@apollo-annotation/shared 0.1.18 → 0.1.20

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Files changed (157) hide show
  1. package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts +33 -0
  2. package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js +83 -0
  3. package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map +1 -0
  4. package/dist/Changes/AddAssemblyFromExternalChange.d.ts +34 -0
  5. package/dist/Changes/AddAssemblyFromExternalChange.js +97 -0
  6. package/dist/Changes/AddAssemblyFromExternalChange.js.map +1 -0
  7. package/dist/Changes/AddAssemblyFromFileChange.d.ts +43 -0
  8. package/dist/Changes/AddAssemblyFromFileChange.js +140 -0
  9. package/dist/Changes/AddAssemblyFromFileChange.js.map +1 -0
  10. package/dist/Changes/AddFeatureChange.d.ts +35 -0
  11. package/dist/Changes/AddFeatureChange.js +169 -0
  12. package/dist/Changes/AddFeatureChange.js.map +1 -0
  13. package/dist/Changes/AddFeaturesFromFileChange.d.ts +32 -0
  14. package/dist/Changes/AddFeaturesFromFileChange.js +76 -0
  15. package/dist/Changes/AddFeaturesFromFileChange.js.map +1 -0
  16. package/dist/Changes/AddRefSeqAliasesChange.d.ts +20 -0
  17. package/dist/Changes/AddRefSeqAliasesChange.js +61 -0
  18. package/dist/Changes/AddRefSeqAliasesChange.js.map +1 -0
  19. package/dist/Changes/DeleteAssemblyChange.d.ts +18 -0
  20. package/dist/Changes/DeleteAssemblyChange.js +72 -0
  21. package/dist/Changes/DeleteAssemblyChange.js.map +1 -0
  22. package/dist/Changes/DeleteFeatureChange.d.ts +42 -0
  23. package/dist/Changes/DeleteFeatureChange.js +143 -0
  24. package/dist/Changes/DeleteFeatureChange.js.map +1 -0
  25. package/dist/Changes/DeleteUserChange.d.ts +25 -0
  26. package/dist/Changes/DeleteUserChange.js +53 -0
  27. package/dist/Changes/DeleteUserChange.js.map +1 -0
  28. package/dist/Changes/FeatureAttributeChange.d.ts +31 -0
  29. package/dist/Changes/FeatureAttributeChange.js +112 -0
  30. package/dist/Changes/FeatureAttributeChange.js.map +1 -0
  31. package/dist/Changes/FromFileBaseChange.d.ts +9 -0
  32. package/dist/Changes/FromFileBaseChange.js +187 -0
  33. package/dist/Changes/FromFileBaseChange.js.map +1 -0
  34. package/dist/Changes/ImportJBrowseConfigChange.d.ts +43 -0
  35. package/dist/Changes/ImportJBrowseConfigChange.js +67 -0
  36. package/dist/Changes/ImportJBrowseConfigChange.js.map +1 -0
  37. package/dist/Changes/LocationEndChange.d.ts +32 -0
  38. package/dist/Changes/LocationEndChange.js +129 -0
  39. package/dist/Changes/LocationEndChange.js.map +1 -0
  40. package/dist/Changes/LocationStartChange.d.ts +32 -0
  41. package/dist/Changes/LocationStartChange.js +129 -0
  42. package/dist/Changes/LocationStartChange.js.map +1 -0
  43. package/dist/Changes/StrandChange.d.ts +31 -0
  44. package/dist/Changes/StrandChange.js +114 -0
  45. package/dist/Changes/StrandChange.js.map +1 -0
  46. package/dist/Changes/TypeChange.d.ts +31 -0
  47. package/dist/Changes/TypeChange.js +114 -0
  48. package/dist/Changes/TypeChange.js.map +1 -0
  49. package/dist/Changes/UserChange.d.ts +25 -0
  50. package/dist/Changes/UserChange.js +51 -0
  51. package/dist/Changes/UserChange.js.map +1 -0
  52. package/dist/Changes/index.d.ts +50 -0
  53. package/dist/Changes/index.js +55 -0
  54. package/dist/Changes/index.js.map +1 -0
