unipept 2.1.1 → 2.2.0
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/.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
|
@@ -0,0 +1,22 @@
|
|
|
1
|
+
[
|
|
2
|
+
{
|
|
3
|
+
"taxon_id": 216816,
|
|
4
|
+
"taxon_name": "Bifidobacterium longum",
|
|
5
|
+
"taxon_rank": "species"
|
|
6
|
+
},
|
|
7
|
+
{
|
|
8
|
+
"taxon_id": 1680,
|
|
9
|
+
"taxon_name": "Bifidobacterium adolescentis",
|
|
10
|
+
"taxon_rank": "species"
|
|
11
|
+
},
|
|
12
|
+
{
|
|
13
|
+
"taxon_id": 1,
|
|
14
|
+
"taxon_name": "root",
|
|
15
|
+
"taxon_rank": "no rank"
|
|
16
|
+
},
|
|
17
|
+
{
|
|
18
|
+
"taxon_id": 2,
|
|
19
|
+
"taxon_name": "Bacteria",
|
|
20
|
+
"taxon_rank": "superkingdom"
|
|
21
|
+
}
|
|
22
|
+
]
|
data/unipept.gemspec
CHANGED
|
@@ -2,16 +2,16 @@
|
|
|
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 2.
|
|
5
|
+
# stub: unipept 2.2.0 ruby lib
|
|
6
6
|
|
|
7
7
|
Gem::Specification.new do |s|
|
|
8
8
|
s.name = "unipept".freeze
|
|
9
|
-
s.version = "2.
|
|
9
|
+
s.version = "2.2.0"
|
|
10
10
|
|
|
11
11
|
s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
|
|
12
12
|
s.require_paths = ["lib".freeze]
|
|
13
13
|
s.authors = ["Bart Mesuere".freeze, "Pieter Verschaffelt".freeze, "Toon Willems".freeze, "Tom Naessens".freeze]
|
|
14
|
-
s.date = "2020-04-
|
|
14
|
+
s.date = "2020-04-27"
|
|
15
15
|
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
|
|
16
16
|
s.email = "unipept@ugent.be".freeze
|
|
17
17
|
s.executables = ["unipept".freeze, "prot2pept".freeze, "peptfilter".freeze, "uniprot".freeze]
|
|
@@ -22,6 +22,7 @@ Gem::Specification.new do |s|
|
|
|
22
22
|
s.files = [
|
|
23
23
|
".document",
|
|
24
24
|
".github/workflows/ci.yml",
|
|
25
|
+
".rakeTasks",
|
|
25
26
|
".rubocop.yml",
|
|
26
27
|
".ruby-version",
|
|
27
28
|
"Gemfile",
|
|
@@ -51,6 +52,7 @@ Gem::Specification.new do |s|
|
|
|
51
52
|
"lib/commands/unipept/pept2taxa.rb",
|
|
52
53
|
"lib/commands/unipept/peptinfo.rb",
|
|
53
54
|
"lib/commands/unipept/taxa2lca.rb",
|
|
55
|
+
"lib/commands/unipept/taxa2tree.rb",
|
|
54
56
|
"lib/commands/unipept/taxonomy.rb",
|
|
55
57
|
"lib/commands/uniprot.rb",
|
|
56
58
|
"lib/configuration.rb",
|
|
@@ -59,6 +61,7 @@ Gem::Specification.new do |s|
|
|
|
59
61
|
"lib/retryable_typhoeus.rb",
|
|
60
62
|
"lib/server_message.rb",
|
|
61
63
|
"lib/version.rb",
|
|
64
|
+
"test.taxa",
|
|
62
65
|
"test/commands/test_peptfilter.rb",
|
|
63
66
|
"test/commands/test_prot2pept.rb",
|
|
64
67
|
"test/commands/test_unipept.rb",
|
|
@@ -74,8 +77,20 @@ Gem::Specification.new do |s|
|
|
|
74
77
|
"test/commands/unipept/test_pept2taxa.rb",
|
|
75
78
|
"test/commands/unipept/test_peptinfo.rb",
|
|
76
79
|
"test/commands/unipept/test_taxa2lca.rb",
|
|
80
|
+
"test/commands/unipept/test_taxa2tree.rb",
|
|
77
81
|
"test/commands/unipept/test_taxonomy.rb",
|
|
78
82
|
"test/helper.rb",
|
|
83
|
+
"test/support/api_stub.rb",
|
|
84
|
+
"test/support/resources/pept2ec.json",
|
|
85
|
+
"test/support/resources/pept2funct.json",
|
|
86
|
+
"test/support/resources/pept2go.json",
|
|
87
|
+
"test/support/resources/pept2interpro.json",
|
|
88
|
+
"test/support/resources/pept2lca.json",
|
|
89
|
+
"test/support/resources/pept2prot.json",
|
|
90
|
+
"test/support/resources/pept2taxa.json",
|
|
91
|
+
"test/support/resources/peptinfo.json",
|
|
92
|
+
"test/support/resources/taxa2tree.json",
|
|
93
|
+
"test/support/resources/taxonomy.json",
|
|
79
94
|
"test/test_batch_iterator.rb",
|
|
80
95
|
"test/test_batch_order.rb",
|
|
81
96
|
"test/test_configuration.rb",
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: unipept
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 2.
