full_lengther_next 0.6.2 → 0.9.8

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.
Files changed (59) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +9 -0
  3. data/.rspec +2 -0
  4. data/.travis.yml +5 -0
  5. data/CODE_OF_CONDUCT.md +49 -0
  6. data/Gemfile +4 -0
  7. data/LICENSE.txt +21 -0
  8. data/{README.rdoc → README.md} +0 -0
  9. data/Rakefile +6 -37
  10. data/bin/console +14 -0
  11. data/bin/download_fln_dbs.rb +2 -7
  12. data/bin/full_lengther_next +85 -6
  13. data/bin/make_user_db.rb +13 -5
  14. data/bin/setup +8 -0
  15. data/full_lengther_next.gemspec +42 -0
  16. data/lib/full_lengther_next.rb +2 -10
  17. data/lib/full_lengther_next/artifacts.rb +74 -0
  18. data/lib/full_lengther_next/{classes/blast_functions.rb → blast_functions.rb} +0 -0
  19. data/lib/full_lengther_next/{classes/cdhit.rb → cdhit.rb} +0 -0
  20. data/lib/full_lengther_next/{classes/chimeric_seqs.rb → chimeric_seqs.rb} +0 -0
  21. data/lib/full_lengther_next/{classes/common_functions.rb → common_functions.rb} +0 -0
  22. data/lib/full_lengther_next/{classes/exonerate_result.rb → exonerate_result.rb} +0 -0
  23. data/lib/full_lengther_next/{classes/fl_analysis.rb → fl_analysis.rb} +0 -0
  24. data/lib/full_lengther_next/{classes/fl_string_utils.rb → fl_string_utils.rb} +0 -0
  25. data/lib/full_lengther_next/fln_stats.rb +613 -0
  26. data/lib/full_lengther_next/go_methods.rb +42 -0
  27. data/lib/full_lengther_next/{classes/handle_db.rb → handle_db.rb} +0 -0
  28. data/lib/full_lengther_next/mapping.rb +296 -0
  29. data/lib/full_lengther_next/{classes/my_worker.rb → my_worker.rb} +71 -9
  30. data/lib/full_lengther_next/{classes/my_worker_EST.rb → my_worker_EST.rb} +0 -0
  31. data/lib/full_lengther_next/{classes/my_worker_manager_EST.rb → my_worker_manager_EST.rb} +0 -0
  32. data/lib/full_lengther_next/{classes/my_worker_manager_fln.rb → my_worker_manager_fln.rb} +181 -16
  33. data/lib/full_lengther_next/{classes/nc_rna.rb → nc_rna.rb} +0 -0
  34. data/lib/full_lengther_next/{classes/orf.rb → orf.rb} +0 -0
  35. data/lib/full_lengther_next/{classes/reptrans.rb → reptrans.rb} +9 -5
  36. data/lib/full_lengther_next/{classes/sequence.rb → sequence.rb} +26 -1
  37. data/lib/full_lengther_next/{classes/test_code.rb → test_code.rb} +1 -1
  38. data/lib/full_lengther_next/{classes/types.rb → types.rb} +3 -2
  39. data/lib/full_lengther_next/{classes/une_los_hit.rb → une_los_hit.rb} +0 -0
  40. data/lib/full_lengther_next/version.rb +3 -0
  41. data/lib/full_lengther_next/{classes/warnings.rb → warnings.rb} +0 -0
  42. data/report_templates/general_summary.erb +140 -0
  43. data/report_templates/mapping_summary.erb +98 -0
  44. data/report_templates/reptrans_summary.erb +32 -0
  45. metadata +112 -134
  46. data/.gemtest +0 -0
  47. data/History.txt +0 -32
  48. data/Manifest.txt +0 -44
  49. data/PostInstall.txt +0 -6
  50. data/bin/plot_fln.rb +0 -270
  51. data/bin/plot_taxonomy.rb +0 -70
  52. data/lib/expresscanvas.zip +0 -0
  53. data/lib/full_lengther_next/classes/artifacts.rb +0 -66
