full_lengther_next 0.6.2 → 0.9.8

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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
data/report_templates/mapping_summary.erb ADDED
@@ -0,0 +1,98 @@
1
+ <%
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+ base_pie_config = {
3
+ header: true,
4
+ 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>
data/report_templates/reptrans_summary.erb ADDED
@@ -0,0 +1,32 @@
1
+ <% base_table_config = {
2
+ header: true,
3
+ border: 2,
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+ 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: []