rbbt-util 1.1.0 → 1.2.1
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.
- data/lib/rbbt-util.rb +2 -0
- data/lib/rbbt.rb +1 -0
- data/lib/rbbt/util/R.rb +24 -0
- data/lib/rbbt/util/bed.rb +325 -0
- data/lib/rbbt/util/cmd.rb +2 -1
- data/lib/rbbt/util/data_module.rb +25 -34
- data/lib/rbbt/util/excel2tsv.rb +2 -3
- data/lib/rbbt/util/log.rb +5 -0
- data/lib/rbbt/util/misc.rb +29 -1
- data/lib/rbbt/util/open.rb +1 -0
- data/lib/rbbt/util/persistence.rb +109 -0
- data/lib/rbbt/util/pkg_data.rb +114 -62
- data/lib/rbbt/util/rake.rb +78 -0
- data/lib/rbbt/util/tc_hash.rb +7 -1
- data/lib/rbbt/util/tsv.rb +582 -153
- data/lib/rbbt/util/workflow.rb +1 -2
- data/share/lib/R/util.R +89 -0
- data/test/rbbt/util/test_R.rb +9 -0
- data/test/rbbt/util/test_bed.rb +136 -0
- data/test/rbbt/util/test_data_module.rb +10 -10
- data/test/rbbt/util/test_misc.rb +1 -0
- data/test/rbbt/util/test_persistence.rb +60 -0
- data/test/rbbt/util/test_pkg_data.rb +113 -0
- data/test/rbbt/util/test_rake.rb +54 -0
- data/test/rbbt/util/test_tsv.rb +91 -46
- data/test/rbbt/util/test_workflow.rb +5 -2
- data/test/test_helper.rb +4 -0
- data/test/test_pkg.rb +0 -10
- data/test/test_rbbt.rb +3 -48
- metadata +21 -6
metadata
CHANGED
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: rbbt-util
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
hash:
|
|
5
|
-
prerelease:
|
|
4
|
+
hash: 29
|
|
5
|
+
prerelease:
|
|
6
6
|
segments:
|
|
7
7
|
- 1
|
|
8
|
+
- 2
|
|
8
9
|
- 1
|
|
9
|
-
|
|
10
|
-
version: 1.1.0
|
|
10
|
+
version: 1.2.1
|
|
11
11
|
platform: ruby
|
|
12
12
|
authors:
|
|
13
13
|
- Miguel Vazquez
|
|
@@ -15,7 +15,7 @@ autorequire:
|
|
|
15
15
|
bindir: bin
|
|
16
16
|
cert_chain: []
|
|
17
17
|
|
|
18
|
-
date:
|
|
18
|
+
date: 2011-01-30 00:00:00 +01:00
|
|
19
19
|
default_executable:
|
|
20
20
|
dependencies:
|
|
21
21
|
- !ruby/object:Gem::Dependency
|
|
@@ -101,6 +101,8 @@ files:
|
|
|
101
101
|
- LICENSE
|
|
102
102
|
- lib/rbbt-util.rb
|
|
103
103
|
- lib/rbbt.rb
|
|
104
|
+
- lib/rbbt/util/R.rb
|
|
105
|
+
- lib/rbbt/util/bed.rb
|
|
104
106
|
- lib/rbbt/util/cachehelper.rb
|
|
105
107
|
- lib/rbbt/util/cmd.rb
|
|
106
108
|
- lib/rbbt/util/data_module.rb
|
|
@@ -109,9 +111,11 @@ files:
|
|
|
109
111
|
- lib/rbbt/util/log.rb
|
|
110
112
|
- lib/rbbt/util/misc.rb
|
|
111
113
|
- lib/rbbt/util/open.rb
|
|
114
|
+
- lib/rbbt/util/persistence.rb
|
|
112
115
|
- lib/rbbt/util/pkg_config.rb
|
|
113
116
|
- lib/rbbt/util/pkg_data.rb
|
|
114
117
|
- lib/rbbt/util/pkg_software.rb
|
|
118
|
+
- lib/rbbt/util/rake.rb
|
|
115
119
|
- lib/rbbt/util/simpleDSL.rb
|
|
116
120
|
- lib/rbbt/util/simpleopt.rb
|
|
117
121
|
- lib/rbbt/util/tc_hash.rb
|
|
@@ -119,12 +123,18 @@ files:
|
|
|
119
123
|
- lib/rbbt/util/tsv.rb
|
|
120
124
|
- lib/rbbt/util/workflow.rb
|
|
121
125
|
- share/install/software/lib/install_helpers
|
|
126
|
+
- share/lib/R/util.R
|
|
127
|
+
- test/rbbt/util/test_R.rb
|
|
128
|
+
- test/rbbt/util/test_bed.rb
|
|
122
129
|
- test/rbbt/util/test_cmd.rb
|
|
123
130
|
- test/rbbt/util/test_data_module.rb
|
|
124
131
|
- test/rbbt/util/test_excel2tsv.rb
|
|
125
132
|
- test/rbbt/util/test_filecache.rb
|
|
126
133
|
- test/rbbt/util/test_misc.rb
|
|
127
134
|
- test/rbbt/util/test_open.rb
|
|
135
|
+
- test/rbbt/util/test_persistence.rb
|
|
136
|
+
- test/rbbt/util/test_pkg_data.rb
|
|
137
|
+
- test/rbbt/util/test_rake.rb
|
|
128
138
|
- test/rbbt/util/test_simpleDSL.rb
|
|
129
139
|
- test/rbbt/util/test_simpleopt.rb
|
|
130
140
|
- test/rbbt/util/test_tc_hash.rb
|
|
@@ -166,17 +176,22 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
166
176
|
requirements: []
|
|
167
177
|
|
|
168
178
|
rubyforge_project:
|
|
169
|
-
rubygems_version: 1.
|
|
179
|
+
rubygems_version: 1.4.2
|
|
170
180
|
signing_key:
|
|
171
181
|
specification_version: 3
|
|
172
182
|
summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
|
|
173
183
|
test_files:
|
|
184
|
+
- test/rbbt/util/test_R.rb
|
|
185
|
+
- test/rbbt/util/test_bed.rb
|
|
174
186
|
- test/rbbt/util/test_cmd.rb
|
|
175
187
|
- test/rbbt/util/test_data_module.rb
|
|
176
188
|
- test/rbbt/util/test_excel2tsv.rb
|
|
177
189
|
- test/rbbt/util/test_filecache.rb
|
|
178
190
|
- test/rbbt/util/test_misc.rb
|
|
179
191
|
- test/rbbt/util/test_open.rb
|
|
192
|
+
- test/rbbt/util/test_persistence.rb
|
|
193
|
+
- test/rbbt/util/test_pkg_data.rb
|
|
194
|
+
- test/rbbt/util/test_rake.rb
|
|
180
195
|
- test/rbbt/util/test_simpleDSL.rb
|
|
181
196
|
- test/rbbt/util/test_simpleopt.rb
|
|
182
197
|
- test/rbbt/util/test_tc_hash.rb
|