  55. package/dist/Checks/CDSCheck.d.ts +8 -0
  56. package/dist/Checks/CDSCheck.js +197 -0
  57. package/dist/Checks/CDSCheck.js.map +1 -0
  58. package/dist/Checks/index.d.ts +1 -0
  59. package/dist/Checks/index.js +5 -0
  60. package/dist/Checks/index.js.map +1 -0
  61. package/dist/Common/index.d.ts +1 -0
  62. package/dist/Common/index.js +5 -0
  63. package/dist/Common/index.js.map +1 -0
  64. package/dist/Common/jwtPayload.d.ts +12 -0
  65. package/dist/Common/jwtPayload.js +16 -0
  66. package/dist/Common/jwtPayload.js.map +1 -0
  67. package/dist/GFF3/gff3ToAnnotationFeature.d.ts +3 -0
  68. package/dist/GFF3/gff3ToAnnotationFeature.js +211 -0
  69. package/dist/GFF3/gff3ToAnnotationFeature.js.map +1 -0
  70. package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts +1 -0
  71. package/dist/GFF3/gff3ToAnnotationFeature.test.js +174 -0
  72. package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -0
  73. package/dist/GFF3/gffReservedKeys.d.ts +5 -0
  74. package/dist/GFF3/gffReservedKeys.js +34 -0
  75. package/dist/GFF3/gffReservedKeys.js.map +1 -0
  76. package/dist/GFF3/index.d.ts +2 -0
  77. package/dist/GFF3/index.js +6 -0
  78. package/dist/GFF3/index.js.map +1 -0
  79. package/dist/Messages.d.ts +28 -0
  80. package/dist/Messages.js +3 -0
  81. package/dist/Messages.js.map +1 -0
  82. package/dist/Operations/GetAssembliesOperation.d.ts +13 -0
  83. package/dist/Operations/GetAssembliesOperation.js +20 -0
  84. package/dist/Operations/GetAssembliesOperation.js.map +1 -0
  85. package/dist/Operations/GetFeaturesOperation.d.ts +26 -0
  86. package/dist/Operations/GetFeaturesOperation.js +42 -0
  87. package/dist/Operations/GetFeaturesOperation.js.map +1 -0
  88. package/dist/Operations/index.d.ts +8 -0
  89. package/dist/Operations/index.js +10 -0
  90. package/dist/Operations/index.js.map +1 -0
  91. package/dist/Validations/CoreValidation.d.ts +17 -0
  92. package/dist/Validations/CoreValidation.js +36 -0
  93. package/dist/Validations/CoreValidation.js.map +1 -0
  94. package/dist/Validations/ParentChildValidation.d.ts +17 -0
  95. package/dist/Validations/ParentChildValidation.js +61 -0
  96. package/dist/Validations/ParentChildValidation.js.map +1 -0
  97. package/dist/Validations/Validation.d.ts +27 -0
  98. package/dist/Validations/Validation.js +27 -0
  99. package/dist/Validations/Validation.js.map +1 -0
  100. package/dist/Validations/ValidationSet.d.ts +24 -0
  101. package/dist/Validations/ValidationSet.js +86 -0
  102. package/dist/Validations/ValidationSet.js.map +1 -0
  103. package/dist/Validations/index.d.ts +4 -0
  104. package/dist/Validations/index.js +8 -0
  105. package/dist/Validations/index.js.map +1 -0
  106. package/dist/Validations/soSequenceTypes.d.ts +2 -0
  107. package/dist/Validations/soSequenceTypes.js +1868 -0
  108. package/dist/Validations/soSequenceTypes.js.map +1 -0
  109. package/dist/index.d.ts +8 -0
  110. package/dist/index.js +12 -0
  111. package/dist/index.js.map +1 -0
  112. package/dist/tsconfig.tsbuildinfo +1 -0
  113. package/dist/util.d.ts +4 -0
  114. package/dist/util.js +102 -0
  115. package/dist/util.js.map +1 -0
  116. package/package.json +17 -8
  117. package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +13 -9
  118. package/src/Changes/AddAssemblyFromFileChange.ts +129 -43
