unipept 2.1.1 → 2.2.0
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- checksums.yaml +4 -4
- data/.rakeTasks +7 -0
- data/VERSION +1 -1
- data/lib/batch_iterator.rb +16 -0
- data/lib/commands/unipept.rb +25 -1
- data/lib/commands/unipept/api_runner.rb +3 -1
- data/lib/commands/unipept/taxa2tree.rb +74 -0
- data/lib/formatters.rb +104 -32
- data/test.taxa +4 -0
- data/test/commands/unipept/test_pept2ec.rb +9 -9
- data/test/commands/unipept/test_pept2funct.rb +13 -13
- data/test/commands/unipept/test_pept2go.rb +8 -8
- data/test/commands/unipept/test_pept2interpro.rb +24 -24
- data/test/commands/unipept/test_peptinfo.rb +14 -14
- data/test/commands/unipept/test_taxa2tree.rb +68 -0
- 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/unipept.gemspec +18 -3
- metadata +17 -2
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@@ -0,0 +1,22 @@
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1
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+
[
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2
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{
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3
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+
"taxon_id": 216816,
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4
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+
"taxon_name": "Bifidobacterium longum",
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5
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+
"taxon_rank": "species"
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6
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+
},
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7
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+
{
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8
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"taxon_id": 1680,
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9
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+
"taxon_name": "Bifidobacterium adolescentis",
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10
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+
"taxon_rank": "species"
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11
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+
},
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12
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{
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13
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"taxon_id": 1,
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14
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+
"taxon_name": "root",
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15
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+
"taxon_rank": "no rank"
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16
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+
},
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17
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{
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18
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"taxon_id": 2,
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19
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"taxon_name": "Bacteria",
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20
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"taxon_rank": "superkingdom"
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21
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}
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22
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]
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data/unipept.gemspec
CHANGED
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@@ -2,16 +2,16 @@
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2
2
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# DO NOT EDIT THIS FILE DIRECTLY
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3
3
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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4
4
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# -*- encoding: utf-8 -*-
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5
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-
# stub: unipept 2.
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5
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+
# stub: unipept 2.2.0 ruby lib
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6
6
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7
7
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Gem::Specification.new do |s|
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8
8
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s.name = "unipept".freeze
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9
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-
s.version = "2.
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9
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+
s.version = "2.2.0"
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10
10
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11
11
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s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
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12
12
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s.require_paths = ["lib".freeze]
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13
13
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s.authors = ["Bart Mesuere".freeze, "Pieter Verschaffelt".freeze, "Toon Willems".freeze, "Tom Naessens".freeze]
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14
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-
s.date = "2020-04-
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14
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+
s.date = "2020-04-27"
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15
15
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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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16
16
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s.email = "unipept@ugent.be".freeze
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17
17
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s.executables = ["unipept".freeze, "prot2pept".freeze, "peptfilter".freeze, "uniprot".freeze]
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@@ -22,6 +22,7 @@ Gem::Specification.new do |s|
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22
22
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s.files = [
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23
23
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".document",
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24
24
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".github/workflows/ci.yml",
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25
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".rakeTasks",
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25
26
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".rubocop.yml",
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26
27
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".ruby-version",
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27
28
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"Gemfile",
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@@ -51,6 +52,7 @@ Gem::Specification.new do |s|
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51
52
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"lib/commands/unipept/pept2taxa.rb",
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52
53
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"lib/commands/unipept/peptinfo.rb",
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53
54
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"lib/commands/unipept/taxa2lca.rb",
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55
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+
"lib/commands/unipept/taxa2tree.rb",
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54
56
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"lib/commands/unipept/taxonomy.rb",
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55
57
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"lib/commands/uniprot.rb",
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56
58
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"lib/configuration.rb",
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@@ -59,6 +61,7 @@ Gem::Specification.new do |s|
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59
61
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"lib/retryable_typhoeus.rb",
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60
62
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"lib/server_message.rb",
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61
63
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"lib/version.rb",
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64
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+
"test.taxa",
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62
65
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"test/commands/test_peptfilter.rb",
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63
66
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"test/commands/test_prot2pept.rb",
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64
67
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"test/commands/test_unipept.rb",
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@@ -74,8 +77,20 @@ Gem::Specification.new do |s|
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74
77
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"test/commands/unipept/test_pept2taxa.rb",
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75
78
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"test/commands/unipept/test_peptinfo.rb",
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76
79
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"test/commands/unipept/test_taxa2lca.rb",
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80
