Skip to content

antismash json2gff module #145

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Ales-ibt wants to merge 4 commits into
base: main
Choose a base branch
from
Open

antismash json2gff module #145

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
113ff76
antismash json2gff module
Ales-ibt Feb 23, 2026
722c584
test fix to use compressed input
Ales-ibt Feb 25, 2026
7888c9b
Fixing manin.nf.test structure
Ales-ibt Feb 25, 2026
49af702
Merge branch 'main' into feature/antismash_convert
mberacochea Feb 27, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
0 modules/ebi-metagenomics/antismash/main.nf → ...-metagenomics/antismash/antismash/main.nf
View file
Open in desktop
File renamed without changes.
0 modules/ebi-metagenomics/antismash/meta.yml → ...metagenomics/antismash/antismash/meta.yml
View file
Open in desktop
File renamed without changes.
1,452 changes: 734 additions & 718 deletions ...antismash_trimmed/as-js/0.13/antismash.js → ...antismash_trimmed/as-js/0.13/antismash.js
View file
Open in desktop

Large diffs are not rendered by default.

0 ...d/nrps_pks/stachelhaus/1.1/signatures.tsv → ...d/nrps_pks/stachelhaus/1.1/signatures.tsv
View file
Open in desktop
File renamed without changes.
16 changes: 8 additions & 8 deletions ...1_LARGE_CLUSTER/[asp,asn,glu,gln,aad].mdl → ...1_LARGE_CLUSTER/[asp,asn,glu,gln,aad].mdl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
SVM-light Version V6.01
2 # kernel type
3 # kernel parameter -d
0.0056731971 # kernel parameter -g
1 # kernel parameter -s
1 # kernel parameter -r
empty# kernel parameter -u
408 # highest feature index
946 # number of training documents
287 # number of support vectors plus 1
3 # kernel parameter -d
0.0056731971 # kernel parameter -g
1 # kernel parameter -s
1 # kernel parameter -r
empty# kernel parameter -u
408 # highest feature index
946 # number of training documents
287 # number of support vectors plus 1
0.57153058 # threshold b, each following line is a SV (starting with alpha*y)
0.2457716618588087209573700420151 1:-0.83854818 2:0.14797908 3:1.1345063 4:-0.83854818 5:-0.83854818 6:0.14797908 7:-0.83854818 8:-0.83854818 9:-0.83854818 10:0.14797908 11:1.1345063 12:0.14797908 13:0.14797908 14:-0.83854818 15:-0.83854818 16:-0.83854818 17:-0.83854818 18:-0.83854818 19:0.14797908 20:0.14797908 21:1.1345063 22:-0.83854818 23:0.14797908 24:-0.83854818 25:-0.83854818 26:0.14797908 27:0.14797908 28:0.14797908 29:0.14797908 30:-0.83854818 31:0.14797908 32:-0.83854818 33:-0.83854818 34:-0.83854818 35:-1.2942894 36:0.61723155 37:0.95284212 38:0.0043775286 39:-1.5277575 40:1.3322279 41:0.38376334 42:0.0043775286 43:-1.2942894 44:1.1571268 45:0.95284212 46:-0.91490352 47:1.3322279 48:-1.1775552 49:-1.0754129 50:-1.1775552 51:0.38376334 52:0.38376334 53:1.1571268 54:0.13570338 55:0.9382503 56:-1.5277575 57:-0.59388471 58:0.38376334 59:0.57345629 