  119. package/src/Changes/AddFeatureChange.ts +2 -3
  120. package/src/Changes/AddFeaturesFromFileChange.ts +8 -3
  121. package/src/Changes/AddRefSeqAliasesChange.ts +88 -0
  122. package/src/Changes/DeleteAssemblyChange.ts +1 -1
  123. package/src/Changes/DeleteFeatureChange.ts +1 -1
  124. package/src/Changes/FeatureAttributeChange.ts +1 -1
  125. package/src/Changes/FromFileBaseChange.ts +221 -0
  126. package/src/Changes/ImportJBrowseConfigChange.ts +116 -0
  127. package/src/Changes/LocationEndChange.ts +25 -18
  128. package/src/Changes/LocationStartChange.ts +25 -18
  129. package/src/Changes/TypeChange.ts +1 -1
  130. package/src/Changes/index.ts +6 -6
  131. package/src/Checks/CDSCheck.ts +125 -173
  132. package/src/Common/jwtPayload.ts +1 -1
  133. package/src/GFF3/gff3ToAnnotationFeature.test.ts +209 -0
  134. package/src/GFF3/gff3ToAnnotationFeature.ts +257 -0
  135. package/src/GFF3/gffReservedKeys.ts +61 -0
  136. package/src/GFF3/index.ts +2 -0
  137. package/src/Operations/GetFeaturesOperation.ts +2 -2
  138. package/src/Validations/ParentChildValidation.ts +5 -5
  139. package/src/index.ts +1 -0
  140. package/src/util.ts +16 -12
  141. package/test_data/braker.gff +13 -0
  142. package/test_data/example01.gff3 +26 -0
  143. package/test_data/example01.json +236 -0
  144. package/test_data/example02.json +225 -0
  145. package/test_data/example04.json +225 -0
  146. package/test_data/example05.gff3 +30 -0
  147. package/test_data/example06.gff3 +30 -0
  148. package/test_data/example07.gff3 +30 -0
  149. package/test_data/gene_mrna.gff3 +4 -0
  150. package/test_data/gene_representations.gff3 +1781 -0
  151. package/test_data/one_cds.gff3 +9 -0
  152. package/test_data/one_cds.json +67 -0
  153. package/test_data/two_cds.gff3 +9 -0
  154. package/test_data/two_cds.json +67 -0
  155. package/tsconfig.json +4 -4
  156. package/src/Changes/DiscontinuousLocationEndChange.ts +0 -182
  157. package/src/Changes/DiscontinuousLocationStartChange.ts +0 -182
package/test_data/example02.json ADDED
@@ -0,0 +1,225 @@
1
+ {
2
+ "_id": "66e049609048deab4117a33e",
3
+ "refSeq": "chr1",
4
+ "type": "gene",
5
+ "min": 10999,
6
+ "max": 19000,
7
+ "strand": 1,
8
+ "children": {
9
+ "66e049609048deab4117a331": {
10
+ "_id": "66e049609048deab4117a331",
11
+ "refSeq": "chr1",
12
+ "type": "mRNA",
13
+ "min": 11049,
14
+ "max": 19000,
15
+ "strand": 1,
16
+ "children": {
17
+ "66e049609048deab4117a32c": {
18
+ "_id": "66e049609048deab4117a32c",
19
+ "refSeq": "chr1",
20
+ "type": "exon",
21
+ "min": 11049,
22
+ "max": 11500,
23
+ "strand": 1,
24
+ "attributes": {
25
+ "gff_id": ["exon20001"]
26
+ }
27
+ },
28
+ "66e049609048deab4117a32d": {
29
+ "_id": "66e049609048deab4117a32d",
30
+ "refSeq": "chr1",
31
+ "type": "exon",
32
+ "min": 12999,
33
+ "max": 13902,
34
+ "strand": 1,
35
+ "attributes": {
36
+ "gff_id": ["exon20004"]
37
+ }
38
+ },
39
+ "66e049609048deab4117a32e": {
40
+ "_id": "66e049609048deab4117a32e",
41
+ "refSeq": "chr1",
42
+ "type": "exon",
43
+ "min": 14999,
44
+ "max": 15500,
45
+ "strand": 1,
46
+ "attributes": {
47
+ "gff_id": ["exon20006"]
48
+ }
49
+ },
50
+ "66e049609048deab4117a32f": {
51
+ "_id": "66e049609048deab4117a32f",
52
+ "refSeq": "chr1",
53
+ "type": "exon",
54
+ "min": 16999,
55
+ "max": 19000,
56
+ "strand": 1,
57
+ "attributes": {
58
+ "gff_id": ["exon20009"]
