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comparison test-data/parseval_output_test2.txt @ 0:1b52f0c8ad7f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
author iuc
date Sun, 03 Jan 2021 14:58:02 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1b52f0c8ad7f
1 |-------------------------------------------------
2 |---- Locus: seqid=Chr1 range=3631-5899
3 |-------------------------------------------------
4 |
5 | reference genes:
6 | AT1G01010
7 |
8 | prediction genes:
9 | AT1G01010
10 |
11 |----------
12 |
13 |--------------------------
14 |---- Begin comparison ----
15 |--------------------------
16 |
17 | reference transcripts:
18 | AT1G01010.1
19 | prediction transcripts:
20 | AT1G01010.1
21 |
22 | reference GFF3:
23 ##gff-version 3
24 Chr1 TAIR9 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1
25 Chr1 TAIR9 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1
26 Chr1 TAIR9 exon 3631 3913 . + . Parent=AT1G01010.1
27 Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1
28 Chr1 TAIR9 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1
29 Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1
30 Chr1 TAIR9 exon 3996 4276 . + . Parent=AT1G01010.1
31 Chr1 TAIR9 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1
32 Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1
33 Chr1 TAIR9 exon 4486 4605 . + . Parent=AT1G01010.1
34 Chr1 TAIR9 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1
35 Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1
36 Chr1 TAIR9 exon 4706 5095 . + . Parent=AT1G01010.1
37 Chr1 TAIR9 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1
38 Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1
39 Chr1 TAIR9 exon 5174 5326 . + . Parent=AT1G01010.1
40 Chr1 TAIR9 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1
41 Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1
42 Chr1 TAIR9 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1
43 Chr1 TAIR9 exon 5439 5899 . + . Parent=AT1G01010.1
44 Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1
45 Chr1 TAIR9 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1
46 ###
47 | prediction GFF3:
48 ##gff-version 3
49 Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1
50 Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1
51 Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1
52 Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1
53 Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS1;Parent=AT1G01010.1
54 Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1
55 Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1
56 Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS1;Parent=AT1G01010.1
57 Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1
58 Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1
59 Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS1;Parent=AT1G01010.1
60 Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1
61 Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1
62 Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS1;Parent=AT1G01010.1
63 Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1
64 Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1
65 Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS1;Parent=AT1G01010.1
66 Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1
67 Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS1;Parent=AT1G01010.1
68 Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1
69 Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1
70 Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1
71 ###
72 |
73 | CDS structure comparison
74 | 6 reference CDS segments
75 | 6 prediction CDS segments
76 | CDS structures match perfectly!
77 |
78 | Exon structure comparison
79 | 6 reference exons
80 | 6 prediction exons
81 | Exon structures match perfectly!
82 |
83 | UTR structure comparison
84 | 2 reference UTR segments
85 | 2 prediction UTR segments
86 | UTR structures match perfectly!
87 |
88 | Gene structures match perfectly!
