+ end
6
+
@@ -0,0 +1,20 @@
1
+ require_relative 'api_runner'
2
+
3
+ module Unipept::Commands
4
+ class Pept2prot < ApiRunner
5
+ def download_xml(result)
6
+ if options[:xml]
7
+ FileUtils.mkdir_p(options[:xml])
8
+ result.first.each do |prot|
9
+ File.open(options[:xml] + "/#{prot['uniprot_id']}.xml", "wb") do |f|
10
+ f.write Typhoeus.get("http://www.uniprot.org/uniprot/#{prot['uniprot_id']}.xml").response_body
11
+ end
12
+ end
13
+ end
14
+ end
15
+
16
+ def batch_size
17
+ 10
18
+ end
19
+ end
20
+ end
@@ -0,0 +1,5 @@
1
+ require_relative 'api_runner'
2
+ module Unipept::Commands
3
+ class Pept2taxa < ApiRunner
4
+ end
5
+ end
@@ -0,0 +1,12 @@
1
+ require_relative 'api_runner'
2
+ module Unipept::Commands
3
+ class Taxa2lca < ApiRunner
4
+ def peptide_iterator(peptides, &block)
5
+ block.call(peptides.to_a, 0)
6
+ end
7
+
8
+ def batch_size
9
+ raise "NOT NEEDED FOR TAXA2LCA"
10
+ end
11
+ end
12
+ end
@@ -0,0 +1,5 @@
1
+ require_relative 'api_runner'
2
+ module Unipept::Commands
3
+ class Taxonomy < ApiRunner
4
+ end
5
+ end
@@ -0,0 +1,7 @@
1
+ ['pept2lca','pept2taxa','pept2prot','taxa2lca','taxonomy'].each do |cmd|
2
+ require_relative File.join('commands',cmd)
3
+ end
4
+ module Unipept
5
+ module Commands
6
+ end
7
+ end
@@ -50,13 +50,13 @@ module Unipept
50
50
 
51
51
  register :csv
52
52
 
53
- def header(data, fasta_mapper = nil)
53
+ def header(data, fasta_input = nil)
54
54
  CSV.generate do |csv|
55
55
  first = data.first
56
56
  if first.kind_of? Array
57
57
  first = first.first
58
58
  end
59
- if fasta_mapper
59
+ if fasta_input
60
60
  csv << (['fasta_header'] + first.keys).map(&:to_s) if first
61
61
  else
62
62
  csv << first.keys.map(&:to_s) if first
@@ -64,26 +64,36 @@ module Unipept
64
64
  end
65
65
  end
66
66
 
67
- def format(data, fasta_mapper = nil)
67
+ def format(data, fasta_input = nil)
68
68
  CSV.generate do |csv|
69
- data.each do |o|
70
- if o.kind_of? Array
71
- o.each do |h|
72
- if fasta_mapper
73
- extra_key = [fasta_mapper[h.values.first]]
74
- csv << (extra_key + h.values).map { |v| v == "" ? nil : v }
75
- else
76
- csv << h.values.map { |v| v == "" ? nil : v }
69
+
70
+ if fasta_input
71
+ # Process the output from {key1: value1, key2: value2, ...}
72
+ # to {value => {key1: value1, key2: value2, ...}}
73
+ data_dict = {}
74
+ data.each do |d|
75
+ data_dict[d.values.first.to_s] ||= []
76
+ data_dict[d.values.first.to_s] << d
77
+ end
78
+
79
+ # Iterate over the input
80
+ fasta_input.each do |input_pair|
81
+ fasta_header, id = input_pair
82
+
83
+ # Retrieve the corresponding API result (if any)
84
+ unless data_dict[id].nil?
85
+ data_dict[id].each do |r|
86
+ csv << ([fasta_header] + r.values).map { |v| v == "" ? nil : v }
77
87
  end
78
88
  end
79
- else
80
- if fasta_mapper
81
- extra_key = [fasta_mapper[o.values.first]]
82
- csv << (extra_key + o.values).map { |v| v == "" ? nil : v }
83
- else
84
- csv << o.values.map { |v| v == "" ? nil : v }
85
- end
86
89
  end
90
+
91
+ else
92
+
93
+ data.each do |o|
94
+ csv << o.values.map { |v| v == "" ? nil : v }
95
+ end
96
+
87
97
  end
88
98
  end
89
99
  end
@@ -0,0 +1,3 @@
1
+ module Unipept
2
+ VERSION = File.read(File.join(File.dirname(__FILE__), "..", "..", "VERSION"))
3
+ end
data/lib/unipept.rb CHANGED
@@ -1,7 +1,8 @@
1
1
  require_relative 'unipept/formatters'
2
2
  require_relative 'unipept/configuration'
3
3
  require_relative 'unipept/batch_order'
4
- require_relative 'unipept/api_runner'
4
+ require_relative 'unipept/commands'
5
+ require_relative 'unipept/version'
5
6
 