59
+ }
60
+ },
61
+ "66e049609048deab4117a330": {
62
+ "_id": "66e049609048deab4117a330",
63
+ "refSeq": "chr1",
64
+ "type": "CDS",
65
+ "min": 11200,
66
+ "max": 17600,
67
+ "strand": 1,
68
+ "attributes": {
69
+ "gff_id": ["cds20001"],
70
+ "gff_name": ["edenprotein.1"]
71
+ }
72
+ }
73
+ },
74
+ "attributes": {
75
+ "gff_id": ["mRNA20001"],
76
+ "gff_name": ["EDEN.1"]
77
+ }
78
+ },
79
+ "66e049609048deab4117a336": {
80
+ "_id": "66e049609048deab4117a336",
81
+ "refSeq": "chr1",
82
+ "type": "mRNA",
83
+ "min": 11049,
84
+ "max": 19000,
85
+ "strand": 1,
86
+ "children": {
87
+ "66e049609048deab4117a332": {
88
+ "_id": "66e049609048deab4117a332",
89
+ "refSeq": "chr1",
90
+ "type": "exon",
91
+ "min": 11049,
92
+ "max": 11500,
93
+ "strand": 1,
94
+ "attributes": {
95
+ "gff_id": ["exon20002"]
96
+ }
97
+ },
98
+ "66e049609048deab4117a333": {
99
+ "_id": "66e049609048deab4117a333",
100
+ "refSeq": "chr1",
101
+ "type": "exon",
102
+ "min": 14999,
103
+ "max": 15500,
104
+ "strand": 1,
105
+ "attributes": {
106
+ "gff_id": ["exon20007"]
107
+ }
108
+ },
109
+ "66e049609048deab4117a334": {
110
+ "_id": "66e049609048deab4117a334",
111
+ "refSeq": "chr1",
112
+ "type": "exon",
113
+ "min": 16999,
114
+ "max": 19000,
115
+ "strand": 1,
116
+ "attributes": {
117
+ "gff_id": ["exon20010"]
118
+ }
119
+ },
120
+ "66e049609048deab4117a335": {
121
+ "_id": "66e049609048deab4117a335",
122
+ "refSeq": "chr1",
123
+ "type": "CDS",
124
+ "min": 11200,
125
+ "max": 17600,
126
+ "strand": 1,
127
+ "attributes": {
128
+ "gff_id": ["cds20002"],
129
+ "gff_name": ["edenprotein.2"]
130
+ }
131
+ }
132
+ },
133
+ "attributes": {
134
+ "gff_id": ["mRNA20002"],
135
+ "gff_name": ["EDEN.2"]
136
+ }
137
+ },
138
+ "66e049609048deab4117a33d": {
139
+ "_id": "66e049609048deab4117a33d",
140
+ "refSeq": "chr1",
141
+ "type": "mRNA",
142
+ "min": 11299,
143
+ "max": 19000,
144
+ "strand": 1,
145
+ "children": {
146
+ "66e049609048deab4117a337": {
147
+ "_id": "66e049609048deab4117a337",
148
+ "refSeq": "chr1",
149
+ "type": "exon",
150
+ "min": 11299,
151
+ "max": 11500,
152
+ "strand": 1,
153
+ "attributes": {
154
+ "gff_id": ["exon20003"]
155
+ }
156
+ },
157
+ "66e049609048deab4117a338": {
158
+ "_id": "66e049609048deab4117a338",
159
+ "refSeq": "chr1",
160
+ "type": "exon",
161
+ "min": 12999,
162
+ "max": 13902,
163
+ "strand": 1,
164
+ "attributes": {
165
+ "gff_id": ["exon20005"]
166
+ }
167
+ },
168
+ "66e049609048deab4117a339": {
169
+ "_id": "66e049609048deab4117a339",
170
+ "refSeq": "chr1",
171
+ "type": "exon",
172
+ "min": 14999,
173
+ "max": 15500,
174
+ "strand": 1,
175
+ "attributes": {
176
+ "gff_id": ["exon20008"]
177
+ }
178
+ },
179
+ "66e049609048deab4117a33a": {
180
+ "_id": "66e049609048deab4117a33a",
181
+ "refSeq": "chr1",
182
+ "type": "exon",
183
+ "min": 16999,
184
+ "max": 19000,
185
+ "strand": 1,
186
+ "attributes": {
187
+ "gff_id": ["exon20011"]
188
+ }
189
+ },
190
+ "66e049609048deab4117a33b": {
191
+ "_id": "66e049609048deab4117a33b",
192
+ "refSeq": "chr1",
193
+ "type": "CDS",
194
+ "min": 13300,
195
+ "max": 17600,
196
+ "strand": 1,
197
+ "attributes": {
198
+ "gff_id": ["cds20003"],
199
+ "gff_name": ["edenprotein.3"]
200
+ }
201
+ },
202
+ "66e049609048deab4117a33c": {
203
+ "_id": "66e049609048deab4117a33c",
204
+ "refSeq": "chr1",
205