  54. data/lib/full_lengther_next/classes/fln_stats.rb +0 -641
  55. data/script/console +0 -10
  56. data/script/destroy +0 -14
  57. data/script/generate +0 -14
  58. data/test/test_full_lengther_next.rb +0 -11
  59. data/test/test_helper.rb +0 -3
@@ -0,0 +1,98 @@
1
+ <%
2
+ base_pie_config = {
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+ header: true,
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+ width: '650px',
5
+ height: '650px',
6
+ responsive: false,
7
+ title: nil,
8
+ config: {
9
+ 'fontName' => 'Arial',
10
+ 'showPieValues' => false,
11
+ 'pieSegmentPrecision' => 3,
12
+ 'maxPieSectors' => 30,
13
+ 'legendBox' => false,
14
+ 'legendScaleFontFactor' => 0.9
15
+ }
16
+ }
17
+ %>
18
+ <center>
19
+ <div style="float: center; font-size: 30; margin:10px">
20
+ <b>Full-LengtherNEXT Mapping Summary</b>
21
+ </div>
22
+ <div style="overflow: hidden; width: 1320px; heigth: 800px; padding: 10">
23
+ <div style="margin: 0; float: left">
24
+ <%= table_title('Mean coverage <br>') %>
25
+ <%=sccater2D(
26
+ id: :mean_coverage,
27
+ x_label: 'Transcripts',
28
+ y_label: 'Coverage (reads)',
29
+ title: nil,
30
+ header: true,
31
+ responsive: false
32
+ )
33
+ %>
34
+ </div>
35
+ <div style="margin: 0; float: rigth">
36
+ <%= table_title('Normalized partial coverage') %>
37
+ <%=sccater2D(
38
+ id: :normalized_partial_coverage,
39
+ x_label: 'Transcript sequence mapped (%)',
40
+ y_label: 'Normalized difference (%)',
41
+ title: nil,
42
+ responsive: false,
43
+ )
44
+ %>
45
+ </div>
46
+ </div>
47
+ <div style="overflow: hidden; width: 1320px; padding: 10">
48
+ <div style="margin: 0; float: left">
49
+ <%= table_title('Coverage analysis on transcripts') %>
50
+ <%=sccater2D(
51
+ id: :normalized_coverages_sorted_by_npc,
52
+ x_label: 'Transcript sequence mapped (%)',
53
+ y_label: 'Mean coverage (reads)',
54
+ title: nil,
55
+ responsive: false,
56
+ )
57
+ %>
58
+ </div>
59
+ <div style="margin: 0; float: rigth">
60
+ </div>
61
+ </div>
62
+
63
+ <div style="overflow: hidden; width: 1320px; padding: 10">
64
+ <div style="margin: 0; float: left">
65
+ <%= table_title('GO: Molecular function') %>
66
+ <%= pie(base_pie_config.merge({
67
+ id: :function_go,
68
+ row_names: true,
69
+ header: true
70
+ }
71
+ ))
72
+ %>
73
+ </div>
74
+ <div style="margin: 0; float: rigth">
75
+ <%= table_title('GO: Biological process') %>
76
+ <%= pie(base_pie_config.merge({
77
+ id: :process_go,
78
+ row_names: true,
79
+ header: true
80
+ }
81
+ ))
82
+ %>
83
+ </div>
84
+ </div>
85
+ <div style="overflow: hidden; width: 1320px; padding: 10">
86
+ <div style="margin: 0; float: left">
87
+ <%= table_title('GO: Cellular component') %>
88
+ <%= pie(base_pie_config.merge({
89
+ id: :component_go,
90
+ row_names: true,
91
+ header: true
92
+ }
93
+ ))
94
+ %>
95
+ </div>
96
+
97
+ </div>
98
+ </center>
@@ -0,0 +1,32 @@
1
+ <% base_table_config = {
2
+ header: true,
3
+ border: 2,
4
+ cell_align: ['left', 'right', 'right'],
5
+ attrib: {
6
+ 'cellspacing' => 0,
7
+ 'cellpadding' => 2
8
+ }
9
+ } %>
10
+ <center>
11
+ <div style="float: center; font-size: 30; margin: 10px">