89 |
90 |
91 |--------------------------
92 |----- End comparison -----
93 |--------------------------
94
95 |-------------------------------------------------
96 |---- Locus: seqid=Chr1 range=5928-8737
97 |-------------------------------------------------
98 |
99 | reference genes:
100 | AT1G01020
101 |
102 | prediction genes:
103 | AT1G01020
104 |
105 |----------
106 |
107 |--------------------------
108 |---- Begin comparison ----
109 |--------------------------
110 |
111 | reference transcripts:
112 | AT1G01020.1
113 | prediction transcripts:
114 | AT1G01020.1
115 |
116 | reference GFF3:
117 ##gff-version 3
118 Chr1 TAIR9 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1
119 Chr1 TAIR9 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1
120 Chr1 TAIR9 exon 5928 6263 . - . Parent=AT1G01020.1
121 Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1
122 Chr1 TAIR9 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1
123 Chr1 TAIR9 exon 6437 7069 . - . Parent=AT1G01020.1
124 Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1
125 Chr1 TAIR9 CDS 6915 7069 . - 2 ID=CDS2;Parent=AT1G01020.1
126 Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1
127 Chr1 TAIR9 CDS 7157 7232 . - 0 ID=CDS2;Parent=AT1G01020.1
128 Chr1 TAIR9 exon 7157 7232 . - . Parent=AT1G01020.1
129 Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1
130 Chr1 TAIR9 CDS 7384 7450 . - 1 ID=CDS2;Parent=AT1G01020.1
131 Chr1 TAIR9 exon 7384 7450 . - . Parent=AT1G01020.1
132 Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1
133 Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.1
134 Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.1
135 Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1
136 Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.1
137 Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.1
138 Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1
139 Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.1
140 Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.1
141 Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1
142 Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.1
143 Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.1
144 Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1
145 Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.1
146 Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.1
147 Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1
148 Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.1
149 Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.1
150 Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1
151 Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1
152 ###
153 | prediction GFF3:
154 ##gff-version 3
155 Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1
156 Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1
157 Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1
158 Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1
159 Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1
160 Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1
161 Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1
162 Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS4;Parent=AT1G01020.1
163 Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1
164 Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS4;Parent=AT1G01020.1
165 Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1
166 Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1
167 Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS4;Parent=AT1G01020.1
168 Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1
169 Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1
170 Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS4;Parent=AT1G01020.1
171 Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1
172 Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1
173 Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS4;Parent=AT1G01020.1
174 Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1
175 Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1
176 Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS4;Parent=AT1G01020.1
177 Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1
178 Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1
179 Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS4;Parent=AT1G01020.1
180 Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1
181 Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1
182 Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS4;Parent=AT1G01020.1
183 Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1
184 Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1
185 Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS4;Parent=AT1G01020.1
186 Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1
187 Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1
188 Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1
189 ###
190 |
191 | CDS structure comparison
192 | 9 reference CDS segments
193 | 9 prediction CDS segments
194 | CDS structures match perfectly!
195 |
196 | Exon structure comparison
197 | 10 reference exons
198 | 10 prediction exons
199 | Exon structures match perfectly!
200 |
201 | UTR structure comparison
202 | 3 reference UTR segments
203 | 3 prediction UTR segments
204 | UTR structures match perfectly!
205 |
206 | Gene structures match perfectly!
207 |
208 |
209 |--------------------------
210 |----- End comparison -----
211 |--------------------------
212 |
213 |--------------------------
214 |---- Begin comparison ----
215 |--------------------------
216 |
217 | reference transcripts:
218 | AT1G01020.2
219 | prediction transcripts:
220 | AT1G01020.2
221 |
222 | reference GFF3:
223 ##gff-version 3
224 Chr1 TAIR9 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1
225 Chr1 TAIR9 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2
226 Chr1 TAIR9 exon 6790 7069 . - . Parent=AT1G01020.2
227 Chr1 TAIR9 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2
228 Chr1 TAIR9 exon 7157 7450 . - . Parent=AT1G01020.2
229 Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2
230 Chr1 TAIR9 CDS 7315 7450 . - 1 ID=CDS3;Parent=AT1G01020.2
231 Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS3;Parent=AT1G01020.2
232 Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.2
233 Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS3;Parent=AT1G01020.2
234 Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.2
235 Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS3;Parent=AT1G01020.2
236 Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.2
237 Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS3;Parent=AT1G01020.2
238 Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.2
239 Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS3;Parent=AT1G01020.2
240 Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.2
241 Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS3;Parent=AT1G01020.2
242 Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.2
243 Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2
244 Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2
245 ###
246 | prediction GFF3:
247 ##gff-version 3
248 Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1
249 Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2
250 Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2
251 Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2
252 Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2
253 Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2
254 Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS5;Parent=AT1G01020.2
255 Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS5;Parent=AT1G01020.2
256 Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2
257 Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS5;Parent=AT1G01020.2
258 Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2
259 Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS5;Parent=AT1G01020.2
260 Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2
261 Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS5;Parent=AT1G01020.2
262 Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2
263 Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS5;Parent=AT1G01020.2
264 Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2
265 Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS5;Parent=AT1G01020.2
266 Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2
267 Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2
268 Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2
269 ###
270 |
271 | CDS structure comparison
272 | 7 reference CDS segments
273 | 7 prediction CDS segments
274 | CDS structures match perfectly!