+ "type": "CDS",
206
+ "min": 13390,
207
+ "max": 17600,
208
+ "strand": 1,
209
+ "attributes": {
210
+ "gff_id": ["cds20004"],
211
+ "gff_name": ["edenprotein.4"]
212
+ }
213
+ }
214
+ },
215
+ "attributes": {
216
+ "gff_id": ["mRNA20003"],
217
+ "gff_name": ["EDEN.3"]
218
+ }
219
+ }
220
+ },
221
+ "attributes": {
222
+ "gff_id": ["gene20001"],
223
+ "gff_name": ["EDEN"]
224
+ }
225
+ }
package/test_data/example04.json ADDED
@@ -0,0 +1,225 @@
1
+ {
2
+ "_id": "66e0555fae0bd7cfcd69912d",
3
+ "refSeq": "chr1",
4
+ "type": "gene",
5
+ "min": 30999,
6
+ "max": 39000,
7
+ "strand": 1,
8
+ "children": {
9
+ "66e0555fae0bd7cfcd699120": {
10
+ "_id": "66e0555fae0bd7cfcd699120",
11
+ "refSeq": "chr1",
12
+ "type": "mRNA",
13
+ "min": 31049,
14
+ "max": 39000,
15
+ "strand": 1,
16
+ "children": {
17
+ "66e0555fae0bd7cfcd69911b": {
18
+ "_id": "66e0555fae0bd7cfcd69911b",
19
+ "refSeq": "chr1",
20
+ "type": "exon",
21
+ "min": 31049,
22
+ "max": 31500,
23
+ "strand": 1,
24
+ "attributes": {
25
+ "gff_id": ["exon40001"]
26
+ }
27
+ },
28
+ "66e0555fae0bd7cfcd69911c": {
29
+ "_id": "66e0555fae0bd7cfcd69911c",
30
+ "refSeq": "chr1",
31
+ "type": "exon",
32
+ "min": 32999,
33
+ "max": 33902,
34
+ "strand": 1,
35
+ "attributes": {
36
+ "gff_id": ["exon40003"]
37
+ }
38
+ },
39
+ "66e0555fae0bd7cfcd69911d": {
40
+ "_id": "66e0555fae0bd7cfcd69911d",
41
+ "refSeq": "chr1",
42
+ "type": "exon",
43
+ "min": 34999,
44
+ "max": 35500,
45
+ "strand": 1,
46
+ "attributes": {
47
+ "gff_id": ["exon40004"]
48
+ }
49
+ },
50
+ "66e0555fae0bd7cfcd69911e": {
51
+ "_id": "66e0555fae0bd7cfcd69911e",
52
+ "refSeq": "chr1",
53
+ "type": "exon",
54
+ "min": 36999,
55
+ "max": 39000,
56
+ "strand": 1,
57
+ "attributes": {
58
+ "gff_id": ["exon40005"]
59
+ }
60
+ },
61
+ "66e0555fae0bd7cfcd69911f": {
62
+ "_id": "66e0555fae0bd7cfcd69911f",
63
+ "refSeq": "chr1",
64
+ "type": "CDS",
65
+ "min": 31200,
66
+ "max": 37600,
67
+ "strand": 1,
68
+ "attributes": {
69
+ "gff_id": ["cds40001"],
70
+ "gff_name": ["edenprotein.1"]
71
+ }
72
+ }
73
+ },
74
+ "attributes": {
75
+ "gff_id": ["mRNA40001"],
76
+ "gff_name": ["EDEN.1"]
77
+ }
78
+ },
79
+ "66e0555fae0bd7cfcd699125": {
80
+ "_id": "66e0555fae0bd7cfcd699125",
81
+ "refSeq": "chr1",
82
+ "type": "mRNA",
83
+ "min": 31049,
84
+ "max": 39000,
85
+ "strand": 1,
86
+ "children": {
87
+ "66e0555fae0bd7cfcd699121": {
88
+ "_id": "66e0555fae0bd7cfcd699121",
89
+ "refSeq": "chr1",
90
+ "type": "exon",
91
+ "min": 31049,
92
+ "max": 31500,
93
+ "strand": 1,
94
+ "attributes": {
95
+ "gff_id": ["exon40001"]
96
+ }
97
+ },
98
+ "66e0555fae0bd7cfcd699122": {
99
+ "_id": "66e0555fae0bd7cfcd699122",
100
+ "refSeq": "chr1",
101
+ "type": "exon",
102
+ "min": 34999,
103
+ "max": 35500,
104
+ "strand": 1,
105
+ "attributes": {
106
+ "gff_id": ["exon40004"]
107
+ }
108
+ },
109
+ "66e0555fae0bd7cfcd699123": {
110
+ "_id": "66e0555fae0bd7cfcd699123",
111
+ "refSeq": "chr1",
112
+ "type": "exon",
113
+ "min": 36999,
114
+ "max": 39000,
115
+ "strand": 1,
116
+ "attributes": {
117
+ "gff_id": ["exon40005"]
118
+ }
119
+ },
120
+ "66e0555fae0bd7cfcd699124": {
121
+ "_id": "66e0555fae0bd7cfcd699124",
122
+ "refSeq": "chr1",
123
+ "type": "CDS",
124
+ "min": 31200,
125
+ "max": 37600,
126
+ "strand": 1,
127
+ "attributes": {
128
+ "gff_id": ["cds40002"],
129
+ "gff_name": ["edenprotein.2"]