12
+ <b> Full-LengtherNEXT Representative Transcriptome Summary </b>
13
+ </div>
14
+ <div style="width: 850px; height: 350px; padding: 10">
15
+ <div style="margin: 0; float:left">
16
+ <%= table_title('Sequences info') %>
17
+ <%= table(base_table_config.merge({
18
+ id: :general_report,
19
+ }
20
+ ))
21
+ %>
22
+ </div>
23
+ <div style="margin: 0; float: rigth">
24
+ <%= table_title('Sequences summary (Acumulative)') %>
25
+ <%= table(base_table_config.merge({
26
+ id: :acumulative_report,
27
+ }
28
+ ))
29
+ %>
30
+ </div>
31
+ </div>
32
+ </center>
metadata CHANGED
@@ -1,176 +1,157 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: full_lengther_next
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.6.2
5
- prerelease:
4
+ version: 0.9.8
6
5
  platform: ruby
7
6
  authors:
8
- - ! 'Pedro Seoane & Noe Fernandez & Dario Guerrero '
7
+ - Pedro Seoane
8
+ - Noe Fernandez
9
+ - Dario Guerrero
9
10
  autorequire:
10
11
  bindir: bin
11
12
  cert_chain: []
12
- date: 2016-05-04 00:00:00.000000000 Z
13
+ date: 2018-02-14 00:00:00.000000000 Z
13
14
  dependencies:
14
15
  - !ruby/object:Gem::Dependency
15
16
  name: xml-simple
16
17
  requirement: !ruby/object:Gem::Requirement
17
- none: false
18
18
  requirements:
19
- - - ! '>='
19
+ - - ">="
20
20
  - !ruby/object:Gem::Version
21
- version: 1.0.12
21
+ version: '0'
22
22
  type: :runtime
23
23
  prerelease: false
24
24
  version_requirements: !ruby/object:Gem::Requirement
25
- none: false
26
25
  requirements:
27
- - - ! '>='
26
+ - - ">="
28
27
  - !ruby/object:Gem::Version
29
- version: 1.0.12
28
+ version: '0'
30
29
  - !ruby/object:Gem::Dependency
31
- name: scbi_blast
30
+ name: scbi_fasta
32
31
  requirement: !ruby/object:Gem::Requirement
33
- none: false
34
32
  requirements:
35
- - - ! '>='
33
+ - - ">="
36
34
  - !ruby/object:Gem::Version
37
- version: 0.0.32
35
+ version: '0'
38
36
  type: :runtime
39
37
  prerelease: false
40
38
  version_requirements: !ruby/object:Gem::Requirement
41
- none: false
42
39
  requirements:
43
- - - ! '>='
40
+ - - ">="
44
41
  - !ruby/object:Gem::Version
45
- version: 0.0.32
42
+ version: '0'
46
43
  - !ruby/object:Gem::Dependency
47
- name: scbi_mapreduce
44
+ name: scbi_blast
48
45
  requirement: !ruby/object:Gem::Requirement
49
- none: false
50
46
  requirements:
51
- - - ! '>='
47
+ - - ">="
52
48
  - !ruby/object:Gem::Version
53
- version: 0.0.29
49
+ version: '0'
54
50
  type: :runtime
55
51
  prerelease: false
56
52
  version_requirements: !ruby/object:Gem::Requirement
57
- none: false
58
53
  requirements:
59
- - - ! '>='
54
+ - - ">="
60
55
  - !ruby/object:Gem::Version
61
- version: 0.0.29
56
+ version: '0'
62
57
  - !ruby/object:Gem::Dependency
63
- name: scbi_zcat
58
+ name: scbi_mapreduce
64
59
  requirement: !ruby/object:Gem::Requirement
65
- none: false
66
60
  requirements:
67
- - - ! '>='
61
+ - - ">="
68
62
  - !ruby/object:Gem::Version
69
63
  version: '0'
70
64
  type: :runtime
71
65
  prerelease: false
72
66
  version_requirements: !ruby/object:Gem::Requirement
73