275 |
276 | Exon structure comparison
277 | 8 reference exons
278 | 8 prediction exons
279 | Exon structures match perfectly!
280 |
281 | UTR structure comparison
282 | 3 reference UTR segments
283 | 3 prediction UTR segments
284 | UTR structures match perfectly!
285 |
286 | Gene structures match perfectly!
287 |
288 |
289 |--------------------------
290 |----- End comparison -----
291 |--------------------------
292
293 |-------------------------------------------------
294 |---- Locus: seqid=Chr1 range=11649-13714
295 |-------------------------------------------------
296 |
297 | reference genes:
298 | AT1G01030
299 |
300 | prediction genes:
301 | AT1G01030
302 |
303 |----------
304 |
305 |--------------------------
306 |---- Begin comparison ----
307 |--------------------------
308 |
309 | reference transcripts:
310 | AT1G01030.1
311 | prediction transcripts:
312 | AT1G01030.1
313 |
314 | reference GFF3:
315 ##gff-version 3
316 Chr1 TAIR9 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1
317 Chr1 TAIR9 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1
318 Chr1 TAIR9 exon 11649 13173 . - . Parent=AT1G01030.1
319 Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1
320 Chr1 TAIR9 CDS 11864 12940 . - 0 Parent=AT1G01030.1
321 Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1
322 Chr1 TAIR9 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1
323 Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1
324 Chr1 TAIR9 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1
325 Chr1 TAIR9 exon 13335 13714 . - . Parent=AT1G01030.1
326 ###
327 | prediction GFF3:
328 ##gff-version 3
329 Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1
330 Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1
331 Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1
332 Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1
333 Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1
334 Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1
335 Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1
336 Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1
337 Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1
338 Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1
339 ###
340 |
341 | CDS structure comparison
342 | 1 reference CDS segments
343 | 1 prediction CDS segments
344 | CDS structures match perfectly!
345 |
346 | Exon structure comparison
347 | 2 reference exons
348 | 2 prediction exons
349 | Exon structures match perfectly!
350 |
351 | UTR structure comparison
352 | 3 reference UTR segments
353 | 3 prediction UTR segments
354 | UTR structures match perfectly!
355 |
356 | Gene structures match perfectly!
357 |
358 |
359 |--------------------------
360 |----- End comparison -----
361 |--------------------------
362
363 |-------------------------------------------------
364 |---- Locus: seqid=Chr1 range=23146-31227
365 |-------------------------------------------------
366 |
367 | reference genes:
368 | AT1G01040
369 |
370 | prediction genes:
371 | AT1G01040
372 |
373 |----------
374 |
375 |--------------------------
376 |---- Begin comparison ----
377 |--------------------------
378 |
379 | reference transcripts:
380 | AT1G01040.1
381 | prediction transcripts:
382 | AT1G01040.1
383 |
384 | reference GFF3:
385 ##gff-version 3
386 Chr1 TAIR9 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1
387 Chr1 TAIR9 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1
388 Chr1 TAIR9 exon 23146 24451 . + . Parent=AT1G01040.1
389 Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1
390 Chr1 TAIR9 CDS 23519 24451 . + 0 ID=CDS6;Parent=AT1G01040.1
391 Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1
392 Chr1 TAIR9 exon 24542 24655 . + . Parent=AT1G01040.1
393 Chr1 TAIR9 CDS 24542 24655 . + 0 ID=CDS6;Parent=AT1G01040.1
394 Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1
395 Chr1 TAIR9 exon 24752 24962 . + . Parent=AT1G01040.1
396 Chr1 TAIR9 CDS 24752 24962 . + 0 ID=CDS6;Parent=AT1G01040.1
397 Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1
398 Chr1 TAIR9 exon 25041 25435 . + . Parent=AT1G01040.1
399 Chr1 TAIR9 CDS 25041 25435 . + 2 ID=CDS6;Parent=AT1G01040.1
400 Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1
401 Chr1 TAIR9 exon 25524 25743 . + . Parent=AT1G01040.1
402 Chr1 TAIR9 CDS 25524 25743 . + 0 ID=CDS6;Parent=AT1G01040.1