60:0.47131392 61:1.1571268 62:-0.59388471 63:0.47131392 64:-1.5423493 65:0.61723155 66:0.0043775286 67:-1.2942894 68:0.38376334 69:0.25011969 70:-0.69372815 71:-0.08022707 72:-1.165652 73:0.86362076 74:-0.36338142 75:-1.4959989 76:-1.165652 77:0.25011969 78:-0.45776621 79:-0.08022707 80:1.4771218 81:-0.36338142 82:-0.88249773 83:-0.033034675 84:-0.88249773 85:-1.4959989 86:-1.4959989 87:-0.45776621 88:-0.12741946 89:-0.26899663 90:0.86362076 91:1.9018534 92:-1.4959989 93:1.0995828 94:-0.45776621 95:-0.45776621 96:1.9018534 97:-0.45776621 98:-0.12741946 99:-0.69372815 100:-1.165652 101:0.25011969 102:-1.4959989 103:-0.45809889 104:0.73458463 105:0.13824286 106:0.84301037 107:0.30088151 108:-0.078608684 109:1.0056491 110:0.84301037 111:-0.45809889 112:-0.78337622 113:0.13824286 114:1.3309263 115:-0.078608684 116:-0.34967312 117:-0.29546022 118:-0.34967312 119:1.0056491 120:1.0056491 121:-0.78337622 122:-1.0544406 123:0.4093073 124:0.30088151 125:-0.62073755 126:1.0056491 127:1.7104166 128:1.0598619 129:-0.78337622 130:-0.62073755 131:1.0598619 132:0.029817088 133:0.73458463 134:0.84301037 135:-0.45809889 136:1.0056491 137:-0.6303606 138:-0.55826056 139:-0.47117865 140:-0.63644701 141:-0.62006062 142:1.690419 143:-0.63644701 144:-0.63644701 145:-0.6303606 146:1.6997826 147:-0.47117865 148:-0.53812873 149:1.690419 150:-0.6303606 151:-0.56949693 152:-0.6303606 153:-0.63644701 154:-0.63644701 155:1.6997826 156:1.7793736 157:-0.47820139 158:-0.62006062 159:-0.56106967 160:-0.63644701 161:-0.56247419 162:-0.55872875 163:1.6997826 164:-0.56106967 165:-0.55872875 166:-0.6303606 167:-0.55826056 168:-0.63644701 169:-0.6303606 170:-0.63644701 171:1.1336221 172:-0.8116802 173:-1.073329 174:-0.31113458 175:1.2018782 176:-1.1529613 177:-0.70929587 178:-0.31113458 179:1.1336221 180:-1.1188332 181:-1.073329 182:0.7582128 183:-1.1529613 184:0.99710959 185:1.2018782 186:0.99710959 187:-0.70929587 188:-0.70929587 189:-1.1188332 190:0.31454739 191:-0.78892809 192:1.2018782 193:0.13253082 194:-0.70929587 195:1.0084856 196:-0.55003136 197:-1.1188332 198:0.13253082 199:-0.55003136 200:1.2473824 201:-0.8116802 202:-0.31113458 203:1.1336221 204:-0.70929587 205:-1.3060657 206:0.33366641 207:0.82939935 208:-0.085799932 209:-1.1916658 210:1.782732 211:0.2573998 212:-0.085799932 213:-1.3060657 214:1.5157988 215:0.82939935 216:-1.1153991 217:1.782732 218:-0.92473263 219:-1.0009992 220:-0.92473263 221:0.2573998 222:0.2573998 223:1.5157988 224:0.79126608 225:1.2488657 226:-1.1916658 227:-0.81033272 228:0.2573998 229:-0.12393324 230:0.10486659 231:1.5157988 232:-0.81033272 233:0.10486659 234:-1.1916658 235:0.33366641 236:-0.085799932 237:-1.3060657 238:0.2573998 239:0.46958315 240:-1.2434403 241:0.10500384 242:-1.3782847 243:1.1662793 244:-0.69657123 245:-2.0050614 246:-1.3782847 247:0.46958315 248:-0.074788705 249:0.10500384 250:2.0727334 251:-0.69657123 