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+
"test/commands/unipept/test_taxa2tree.rb",
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77
81
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"test/commands/unipept/test_taxonomy.rb",
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78
82
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"test/helper.rb",
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83
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+
"test/support/api_stub.rb",
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84
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"test/support/resources/pept2ec.json",
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85
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"test/support/resources/pept2funct.json",
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86
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+
"test/support/resources/pept2go.json",
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87
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"test/support/resources/pept2interpro.json",
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88
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"test/support/resources/pept2lca.json",
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89
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"test/support/resources/pept2prot.json",
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90
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+
"test/support/resources/pept2taxa.json",
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91
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+
"test/support/resources/peptinfo.json",
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92
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"test/support/resources/taxa2tree.json",
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93
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+
"test/support/resources/taxonomy.json",
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79
94
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"test/test_batch_iterator.rb",
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80
95
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"test/test_batch_order.rb",
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81
96
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"test/test_configuration.rb",
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: unipept
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 2.
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4
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+
version: 2.2.0
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Bart Mesuere
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@@ -11,7 +11,7 @@ authors:
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11
11
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autorequire:
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12
12
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bindir: bin
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13
13
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cert_chain: []
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14
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-
date: 2020-04-
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14
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date: 2020-04-27 00:00:00.000000000 Z
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15
15
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dependencies:
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16
16
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- !ruby/object:Gem::Dependency
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17
17
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name: cri
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@@ -100,6 +100,7 @@ extra_rdoc_files:
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100
100
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files:
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101
101
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- ".document"
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102
102
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- ".github/workflows/ci.yml"
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103
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+
- ".rakeTasks"
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103
104
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- ".rubocop.yml"
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104
105
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- ".ruby-version"
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105
106
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- Gemfile
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@@ -129,6 +130,7 @@ files:
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129
130
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- lib/commands/unipept/pept2taxa.rb
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130
131
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- lib/commands/unipept/peptinfo.rb
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131
132
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- lib/commands/unipept/taxa2lca.rb
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133
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+
- lib/commands/unipept/taxa2tree.rb
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132
134
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- lib/commands/unipept/taxonomy.rb
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133
135
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- lib/commands/uniprot.rb
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134
136
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- lib/configuration.rb
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@@ -137,6 +139,7 @@ files:
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137
139
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- lib/retryable_typhoeus.rb
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138
140
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- lib/server_message.rb
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139
141
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- lib/version.rb
|
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142
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+
- test.taxa
|
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140
143
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- test/commands/test_peptfilter.rb
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141
144
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- test/commands/test_prot2pept.rb
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142
145
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- test/commands/test_unipept.rb
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@@ -152,8 +155,20 @@ files:
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152
155
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- test/commands/unipept/test_pept2taxa.rb
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153
156
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- test/commands/unipept/test_peptinfo.rb
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154
157
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- test/commands/unipept/test_taxa2lca.rb
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158
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+
- test/commands/unipept/test_taxa2tree.rb
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155
159
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- test/commands/unipept/test_taxonomy.rb
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156
160
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- test/helper.rb
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161
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+
- test/support/api_stub.rb
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162
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+
- test/support/resources/pept2ec.json
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163
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+
- test/support/resources/pept2funct.json
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164
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+
- test/support/resources/pept2go.json
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165
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+
- test/support/resources/pept2interpro.json
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166
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+
- test/support/resources/pept2lca.json
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167
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+
- test/support/resources/pept2prot.json
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168
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+
- test/support/resources/pept2taxa.json
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169
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+
- test/support/resources/peptinfo.json
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170
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+
- test/support/resources/taxa2tree.json
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171
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+
- test/support/resources/taxonomy.json
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157
172
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- test/test_batch_iterator.rb
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158
173
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- test/test_batch_order.rb
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159
174
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- test/test_configuration.rb
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