Galaxy |

Changeset 6:d0d4cef4f967 (2021-02-01)

Previous changeset 5:c6334cb383ff (2020-10-08) Next changeset 7:ffd1300599a1 (2021-10-22)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"

modified:
test-data/transcripts.fasta
transdecoder.xml

added:
test-data/blastp.outfmt6
test-data/pasa_assemblies.fasta
test-data/pasa_genetransmap.txt
test-data/pfam.domtblout

diff -r c6334cb383ff -r d0d4cef4f967 test-data/blastp.outfmt6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastp.outfmt6 Mon Feb 01 20:51:40 2021 +0000

@@ -0,0 +1,79 @@
+CUFF.29.1.p1 ISP3_SCHPO 100.000 182 0 0 1 182 1 182 2.18e-138 377
+CUFF.50.1.p1 ADH4_SCHPO 100.000 422 0 0 1 422 1 422 0.0 874
+CUFF.50.1.p2 PANC_SCHPO 100.000 283 0 0 1 283 1 283 0.0 586
+CUFF.50.1.p3 PANB_SCHPO 100.000 267 0 0 1 267 1 267 0.0 554
+CUFF.60.2.p1 CHS1_SCHPO 100.000 832 0 0 1 832 1 832 0.0 1727
+CUFF.60.2.p2 KIME_SCHPO 100.000 404 0 0 1 404 1 404 0.0 823
+CUFF.60.1.p1 CHS1_SCHPO 100.000 832 0 0 1 832 1 832 0.0 1727
+CUFF.60.1.p2 KIME_SCHPO 100.000 353 0 0 1 353 52 404 0.0 723
+CUFF.34.1.p1 YAO3_SCHPO 100.000 302 0 0 1 302 1 302 0.0 634
+CUFF.34.1.p2 YAO2_SCHPO 100.000 146 0 0 1 146 1 146 8.40e-110 302
+CUFF.41.1.p1 YAOB_SCHPO 100.000 325 0 0 1 325 33 357 0.0 678
+CUFF.41.1.p2 YCV2_SCHPO 46.875 256 128 5 4 257 361 610 2.86e-69 220
+CUFF.41.1.p3 YAOA_SCHPO 100.000 119 0 0 1 119 316 434 1.41e-83 245
+CUFF.13.2.p1 NAH_SCHPO 100.000 224 0 0 68 291 1 224 1.27e-163 457
+CUFF.13.1.p1 NAH_SCHPO 100.000 41 0 0 76 116 1 41 7.94e-24 89.0
+CUFF.13.1.p2 NAH_SCHPO 100.000 119 0 0 1 119 106 224 5.44e-82 242
+CUFF.13.3.p1 NAH_SCHPO 92.063 126 10 0 68 193 1 126 2.24e-80 241
+CUFF.11.1.p1 YI48_SCHPO 100.000 293 0 0 1 293 124 416 0.0 597
+CUFF.9.1.p1 YI74_SCHPO 100.000 155 0 0 1 155 1 155 3.11e-113 312
+CUFF.38.1.p1 YAO7_SCHPO 100.000 637 0 0 1 637 1 637 0.0 1321
+CUFF.38.1.p2 YAO8_SCHPO 100.000 550 0 0 1 550 1 550 0.0 1107
+CUFF.38.1.p3 YAO6_SCHPO 100.000 455 0 0 1 455 1 455 0.0 902
+CUFF.38.1.p4 SPEB1_SCHPO 100.000 374 0 0 1 374 1 374 0.0 764
+CUFF.7.1.p1 YI7I_SCHPO 100.000 133 0 0 1 133 1 133 1.05e-98 273
+CUFF.27.1.p1 YDI4_SCHPO 100.000 463 0 0 1 463 1 463 0.0 951
+CUFF.36.1.p1 YAO4_SCHPO 100.000 130 0 0 1 130 1 130 2.80e-95 264
+CUFF.1.1.p1 MAOX_SCHPO 98.148 108 2 0 1 108 51 158 3.27e-73 222
+CUFF.57.1.p1 GCSP_SCHPO 100.000 1031 0 0 1 1031 1 1031 0.0 2161
+CUFF.47.1.p1 HSP32_SCHPO 100.000 178 0 0 22 199 1 178 9.43e-134 369
+CUFF.44.1.p1 YAOF_SCHPO 100.000 1317 0 0 1 1317 1 1317 0.0 2711
+CUFF.37.1.p1 MFS2_SCHPO 100.000 546 0 0 1 546 1 546 0.0 1115
+CUFF.32.1.p1 PDC2_SCHPO 98.940 566 1 1 1 561 1 566 0.0 1155
+CUFF.32.1.p3 YDI8_SCHPO 100.000 120 0 0 1 120 1 120 9.25e-88 244
+CUFF.39.1.p1 YAO6_SCHPO 100.000 455 0 0 1 455 1 455 0.0 902
+CUFF.2.1.p1 YM0C_SCHPO 100.000 123 0 0 1 123 1 123 2.84e-88 246
+CUFF.40.1.p1 YAOA_SCHPO 100.000 434 0 0 1 434 1 434 0.0 897