130
+ }
131
+ }
132
+ },
133
+ "attributes": {
134
+ "gff_id": ["mRNA40002"],
135
+ "gff_name": ["EDEN.2"]
136
+ }
137
+ },
138
+ "66e0555fae0bd7cfcd69912c": {
139
+ "_id": "66e0555fae0bd7cfcd69912c",
140
+ "refSeq": "chr1",
141
+ "type": "mRNA",
142
+ "min": 31299,
143
+ "max": 39000,
144
+ "strand": 1,
145
+ "children": {
146
+ "66e0555fae0bd7cfcd699126": {
147
+ "_id": "66e0555fae0bd7cfcd699126",
148
+ "refSeq": "chr1",
149
+ "type": "exon",
150
+ "min": 31299,
151
+ "max": 31500,
152
+ "strand": 1,
153
+ "attributes": {
154
+ "gff_id": ["exon40002"]
155
+ }
156
+ },
157
+ "66e0555fae0bd7cfcd699127": {
158
+ "_id": "66e0555fae0bd7cfcd699127",
159
+ "refSeq": "chr1",
160
+ "type": "exon",
161
+ "min": 32999,
162
+ "max": 33902,
163
+ "strand": 1,
164
+ "attributes": {
165
+ "gff_id": ["exon40003"]
166
+ }
167
+ },
168
+ "66e0555fae0bd7cfcd699128": {
169
+ "_id": "66e0555fae0bd7cfcd699128",
170
+ "refSeq": "chr1",
171
+ "type": "exon",
172
+ "min": 34999,
173
+ "max": 35500,
174
+ "strand": 1,
175
+ "attributes": {
176
+ "gff_id": ["exon40004"]
177
+ }
178
+ },
179
+ "66e0555fae0bd7cfcd699129": {
180
+ "_id": "66e0555fae0bd7cfcd699129",
181
+ "refSeq": "chr1",
182
+ "type": "exon",
183
+ "min": 36999,
184
+ "max": 39000,
185
+ "strand": 1,
186
+ "attributes": {
187
+ "gff_id": ["exon40005"]
188
+ }
189
+ },
190
+ "66e0555fae0bd7cfcd69912a": {
191
+ "_id": "66e0555fae0bd7cfcd69912a",
192
+ "refSeq": "chr1",
193
+ "type": "CDS",
194
+ "min": 33300,
195
+ "max": 37600,
196
+ "strand": 1,
197
+ "attributes": {
198
+ "gff_id": ["cds40003"],
199
+ "gff_name": ["edenprotein.3"]
200
+ }
201
+ },
202
+ "66e0555fae0bd7cfcd69912b": {
203
+ "_id": "66e0555fae0bd7cfcd69912b",
204
+ "refSeq": "chr1",
205
+ "type": "CDS",
206
+ "min": 33390,
207
+ "max": 37600,
208
+ "strand": 1,
209
+ "attributes": {
210
+ "gff_id": ["cds40004"],
211
+ "gff_name": ["edenprotein.4"]
212
+ }
213
+ }
214
+ },
215
+ "attributes": {
216
+ "gff_id": ["mRNA40003"],
217
+ "gff_name": ["EDEN.3"]
218
+ }
219
+ }
220
+ },
221
+ "attributes": {
222
+ "gff_id": ["gene40001"],
223
+ "gff_name": ["EDEN"]
224
+ }
225
+ }
package/test_data/example05.gff3 ADDED
@@ -0,0 +1,30 @@
1
+ ##gff-version 3
2
+ # example 5
3
+ chr1 . gene 1000 9000 . + . ID=gene10001;Name=EDEN;testid=t003
4
+ chr1 . mRNA 1050 9000 . + . ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004
5
+ chr1 . mRNA 1050 9000 . + . ID=mRNA10002;Parent=gene10001;Name=EDEN.2;testid=t005
6
+ chr1 . mRNA 1300 9000 . + . ID=mRNA10003;Parent=gene10001;Name=EDEN.3;testid=t006
7
+ chr1 . exon 1050 1500 . + . ID=exon10001;Parent=mRNA10001,mRNA10002;testid=t007
8
+ chr1 . exon 1300 1500 . + . ID=exon10002;Parent=mRNA10003;testid=t008
9
+ chr1 . exon 3000 3902 . + . ID=exon10003;Parent=mRNA10001,mRNA10003;testid=t009
10
+ chr1 . exon 5000 5500 . + . ID=exon10004;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t010
11
+ chr1 . exon 7000 9000 . + . ID=exon10005;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t011
12
+ chr1 . five_prime_UTR 1050 1200 . + . ID=five_prime_UTR10001;Parent=mRNA10001,mRNA10002;testid=t012
13
+ chr1 . five_prime_UTR 1300 1500 . + . ID=five_prime_UTR10002;Parent=mRNA10003;testid=t013
14
+ chr1 . five_prime_UTR 3000 3300 . + . ID=five_prime_UTR10003;Parent=mRNA10003;testid=t014
15