- none: false
74
67
  requirements:
75
- - - ! '>='
68
+ - - ">="
76
69
  - !ruby/object:Gem::Version
77
70
  version: '0'
78
71
  - !ruby/object:Gem::Dependency
79
- name: bio-cd-hit-report
72
+ name: scbi_zcat
80
73
  requirement: !ruby/object:Gem::Requirement
81
- none: false
82
74
  requirements:
83
- - - ! '>='
75
+ - - ">="
84
76
  - !ruby/object:Gem::Version
85
- version: 0.1.0
77
+ version: '0'
86
78
  type: :runtime
87
79
  prerelease: false
88
80
  version_requirements: !ruby/object:Gem::Requirement
89
- none: false
90
81
  requirements:
91
- - - ! '>='
82
+ - - ">="
92
83
  - !ruby/object:Gem::Version
93
- version: 0.1.0
84
+ version: '0'
94
85
  - !ruby/object:Gem::Dependency
95
- name: bio
86
+ name: bio-cd-hit-report
96
87
  requirement: !ruby/object:Gem::Requirement
97
- none: false
98
88
  requirements:
99
- - - ! '>='
89
+ - - ">="
100
90
  - !ruby/object:Gem::Version
101
- version: 1.4.3
91
+ version: '0'
102
92
  type: :runtime
103
93
  prerelease: false
104
94
  version_requirements: !ruby/object:Gem::Requirement
105
- none: false
106
95
  requirements:
107
- - - ! '>='
96
+ - - ">="
108
97
  - !ruby/object:Gem::Version
109
- version: 1.4.3
98
+ version: '0'
110
99
  - !ruby/object:Gem::Dependency
111
- name: scbi_plot
100
+ name: report_html
112
101
  requirement: !ruby/object:Gem::Requirement
113
- none: false
114
102
  requirements:
115
- - - ! '>='
103
+ - - ">="
116
104
  - !ruby/object:Gem::Version
117
- version: 0.0.6
105
+ version: '0'
118
106
  type: :runtime
119
107
  prerelease: false
120
108
  version_requirements: !ruby/object:Gem::Requirement
121
- none: false
122
109
  requirements:
123
- - - ! '>='
110
+ - - ">="
124
111
  - !ruby/object:Gem::Version
125
- version: 0.0.6
112
+ version: '0'
126
113
  - !ruby/object:Gem::Dependency
127
- name: rdoc
114
+ name: bundler
128
115
  requirement: !ruby/object:Gem::Requirement
129
- none: false
130
116
  requirements:
131
- - - ~>
117
+ - - "~>"
132
118
  - !ruby/object:Gem::Version
133
- version: '3.10'
119
+ version: '1.12'
134
120
  type: :development
135
121
  prerelease: false
136
122
  version_requirements: !ruby/object:Gem::Requirement
137
- none: false
138
123
  requirements:
139
- - - ~>
124
+ - - "~>"
140
125
  - !ruby/object:Gem::Version
141
- version: '3.10'
126
+ version: '1.12'
142
127
  - !ruby/object:Gem::Dependency
143
- name: newgem
128
+ name: rake
144
129
  requirement: !ruby/object:Gem::Requirement
145
- none: false
146
130
  requirements:
147
- - - ! '>='
131
+ - - "~>"
148
132
  - !ruby/object:Gem::Version
149
- version: 1.5.3
133
+ version: '10.0'
150
134
  type: :development
151
135
  prerelease: false
152
136
  version_requirements: !ruby/object:Gem::Requirement
153
- none: false
154
137
  requirements:
155
- - - ! '>='
138
+ - - "~>"
156
139
  - !ruby/object:Gem::Version
157
- version: 1.5.3
140
+ version: '10.0'
158
141
  - !ruby/object:Gem::Dependency
159
- name: hoe
142
+ name: rspec
160
143
  requirement: !ruby/object:Gem::Requirement
161
- none: false
162
144
  requirements:
163
- - - ~>
145
+ - - "~>"
164
146
