Mercurial > repos > iuc > aegean_parseval
comparison test-data/parseval_output_test1.txt @ 0:1b52f0c8ad7f draft
"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=3626-5904 | |
| 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=5923-8742 | |
| 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=11644-13719 | |
| 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=23141-31232 | |
| 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/5/1/b/dataset_51bd183d-470e-4a87-a230-5a73a406179d.dat | |
| 497 Prediction annotations: /tmp/tmpuaspc0eb/files/6/f/b/dataset_6fba7592-2a44-4ea7-ae0a-ba0c87badb42.dat | |
| 498 Executing command: parseval -l 5 -t 20 -w -f text -o /tmp/tmpuaspc0eb/files/9/2/0/dataset_92006ba5-932e-40f8-a785-2a9b2932d88a.dat /tmp/tmpuaspc0eb/files/5/1/b/dataset_51bd183d-470e-4a87-a230-5a73a406179d.dat /tmp/tmpuaspc0eb/files/6/f/b/dataset_6fba7592-2a44-4ea7-ae0a-ba0c87badb42.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..........................3617.40 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 -- |