+ chr1 . five_prime_UTR 3000 3390 . + . ID=five_prime_UTR10004;Parent=mRNA10003;testid=t015
16
+ chr1 . five_prime_UTR 3000 3390 . + . ID=five_prime_UTR10004;Parent=mRNA10003;testid=t016
17
+ chr1 . three_prime_UTR 7601 9000 . + . ID=three_prime_UTR10001;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t017
18
+ chr1 . CDS 1201 1500 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t018
19
+ chr1 . CDS 3000 3902 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t019
20
+ chr1 . CDS 5000 5500 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t020
21
+ chr1 . CDS 7000 7600 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t021
22
+ chr1 . CDS 1201 1500 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t022
23
+ chr1 . CDS 5000 5500 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t023
24
+ chr1 . CDS 7000 7600 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t024
25
+ chr1 . CDS 3301 3902 . + 0 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t025
26
+ chr1 . CDS 5000 5500 . + 1 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t026
27
+ chr1 . CDS 7000 7600 . + 1 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t027
28
+ chr1 . CDS 3391 3902 . + 0 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t028
29
+ chr1 . CDS 5000 5500 . + 1 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t029
30
+ chr1 . CDS 7000 7600 . + 1 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t030
package/test_data/example06.gff3 ADDED
@@ -0,0 +1,30 @@
1
+ ##gff-version 3
2
+ # example 6
3
+ chr1 . gene 1000 9000 . + . ID=gene10001;Name=EDEN;testid=t003
4
+ chr1 . mRNA 1050 9000 . + . ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004
5
+ chr1 . mRNA 1050 9000 . + . ID=mRNA10002;Parent=gene10001;Name=EDEN.2;testid=t005
6
+ chr1 . mRNA 1300 9000 . + . ID=mRNA10003;Parent=gene10001;Name=EDEN.3;testid=t006
7
+ chr1 . exon 1050 1500 . + . ID=exon10001;Parent=mRNA10001,mRNA10002;testid=t007
8
+ chr1 . exon 1300 1500 . + . ID=exon10002;Parent=mRNA10003;testid=t008
9
+ chr1 . exon 3000 3902 . + . ID=exon10003;Parent=mRNA10001,mRNA10003;testid=t009
10
+ chr1 . exon 5000 5500 . + . ID=exon10004;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t010
11
+ chr1 . exon 7000 9000 . + . ID=exon10005;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t011
12
+ chr1 . five_prime_UTR 1050 1200 . + . ID=five_prime_UTR10001;Parent=mRNA10001,mRNA10002;testid=t012
13
+ chr1 . five_prime_UTR 1300 1500 . + . ID=five_prime_UTR10002;Parent=mRNA10003;testid=t013
14
+ chr1 . five_prime_UTR 3000 3300 . + . ID=five_prime_UTR10003;Parent=mRNA10003;testid=t014
15
+ chr1 . five_prime_UTR 3000 3390 . + . ID=five_prime_UTR10004;Parent=mRNA10003;testid=t015
16
+ chr1 . five_prime_UTR 3000 3390 . + . ID=five_prime_UTR10004;Parent=mRNA10003;testid=t016
17
+ chr1 . three_prime_UTR 7601 9000 . + . ID=three_prime_UTR10001;Parent=mRNA10001,mRNA10002,mRNA10003;testid=t017
18
+ chr1 . CDS 1201 1500 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t018
19
+ chr1 . CDS 3000 3902 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t019
20
+ chr1 . CDS 5000 5500 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t020
21
+ chr1 . CDS 7000 7600 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t021
22
+ chr1 . CDS 1201 1500 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t022
23