  - !ruby/object:Gem::Version
165
- version: '3.3'
147
+ version: '3.0'
166
148
  type: :development
167
149
  prerelease: false
168
150
  version_requirements: !ruby/object:Gem::Requirement
169
- none: false
170
151
  requirements:
171
- - - ~>
152
+ - - "~>"
172
153
  - !ruby/object:Gem::Version
173
- version: '3.3'
154
+ version: '3.0'
174
155
  description: FULL-LENGTHERNEXT is a tool adapted to NGS technologies, able to work
175
156
  in parallel and in a distributed way to minimise computing time. It is able to classify
176
157
  unigenes to full-length, 5’-end, 3’-end and internal, suggesting which unknown genes
@@ -178,89 +159,86 @@ description: FULL-LENGTHERNEXT is a tool adapted to NGS technologies, able to wo
178
159
  one of the main mistake found in wrong entries of full-length sequences databases,
179
160
  and it is a fast tool to compare different transcriptome assemblies.
180
161
  email:
181
- - seoanezonjic@hotmail.com & noeisneo@gmail.com & dariogf@gmail.com
162
+ - seoanezonjic@hotmail.com
163
+ - noeisneo@gmail.com
164
+ - dariogf@gmail.com
182
165
  executables:
183
- - plot_taxonomy.rb
184
- - plot_fln.rb
166
+ - console
185
167
  - download_fln_dbs.rb
186
168
  - full_lengther_next
187
- - make_user_db.rb
188
169
  - make_test_dataset.rb
170
+ - make_user_db.rb
171
+ - setup
189
172
  extensions: []
190
- extra_rdoc_files:
191
- - PostInstall.txt
192
- - README.rdoc
193
- - History.txt
194
- - Manifest.txt
173
+ extra_rdoc_files: []
195
174
  files:
175
+ - ".gitignore"
176
+ - ".rspec"
177
+ - ".travis.yml"
178
+ - CODE_OF_CONDUCT.md
179
+ - Gemfile
180
+ - LICENSE.txt
181
+ - README.md
196
182
  - Rakefile
197
- - script/generate
198
- - script/destroy
199
- - script/console
200
- - test/test_full_lengther_next.rb
201
- - test/test_helper.rb
202
- - bin/plot_taxonomy.rb
203
- - bin/plot_fln.rb
183
+ - bin/console
204
184
  - bin/download_fln_dbs.rb
205
185
  - bin/full_lengther_next
206
- - bin/make_user_db.rb
207
186
  - bin/make_test_dataset.rb
208
- - PostInstall.txt
209
- - README.rdoc
210
- - History.txt
211
- - Manifest.txt
212
- - lib/full_lengther_next/classes/blast_functions.rb
213
- - lib/full_lengther_next/classes/my_worker_manager_fln.rb
214
- - lib/full_lengther_next/classes/types.rb
215
- - lib/full_lengther_next/classes/chimeric_seqs.rb
216
- - lib/full_lengther_next/classes/artifacts.rb
217
- - lib/full_lengther_next/classes/cdhit.rb
218
- - lib/full_lengther_next/classes/fl_analysis.rb
219
- - lib/full_lengther_next/classes/fl_string_utils.rb
220
- - lib/full_lengther_next/classes/my_worker.rb
221
- - lib/full_lengther_next/classes/sequence.rb
222
- - lib/full_lengther_next/classes/my_worker_EST.rb
223
- - lib/full_lengther_next/classes/test_code.rb
224
- - lib/full_lengther_next/classes/orf.rb
225
- - lib/full_lengther_next/classes/une_los_hit.rb
226
- - lib/full_lengther_next/classes/warnings.rb
227
- - lib/full_lengther_next/classes/fln_stats.rb
228
- - lib/full_lengther_next/classes/my_worker_manager_EST.rb
229
- - lib/full_lengther_next/classes/nc_rna.rb
230