252:-0.15469651 253:0.54449672 254:-0.15469651 255:-2.0050614 256:-2.0050614 257:-0.074788705 258:0.36969844 259:-0.51178449 260:1.1662793 261:1.2936324 262:-2.0050614 263:-0.55673259 264:-0.59169227 265:-0.074788705 266:1.2936324 267:-0.59169227 268:0.46708605 269:-1.2434403 270:-1.3782847 271:0.46958315 272:-2.0050614 273:-1.3739842 274:1.2258232 275:-0.088057987 276:-0.70306617 277:-0.92670554 278:1.4774173 279:1.5892371 280:-0.70306617 281:-1.3739842 282:-0.11601291 283:-0.088057987 284:-1.094435 285:1.4774173 286:-1.1223899 287:-1.094435 288:-1.1223899 289:1.5892371 290:1.5892371 291:-0.11601291 292:-0.11601291 293:1.3096879 294:-0.92670554 295:0.41513053 296:1.5892371 297:1.5892371 298:-0.032148156 299:-0.11601291 300:0.41513053 301:-0.032148156 302:-1.4578489 303:1.2258232 304:-0.70306617 305:-1.3739842 306:1.5892371 307:0.75635028 308:-0.77585107 309:0.19918618 310:-0.55298543 311:0.97921598 312:-1.3608733 313:-0.77585107 314:-0.55298543 315:0.75635028 316:-1.8344629 317:0.19918618 318:0.95135778 319:-1.3608733 320:1.8706785 321:0.059895143 322:1.8706785 323:-0.77585107 324:-0.77585107 325:-1.8344629 326:-0.44155258 327:-0.38583615 328:0.97921598 329:1.2299398 330:-0.77585107 331:-1.3330152 332:0.44991004 333:-1.8344629 334:1.2299398 335:0.44991004 336:1.5920964 337:-0.77585107 338:-0.55298543 339:0.75635028 340:-0.77585107 341:0.76650506 342:-0.83950549 343:0.40150264 344:1.5330101 345:0.47450313 346:0.036500242 347:-1.5695103 348:1.5330101 349:0.76650506 350:1.8615122 351:0.40150264 352:0.29200193 353:0.036500242 354:0.21900144 355:1.6425108 356:0.21900144 357:-1.5695103 358:-1.5695103 359:1.8615122 360:-8.1046812e-16 361:-1.2045079 362:0.47450313 363:-1.1315074 364:-1.5695103 365:-1.5695103 366:-0.62050408 367:1.8615122 368:-1.1315074 369:-0.62050408 370:0.29200193 371:-0.83950549 372:1.5330101 373:0.76650506 374:-1.5695103 375:-0.026966004 376:-0.20094022 377:-0.21833764 378:-0.015367722 379:-0.31692302 380:-1.8884901 381:-0.032765143 382:-0.015367722 383:-0.026966004 384:-1.6275288 385:-0.21833764 386:-0.079158269 387:-1.8884901 388:-0.038564283 389:-0.16614538 390:-0.038564283 391:-0.032765143 392:-0.032765143 393:-1.6275288 394:0.9066956 395:-0.357517 396:-0.31692302 397:-0.2125385 398:-0.032765143 399:0.1586065 400:-0.2125385 401:-1.6275288 402:-0.2125385 403:-0.2125385 404:-0.0037694413 405:-0.20094022 406:-0.015367722 407:-0.026966004 408:-0.032765143 # Q7NVV9_m1_unknownspec
-0.11455293321872014877804701882269 1:3.1075609 2:0.14797908 3:-0.83854818 4:0.14797908 5:-0.83854818 6:0.14797908 7:-0.83854818 8:0.14797908 9:-0.83854818 10:-0.83854818 11:0.14797908 12:0.14797908 13:0.14797908 14:-0.83854818 15:-0.83854818 16:-0.83854818 17:0.14797908 18:-0.83854818 19:0.14797908 20:0.14797908 21:1.1345063 22:-0.83854818 23:0.14797908 24:-0.83854818 25:-0.83854818 26:0.14797908 27:0.14797908 28:-0.83854818 29:-0.83854818 