+ chr1 . CDS 5000 5500 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t023
24
+ chr1 . CDS 7000 7600 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t024
25
+ chr1 . CDS 3301 3902 . + 0 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t025
26
+ chr1 . CDS 5000 5500 . + 1 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t026
27
+ chr1 . CDS 7000 7600 . + 1 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t027
28
+ chr1 . CDS 3391 3902 . + 0 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t028
29
+ chr1 . CDS 5000 5500 . + 1 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t029
30
+ chr1 . CDS 7000 7600 . + 1 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t030
package/test_data/example07.gff3 ADDED
@@ -0,0 +1,30 @@
1
+ ##gff-version 3
2
+ # example 2
3
+ chr1 . gene 1000 9000 . + . ID=gene10001;Name=EDEN;testid=t003
4
+ chr1 . mRNA 1050 9000 . + . ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004
5
+ chr1 . mRNA 1050 9000 . + . ID=mRNA10002;Parent=gene10001;Name=EDEN.2;testid=t005
6
+ chr1 . mRNA 1300 9000 . + . ID=mRNA10003;Parent=gene10001;Name=EDEN.3;testid=t006
7
+ chr1 . exon 1050 1500 . + . ID=exon10001;Parent=mRNA10001;testid=t007
8
+ chr1 . exon 1050 1500 . + . ID=exon10002;Parent=mRNA10002;testid=t008
9
+ chr1 . exon 1300 1500 . + . ID=exon10003;Parent=mRNA10003;testid=t009
10
+ chr1 . exon 3000 3902 . + . ID=exon10004;Parent=mRNA10001;testid=t010
11
+ chr1 . exon 3000 3902 . + . ID=exon10005;Parent=mRNA10003;testid=t011
12
+ chr1 . exon 5000 5500 . + . ID=exon10006;Parent=mRNA10001;testid=t012
13
+ chr1 . exon 5000 5500 . + . ID=exon10007;Parent=mRNA10002;testid=t013
14
+ chr1 . exon 5000 5500 . + . ID=exon10008;Parent=mRNA10003;testid=t014
15
+ chr1 . exon 7000 9000 . + . ID=exon10009;Parent=mRNA10001;testid=t015
16
+ chr1 . exon 7000 9000 . + . ID=exon20010;Parent=mRNA10002;testid=t016
17
+ chr1 . exon 7000 9000 . + . ID=exon20011;Parent=mRNA10003;testid=t017
18
+ chr1 . CDS 1201 1500 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t018
19
+ chr1 . CDS 3000 3902 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t019
20
+ chr1 . CDS 5000 5500 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t020
21
+ chr1 . CDS 7000 7600 . + 0 ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t021
22
+ chr1 . CDS 1201 1500 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t022
23
+ chr1 . CDS 5000 5500 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t023
24
+ chr1 . CDS 7000 7600 . + 0 ID=cds10002;Parent=mRNA10002;Name=edenprotein.2;testid=t024
25
+ chr1 . CDS 3301 3902 . + 0 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t025
26
+ chr1 . CDS 5000 5500 . + 1 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t026
27
+ chr1 . CDS 7000 7600 . + 1 ID=cds10003;Parent=mRNA10003;Name=edenprotein.3;testid=t027
28
+ chr1 . CDS 3391 3902 . + 0 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t028
29
+ chr1 . CDS 5000 5500 . + 1 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t029
30
+ chr1 . CDS 7000 7600 . + 1 ID=cds10004;Parent=mRNA10003;Name=edenprotein.4;testid=t030
package/test_data/gene_mrna.gff3 ADDED
@@ -0,0 +1,4 @@
1
+ ##gff-version 3
2
+ ##sequence-region ctgA 1000 2000
3
+ ctgA example gene 1000 2000 . . . ID=gene01;Name=geneA;Alias=hga
4
+ ctgA example mRNA 1000 2000 . . . Parent=gene01;Name=mrnaA;Alias=hga