- - lib/full_lengther_next/classes/reptrans.rb
231
- - lib/full_lengther_next/classes/common_functions.rb
232
- - lib/full_lengther_next/classes/exonerate_result.rb
233
- - lib/full_lengther_next/classes/handle_db.rb
187
+ - bin/make_user_db.rb
188
+ - bin/setup
189
+ - full_lengther_next.gemspec
234
190
  - lib/full_lengther_next.rb
235
- - lib/expresscanvas.zip
236
- - .gemtest
237
- homepage: http://www.scbi.uma.es/downloads
238
- licenses: []
239
- post_install_message: PostInstall.txt
240
- rdoc_options:
241
- - --main
242
- - README.rdoc
191
+ - lib/full_lengther_next/artifacts.rb
192
+ - lib/full_lengther_next/blast_functions.rb
193
+ - lib/full_lengther_next/cdhit.rb
194
+ - lib/full_lengther_next/chimeric_seqs.rb
195
+ - lib/full_lengther_next/common_functions.rb
196
+ - lib/full_lengther_next/exonerate_result.rb
197
+ - lib/full_lengther_next/fl_analysis.rb
198
+ - lib/full_lengther_next/fl_string_utils.rb
199
+ - lib/full_lengther_next/fln_stats.rb
200
+ - lib/full_lengther_next/go_methods.rb
201
+ - lib/full_lengther_next/handle_db.rb
202
+ - lib/full_lengther_next/mapping.rb
203
+ - lib/full_lengther_next/my_worker.rb
204
+ - lib/full_lengther_next/my_worker_EST.rb
205
+ - lib/full_lengther_next/my_worker_manager_EST.rb
206
+ - lib/full_lengther_next/my_worker_manager_fln.rb
207
+ - lib/full_lengther_next/nc_rna.rb
208
+ - lib/full_lengther_next/orf.rb
209
+ - lib/full_lengther_next/reptrans.rb
210
+ - lib/full_lengther_next/sequence.rb
211
+ - lib/full_lengther_next/test_code.rb
212
+ - lib/full_lengther_next/types.rb
213
+ - lib/full_lengther_next/une_los_hit.rb
214
+ - lib/full_lengther_next/version.rb
215
+ - lib/full_lengther_next/warnings.rb
216
+ - report_templates/general_summary.erb
217
+ - report_templates/mapping_summary.erb
218
+ - report_templates/reptrans_summary.erb
219
+ homepage: https://github.com/seoanezonjic
220
+ licenses:
221
+ - MIT
222
+ metadata: {}
223
+ post_install_message:
224
+ rdoc_options: []
243
225
  require_paths:
244
226
  - lib
245
227
  required_ruby_version: !ruby/object:Gem::Requirement
246
- none: false
247
228
  requirements:
248
- - - ! '>='
229
+ - - ">="
249
230
  - !ruby/object:Gem::Version
250
231
  version: '0'
251
232
  required_rubygems_version: !ruby/object:Gem::Requirement
252
- none: false
253
233
  requirements:
254
- - - ! '>='
234
+ - - ">="
255
235
  - !ruby/object:Gem::Version
256
236
  version: '0'
257
237
  requirements: []
258
- rubyforge_project: full_lengther_next
259
- rubygems_version: 1.8.23
238
+ rubyforge_project:
239
+ rubygems_version: 2.4.8
260
240
  signing_key:
261
- specification_version: 3
262
- summary: FULL-LENGTHERNEXT is a tool adapted to NGS technologies, able to work in
263
- parallel and in a distributed way to minimise computing time
264
- test_files:
265
- - test/test_full_lengther_next.rb
266
- - test/test_helper.rb
241
+ specification_version: 4
242
+ summary: Tool to annotate transcriptomes and it is able to stablish the integrity
243
+ of each transcript. Also, FLN can detect novel genes on a target organism.
244
+ test_files: []