|
|
4
|
+
version: 2.2.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Bart Mesuere
|
|
@@ -11,7 +11,7 @@ authors:
|
|
|
11
11
|
autorequire:
|
|
12
12
|
bindir: bin
|
|
13
13
|
cert_chain: []
|
|
14
|
-
date: 2020-04-
|
|
14
|
+
date: 2020-04-27 00:00:00.000000000 Z
|
|
15
15
|
dependencies:
|
|
16
16
|
- !ruby/object:Gem::Dependency
|
|
17
17
|
name: cri
|
|
@@ -100,6 +100,7 @@ extra_rdoc_files:
|
|
|
100
100
|
files:
|
|
101
101
|
- ".document"
|
|
102
102
|
- ".github/workflows/ci.yml"
|
|
103
|
+
- ".rakeTasks"
|
|
103
104
|
- ".rubocop.yml"
|
|
104
105
|
- ".ruby-version"
|
|
105
106
|
- Gemfile
|
|
@@ -129,6 +130,7 @@ files:
|
|
|
129
130
|
- lib/commands/unipept/pept2taxa.rb
|
|
130
131
|
- lib/commands/unipept/peptinfo.rb
|
|
131
132
|
- lib/commands/unipept/taxa2lca.rb
|
|
133
|
+
- lib/commands/unipept/taxa2tree.rb
|
|
132
134
|
- lib/commands/unipept/taxonomy.rb
|
|
133
135
|
- lib/commands/uniprot.rb
|
|
134
136
|
- lib/configuration.rb
|
|
@@ -137,6 +139,7 @@ files:
|
|
|
137
139
|
- lib/retryable_typhoeus.rb
|
|
138
140
|
- lib/server_message.rb
|
|
139
141
|
- lib/version.rb
|
|
142
|
+
- test.taxa
|
|
140
143
|
- test/commands/test_peptfilter.rb
|
|
141
144
|
- test/commands/test_prot2pept.rb
|
|
142
145
|
- test/commands/test_unipept.rb
|
|
@@ -152,8 +155,20 @@ files:
|
|
|
152
155
|
- test/commands/unipept/test_pept2taxa.rb
|
|
153
156
|
- test/commands/unipept/test_peptinfo.rb
|
|
154
157
|
- test/commands/unipept/test_taxa2lca.rb
|
|
158
|
+
- test/commands/unipept/test_taxa2tree.rb
|
|
155
159
|
- test/commands/unipept/test_taxonomy.rb
|
|
156
160
|
- test/helper.rb
|
|
161
|
+
- test/support/api_stub.rb
|
|
162
|
+
- test/support/resources/pept2ec.json
|
|
163
|
+
- test/support/resources/pept2funct.json
|
|
164
|
+
- test/support/resources/pept2go.json
|
|
165
|
+
- test/support/resources/pept2interpro.json
|
|
166
|
+
- test/support/resources/pept2lca.json
|
|
167
|
+
- test/support/resources/pept2prot.json
|
|
168
|
+
- test/support/resources/pept2taxa.json
|
|
169
|
+
- test/support/resources/peptinfo.json
|
|
170
|
+
- test/support/resources/taxa2tree.json
|
|
171
|
+
- test/support/resources/taxonomy.json
|
|
157
172
|
- test/test_batch_iterator.rb
|
|
158
173
|
- test/test_batch_order.rb
|
|
159
174
|
- test/test_configuration.rb
|