6
7
  module Unipept
7
8
  end
data/unipept.gemspec CHANGED
@@ -2,29 +2,29 @@
2
2
  # DO NOT EDIT THIS FILE DIRECTLY
3
3
  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
4
4
  # -*- encoding: utf-8 -*-
5
- # stub: unipept 0.5.7 ruby lib
5
+ # stub: unipept 0.6.1 ruby lib
6
6
 
7
7
  Gem::Specification.new do |s|
8
8
  s.name = "unipept"
9
- s.version = "0.5.7"
9
+ s.version = "0.6.1"
10
10
 
11
11
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
12
12
  s.require_paths = ["lib"]
13
- s.authors = ["Toon Willems"]
14
- s.date = "2014-06-25"
15
- s.description = "CLI interface to unipept"
16
- s.email = "willemstoon@gmail.com"
13
+ s.authors = ["Toon Willems", "Bart Mesuere", "Tom Naessens"]
14
+ s.date = "2015-04-22"
15
+ s.description = "Command line interface to Unipept web services."
16
+ s.email = "unipept@ugent.be"
17
17
  s.executables = ["unipept", "prot2pept", "peptfilter", "uniprot"]
18
18
  s.extra_rdoc_files = [
19
19
  "LICENSE.txt",
20
- "README.rdoc"
20
+ "README.md"
21
21
  ]
22
22
  s.files = [
23
23
  ".document",
24
24
  "Gemfile",
25
25
  "Gemfile.lock",
26
26
  "LICENSE.txt",
27
- "README.rdoc",
27
+ "README.md",
28
28
  "Rakefile",
29
29
  "VERSION",
30
30
  "bin/peptfilter",
@@ -32,18 +32,26 @@ Gem::Specification.new do |s|
32
32
  "bin/unipept",
33
33
  "bin/uniprot",
34
34
  "lib/unipept.rb",
35
- "lib/unipept/api_runner.rb",
36
35
  "lib/unipept/batch_order.rb",
36
+ "lib/unipept/commands.rb",
37
+ "lib/unipept/commands/api_runner.rb",
38
+ "lib/unipept/commands/pept2lca.rb",
39
+ "lib/unipept/commands/pept2prot.rb",
40
+ "lib/unipept/commands/pept2taxa.rb",
41
+ "lib/unipept/commands/taxa2lca.rb",
42
+ "lib/unipept/commands/taxonomy.rb",
37
43
  "lib/unipept/configuration.rb",
38
44
  "lib/unipept/formatters.rb",
45
+ "lib/unipept/version.rb",
39
46
  "test/helper.rb",
40
47
  "test/test_unipept.rb",
41
48
  "unipept.gemspec"
42
49
  ]
43
- s.homepage = "http://github.ugent.be/bmesuere/unipept/"
50
+ s.homepage = "https://github.com/unipept/unipept/"
44
51
  s.licenses = ["MIT"]
52
+ s.required_ruby_version = Gem::Requirement.new(">= 1.9.3")
45
53
  s.rubygems_version = "2.2.2"
46
- s.summary = "CLI interface to unipept"
54
+ s.summary = "Command line interface to Unipept web services."
47
55
 