403 Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1
404 Chr1 TAIR9 exon 25825 25997 . + . Parent=AT1G01040.1
405 Chr1 TAIR9 CDS 25825 25997 . + 2 ID=CDS6;Parent=AT1G01040.1
406 Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1
407 Chr1 TAIR9 exon 26081 26203 . + . Parent=AT1G01040.1
408 Chr1 TAIR9 CDS 26081 26203 . + 0 ID=CDS6;Parent=AT1G01040.1
409 Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1
410 Chr1 TAIR9 exon 26292 26452 . + . Parent=AT1G01040.1
411 Chr1 TAIR9 CDS 26292 26452 . + 0 ID=CDS6;Parent=AT1G01040.1
412 Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1
413 Chr1 TAIR9 exon 26543 26776 . + . Parent=AT1G01040.1
414 Chr1 TAIR9 CDS 26543 26776 . + 1 ID=CDS6;Parent=AT1G01040.1
415 Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1
416 Chr1 TAIR9 exon 26862 27012 . + . Parent=AT1G01040.1
417 Chr1 TAIR9 CDS 26862 27012 . + 1 ID=CDS6;Parent=AT1G01040.1
418 Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1
419 Chr1 TAIR9 exon 27099 27281 . + . Parent=AT1G01040.1
420 Chr1 TAIR9 CDS 27099 27281 . + 0 ID=CDS6;Parent=AT1G01040.1
421 Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1
422 Chr1 TAIR9 exon 27372 27533 . + . Parent=AT1G01040.1
423 Chr1 TAIR9 CDS 27372 27533 . + 0 ID=CDS6;Parent=AT1G01040.1
424 Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1
425 ###
426 | prediction GFF3:
427 ##gff-version 3
428 Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1
429 Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1
430 Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1
431 Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1
432 Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS7;Parent=AT1G01040.1
433 Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1
434 Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1
435 Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS7;Parent=AT1G01040.1
436 Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1
437 Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1
438 Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS7;Parent=AT1G01040.1
439 Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1
440 Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1
441 Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS7;Parent=AT1G01040.1
442 Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1
443 Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1
444 Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS7;Parent=AT1G01040.1
445 Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1
446 Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1
447 Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS7;Parent=AT1G01040.1
448 Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1
449 Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1
450 Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS7;Parent=AT1G01040.1
451 Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1
452 Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1
453 Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS7;Parent=AT1G01040.1
454 Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1
455 Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1
456 Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS7;Parent=AT1G01040.1
457 Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1
458 Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1
459 Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS7;Parent=AT1G01040.1
460 Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1
461 Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1
462 Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS7;Parent=AT1G01040.1
463 Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1
464 Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1
465 Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS7;Parent=AT1G01040.1
466 Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1
467 ###
468 |
469 | CDS structure comparison
470 | 12 reference CDS segments
471 | 12 prediction CDS segments
472 | CDS structures match perfectly!
473 |
474 | Exon structure comparison
475 | 12 reference exons
476 | 12 prediction exons
477 | Exon structures match perfectly!
478 |
479 | UTR structure comparison
480 | 1 reference UTR segments
481 | 1 prediction UTR segments
482 | UTR structures match perfectly!