30:-0.83854818 31:0.14797908 32:-0.83854818 33:0.14797908 34:-0.83854818 35:1.084168 36:-0.91490352 37:-1.0754129 38:0.47131392 39:-1.5277575 40:1.3322279 41:-1.1775552 42:0.61723155 43:-1.1775552 44:0.57345629 45:1.1571268 46:-0.91490352 47:0.13570338 48:-1.5277575 49:-1.2942894 50:-0.90031177 51:0.61723155 52:0.38376334 53:1.1571268 54:0.13570338 55:0.9382503 56:-1.2942894 57:-0.59388471 58:0.38376334 59:0.57345629 60:0.47131392 61:1.1571268 62:0.0043775286 63:0.0043775286 64:-1.1775552 65:1.1571268 66:-1.1775552 67:0.47131392 68:-0.90031177 69:0.91081315 70:1.4771218 71:-0.033034675 72:-0.45776621 73:0.86362076 74:-0.36338142 75:-0.88249773 76:-0.69372815 77:-0.88249773 78:1.0995828 79:-0.45776621 80:1.4771218 81:-0.12741946 82:0.86362076 83:0.25011969 84:-1.873538 85:-0.69372815 86:-1.4959989 87:-0.45776621 88:-0.12741946 89:-0.26899663 90:0.25011969 91:1.9018534 92:-1.4959989 93:1.0995828 94:-0.45776621 95:-0.45776621 96:-1.165652 97:-1.165652 98:-0.88249773 99:-0.45776621 100:-0.88249773 101:-0.45776621 102:-1.873538 103:-2.7350402 104:1.3309263 105:-0.29546022 106:1.0598619 107:0.30088151 108:-0.078608684 109:-0.34967312 110:0.73458463 111:-0.34967312 112:1.7104166 113:-0.78337622 114:1.3309263 115:-1.0544406 116:0.30088151 117:-0.45809889 118:-1.2712922 119:0.73458463 120:1.0056491 121:-0.78337622 122:-1.0544406 123:0.4093073 124:-0.45809889 125:-0.62073755 126:1.0056491 127:1.7104166 128:1.0598619 129:-0.78337622 130:0.84301037 131:0.84301037 132:-0.34967312 133:-0.78337622 134:-0.34967312 135:1.0598619 136:-1.2712922 137:1.7981009 138:-0.53812873 139:-0.56949693 140:-0.55872875 141:-0.62006062 142:1.690419 143:-0.6303606 144:-0.55826056 145:-0.6303606 146:-0.56247419 147:1.6997826 148:-0.53812873 149:1.7793736 150:-0.62006062 151:-0.6303606 152:-0.56715602 153:-0.55826056 154:-0.63644701 155:1.6997826 156:1.7793736 157:-0.47820139 158:-0.6303606 159:-0.56106967 160:-0.63644701 161:-0.56247419 162:-0.55872875 163:1.6997826 164:-0.63644701 165:-0.63644701 166:-0.6303606 167:1.6997826 168:-0.6303606 169:-0.55872875 170:-0.56715602 171:-1.1984653 172:0.7582128 173:1.2018782 174:-0.55003136 175:1.2018782 176:-1.1529613 177:0.99710959 178:-0.8116802 179:0.99710959 180:1.0084856 181:-1.1188332 182:0.7582128 183:0.31454739 184:1.2018782 185:1.1336221 186:1.3042625 187:-0.8116802 188:-0.70929587 189:-1.1188332 190:0.31454739 191:-0.78892809 192:1.1336221 193:0.13253082 194:-0.70929587 195:1.0084856 196:-0.55003136 197:-1.1188332 198:-0.31113458 199:-0.31113458 200:0.99710959 201:-1.1188332 202:0.99710959 203:-0.55003136 204:1.3042625 205:0.82939935 206:-1.1153991 207:-1.0009992 208:0.10486659 209:-1.1916658 210:1.782732 211:-0.92473263 212:0.33366641 213:-0.92473263 214:-0.12393324 215:1.5157988 216:-1.1153991 217:0.79126608 218:-1.1916658 219:-1.3060657 220:-1.0772659 221:0.33366641 222:0.2573998 223:1.5157988 224:0.79126608 