48
56
  if s.respond_to? :specification_version then
49
57
  s.specification_version = 4
metadata CHANGED
@@ -1,14 +1,16 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: unipept
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.5.7
4
+ version: 0.6.1
5
5
  platform: ruby
6
6
  authors:
7
7
  - Toon Willems
8
+ - Bart Mesuere
9
+ - Tom Naessens
8
10
  autorequire:
9
11
  bindir: bin
10
12
  cert_chain: []
11
- date: 2014-06-25 00:00:00.000000000 Z
13
+ date: 2015-04-22 00:00:00.000000000 Z
12
14
  dependencies:
13
15
  - !ruby/object:Gem::Dependency
14
16
  name: shoulda
@@ -108,8 +110,8 @@ dependencies:
108
110
  - - "~>"
109
111
  - !ruby/object:Gem::Version
110
112
  version: '2.6'
111
- description: CLI interface to unipept
112
- email: willemstoon@gmail.com
113
+ description: Command line interface to Unipept web services.
114
+ email: unipept@ugent.be
113
115
  executables:
114
116
  - unipept
115
117
  - prot2pept
@@ -118,13 +120,13 @@ executables:
118
120
  extensions: []
119
121
  extra_rdoc_files:
120
122
  - LICENSE.txt
121
- - README.rdoc
123
+ - README.md
122
124
  files:
123
125
  - ".document"
124
126
  - Gemfile
125
127
  - Gemfile.lock
126
128
  - LICENSE.txt
127
- - README.rdoc
129
+ - README.md
128
130
  - Rakefile
129
131
  - VERSION
130
132
  - bin/peptfilter
@@ -132,14 +134,21 @@ files:
132
134
  - bin/unipept
133
135
  - bin/uniprot
134
136
  - lib/unipept.rb
135
- - lib/unipept/api_runner.rb
136
137
  - lib/unipept/batch_order.rb
138
+ - lib/unipept/commands.rb
139
+ - lib/unipept/commands/api_runner.rb
140
+ - lib/unipept/commands/pept2lca.rb
141
+ - lib/unipept/commands/pept2prot.rb
142
+ - lib/unipept/commands/pept2taxa.rb
143
+ - lib/unipept/commands/taxa2lca.rb
144
+ - lib/unipept/commands/taxonomy.rb
137
145
  - lib/unipept/configuration.rb
138
146
  - lib/unipept/formatters.rb
147
+ - lib/unipept/version.rb
139
148
  - test/helper.rb
140
149
  - test/test_unipept.rb
141
150
  - unipept.gemspec
142
- homepage: http://github.ugent.be/bmesuere/unipept/
151
+ homepage: https://github.com/unipept/unipept/
143
152
  licenses:
144
153
  - MIT
145
154
  metadata: {}
@@ -151,7 +160,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
151
160
  requirements:
152
161
  - - ">="
153
162
  - !ruby/object:Gem::Version
154
- version: '0'
163
+ version: 1.9.3
155
164
  required_rubygems_version: !ruby/object:Gem::Requirement
156
165
  requirements:
157
166
  - - ">="
@@ -162,5 +171,5 @@ rubyforge_project:
162
171
  rubygems_version: 2.2.2
163
172
  signing_key:
164
173
  specification_version: 4
165
- summary: CLI interface to unipept
174
+ summary: Command line interface to Unipept web services.
166
175
  test_files: []
data/README.rdoc DELETED
@@ -1,19 +0,0 @@
1
- = unipept
2
-
3
- Description goes here.
4
-
5
- == Contributing to unipept
6
-
7
- * Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
8
- * Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
9
- * Fork the project.
10
- * Start a feature/bugfix branch.
11
- * Commit and push until you are happy with your contribution.
12
- * Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
13
- * Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
14
-
15
- == Copyright
16
-
17
- Copyright (c) 2014 Toon Willems. See LICENSE.txt for
18
- further details.
19
-