483 |
484 | Gene structures match perfectly!
485 |
486 |
487 |--------------------------
488 |----- End comparison -----
489 |--------------------------
490
491 ============================================================
492 ========== ParsEval Summary
493 ============================================================
494
495 Started: 31 Dec 2020, 08:38PM
496 Reference annotations: /tmp/tmpuaspc0eb/files/0/4/3/dataset_0436aebb-5e69-4845-b8d6-cc6932c61142.dat
497 Prediction annotations: /tmp/tmpuaspc0eb/files/f/a/e/dataset_fae0f82b-28de-405b-9da1-0a227c4b4b92.dat
498 Executing command: parseval -l 0 -t 32 -w -f text -o /tmp/tmpuaspc0eb/files/3/2/7/dataset_327cf1a1-a7ea-412e-ac0f-e23f78ff553a.dat /tmp/tmpuaspc0eb/files/0/4/3/dataset_0436aebb-5e69-4845-b8d6-cc6932c61142.dat /tmp/tmpuaspc0eb/files/f/a/e/dataset_fae0f82b-28de-405b-9da1-0a227c4b4b92.dat
499
500 Sequences compared
501 Chr1
502
503 Gene loci................................4
504 shared.................................4
505 unique to reference....................0
506 unique to prediction...................0
507
508 Reference annotations
509 genes..................................4
510 average per locus....................1.000
511 transcripts............................5
512 average per locus....................1.250
513 average per gene.....................1.250
514
515 Prediction annotations
516 genes..................................4
517 average per locus....................1.000
518 transcripts............................5
519 average per locus....................1.250
520 average per gene.....................1.250
521
522 Total comparisons........................5
523 perfect matches........................5 (100.0%)
524 avg. length..........................3607.40 bp
525 avg. # refr exons....................7.60
526 avg. # pred exons....................7.60
527 avg. refr CDS length.................449.40 aa
528 avg. pred CDS length.................449.40 aa
529 perfect matches with mislabeled UTRs...0 (0.0%)
530 CDS structure matches..................0 (0.0%)
531 exon structure matches.................0 (0.0%)
532 UTR structure matches..................0 (0.0%)
533 non-matches............................0 (0.0%)
534
535 CDS structure comparison
536 reference CDS segments.................35
537 match prediction.....................35 (100.0%)
538 don't match prediction...............0 (0.0%)
539 prediction CDS segments................35
540 match reference......................35 (100.0%)
541 don't match reference................0 (0.0%)
542 Sensitivity............................1.000
543 Specificity............................1.000
544 F1 Score...............................1.000
545 Annotation edit distance...............0.000
546
547 Exon structure comparison
548 reference exons........................38
549 match prediction.....................38 (100.0%)
550 don't match prediction...............0 (0.0%)
551 prediction exons.......................38
552 match reference......................38 (100.0%)
553 don't match reference................0 (0.0%)
554 Sensitivity............................1.000
555 Specificity............................1.000
556 F1 Score...............................1.000
557 Annotation edit distance...............0.000
558
559 UTR structure comparison
560 reference UTR segments.................12
561 match prediction.....................12 (100.0%)
562 don't match prediction...............0 (0.0%)
563 prediction UTR segments................12
564 match reference......................12 (100.0%)
565 don't match reference................0 (0.0%)
566 Sensitivity............................1.000
567 Specificity............................1.000
568 F1 Score...............................1.000
569 Annotation edit distance...............0.000
570
571 Nucleotide-level comparison CDS UTRs Overall
572 Matching coefficient: 1.000 1.000 1.000
573 Correlation coefficient: 1.000 1.000 --
574 Sensitivity: 1.000 1.000 --
575 Specificity: 1.000 1.000 --
576 F1 Score: 1.000 1.000 --
577 Annotation edit distance: 0.000 0.000 --