225:1.2488657 226:-1.3060657 227:-0.81033272 228:0.2573998 229:-0.12393324 230:0.10486659 231:1.5157988 232:-0.085799932 233:-0.085799932 234:-0.92473263 235:1.5157988 236:-0.92473263 237:0.10486659 238:-1.0772659 239:1.2187188 240:2.0727334 241:0.54449672 242:-0.59169227 243:1.1662793 244:-0.69657123 245:-0.15469651 246:-1.2434403 247:-0.15469651 248:-0.55673259 249:-0.074788705 250:2.0727334 251:0.36969844 252:1.1662793 253:0.46958315 254:-1.0461679 255:-1.2434403 256:-2.0050614 257:-0.074788705 258:0.36969844 259:-0.51178449 260:0.46958315 261:1.2936324 262:-2.0050614 263:-0.55673259 264:-0.59169227 265:-0.074788705 266:-1.3782847 267:-1.3782847 268:-0.15469651 269:-0.074788705 270:-0.15469651 271:-0.59169227 272:-1.0461679 273:0.051716596 274:-1.094435 275:-1.094435 276:-0.032148156 277:-0.92670554 278:1.4774173 279:-1.1223899 280:1.2258232 281:-1.1223899 282:1.5892371 283:-0.11601291 284:-1.094435 285:-0.11601291 286:-0.92670554 287:-1.3739842 288:-0.088057987 289:1.2258232 290:1.5892371 291:-0.11601291 292:-0.11601291 293:1.3096879 294:-1.3739842 295:0.41513053 296:1.5892371 297:1.5892371 298:-0.032148156 299:-0.11601291 300:-0.70306617 301:-0.70306617 302:-1.1223899 303:-0.11601291 304:-1.1223899 305:-0.032148156 306:-0.088057987 307:-0.27440333 308:0.95135778 309:0.059895143 310:0.44991004 311:0.97921598 312:-1.3608733 313:1.8706785 314:-0.77585107 315:1.8706785 316:-1.3330152 317:-1.8344629 318:0.95135778 319:-0.44155258 320:0.97921598 321:0.75635028 322:0.44991004 323:-0.77585107 324:-0.77585107 325:-1.8344629 326:-0.44155258 327:-0.38583615 328:0.75635028 329:1.2299398 330:-0.77585107 331:-1.3330152 332:0.44991004 333:-1.8344629 334:-0.55298543 335:-0.55298543 336:1.8706785 337:-1.8344629 338:1.8706785 339:0.44991004 340:0.44991004 341:-0.073000483 342:0.29200193 343:1.6425108 344:-0.62050408 345:0.47450313 346:0.036500242 347:0.21900144 348:-0.83950549 349:0.21900144 350:-1.5695103 351:1.8615122 352:0.29200193 353:-8.1046812e-16 354:0.47450313 355:0.76650506 356:-1.0950072 357:-0.83950549 358:-1.5695103 359:1.8615122 360:-8.1046812e-16 361:-1.2045079 362:0.76650506 363:-1.1315074 364:-1.5695103 365:-1.5695103 366:-0.62050408 367:1.8615122 368:1.5330101 369:1.5330101 370:0.21900144 371:1.8615122 372:0.21900144 373:-0.62050408 374:-1.0950072 375:2.7450233 376:-0.079158269 377:-0.16614538 378:-0.2125385 379:-0.31692302 380:-1.8884901 381:-0.038564283 382:-0.20094022 383:-0.038564283 384:0.1586065 385:-1.6275288 386:-0.079158269 387:0.9066956 388:-0.31692302 389:-0.026966004 390:-0.56628609 391:-0.20094022 392:-0.032765143 393:-1.6275288 394:0.9066956 395:-0.357517 396:-0.026966004 397:-0.2125385 398:-0.032765143 399:0.1586065 400:-0.2125385 401:-1.6275288 402:-0.015367722 403:-0.015367722 404:-0.038564283 405:-1.6275288 406:-0.038564283 407:-0.2125385 408:-0.56628609 # Q5YPH7_m3_unknownspec
Expand Down
Loading