+CUFF.40.1.p2 YAOB_SCHPO 100.000 325 0 0 1 325 33 357 0.0 678
+CUFF.40.1.p3 YCV2_SCHPO 46.875 256 128 5 4 257 361 610 2.86e-69 220
+CUFF.26.1.p1 YDI4_SCHPO 100.000 461 0 0 1 461 3 463 0.0 946
+CUFF.45.1.p1 YAOH_SCHPO 100.000 585 0 0 1 585 1 585 0.0 1207
+CUFF.45.1.p2 YAOI_SCHPO 100.000 498 0 0 1 498 1 498 0.0 1021
+CUFF.54.1.p1 RS3A1_SCHPO 100.000 252 0 0 1 252 1 252 0.0 517
+CUFF.18.1.p1 YI7F_SCHPO 100.000 247 0 0 10 256 1 247 0.0 519
+CUFF.49.1.p1 OYEA_SCHPO 100.000 382 0 0 1 382 1 382 0.0 798
+CUFF.49.1.p2 YA05_SCHPO 100.000 196 0 0 1 196 1 196 1.96e-151 412
+CUFF.5.1.p1 YP44_SCHPO 100.000 163 0 0 1 163 1 163 7.87e-122 339
+CUFF.58.1.p1 RS6A_SCHPO 100.000 191 0 0 11 201 1 191 5.28e-142 390
+CUFF.43.1.p1 YAOG_SCHPO 100.000 131 0 0 1 131 1 131 4.70e-98 271
+CUFF.28.1.p1 ISP3_SCHPO 100.000 182 0 0 1 182 1 182 2.18e-138 377
+CUFF.25.1.p1 STR3_SCHPO 100.000 630 0 0 1 630 1 630 0.0 1294
+CUFF.24.1.p1 GHT3_SCHPO 100.000 555 0 0 1 555 1 555 0.0 1140
+CUFF.19.1.p1 DAK2_SCHPO 100.000 591 0 0 57 647 1 591 0.0 1201
+CUFF.6.1.p1 YI42_SCHPO 100.000 316 0 0 1 316 29 344 0.0 650
+CUFF.30.2.p1 FTA5_SCHPO 99.355 155 1 0 95 249 181 335 3.84e-116 332
+CUFF.30.1.p1 FTA5_SCHPO 100.000 335 0 0 1 335 1 335 0.0 653
+CUFF.15.1.p1 ASPG2_SCHPO 100.000 356 0 0 11 366 1 356 0.0 726
+CUFF.31.1.p1 FTA5_SCHPO 100.000 385 0 0 1 385 1 385 0.0 752
+CUFF.48.1.p1 OYEA_SCHPO 100.000 382 0 0 1 382 1 382 0.0 798
+CUFF.48.1.p2 YA03_SCHPO 100.000 219 0 0 1 219 1 219 6.12e-167 453
+CUFF.48.1.p3 YA05_SCHPO 100.000 196 0 0 1 196 1 196 1.96e-151 412
+CUFF.12.1.p1 PLB7_SCHPO 100.000 673 0 0 1 673 1 673 0.0 1393
+CUFF.14.1.p1 FEX2_SCHPO 100.000 311 0 0 1 311 1 311 0.0 634
+CUFF.3.1.p1 YM04_SCHPO 100.000 288 0 0 1 288 1 288 0.0 588
+CUFF.4.1.p1 YP42_SCHPO 100.000 119 0 0 1 119 1 119 7.65e-87 242
+CUFF.53.1.p1 GPI7_SCHPO 100.000 758 0 0 1 758 1 758 0.0 1550
+CUFF.51.1.p1 YA0C_SCHPO 100.000 371 0 0 1 371 1 371 0.0 769
+CUFF.51.1.p2 GMH2_SCHPO 100.000 346 0 0 1 346 1 346 0.0 719
+CUFF.46.1.p1 HSP32_SCHPO 100.000 240 0 0 1 240 1 240 0.0 491
+CUFF.42.1.p1 YAOE_SCHPO 100.000 989 0 0 1 989 272 1260 0.0 2059
+CUFF.42.1.p2 HSP34_SCHPO 100.000 222 0 0 1 222 1 222 1.08e-168 457
+CUFF.55.1.p1 YA95_SCHPO 92.617 149 4 1 19 167 1 142 5.46e-101 285
+CUFF.35.1.p1 YAO2_SCHPO 100.000 150 0 0 1 150 1 150 1.18e-112 310
+CUFF.17.1.p1 YI7E_SCHPO 100.000 351 0 0 1 351 1 351 0.0 726
+CUFF.59.1.p1 ASL1_SCHPO 100.000 530 0 0 1 530 1 530 0.0 1019
+CUFF.52.1.p1 OYEB_SCHPO 100.000 392 0 0 1 392 1 392 0.0 824
+CUFF.52.1.p2 GMH1_SCHPO 100.000 329 0 0 1 329 1 329 0.0 683
+CUFF.52.1.p3 PANB_SCHPO 100.000 240 0 0 1 240 1 240 0.0 497
+CUFF.20.1.p1 YI7H_SCHPO 100.000 598 0 0 1 598 1 598 0.0 1234
+CUFF.20.1.p2 DAK2_SCHPO 100.000 148 0 0 57 204 1 148 2.26e-102 301

diff -r c6334cb383ff -r d0d4cef4f967 test-data/pasa_assemblies.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pasa_assemblies.fasta Mon Feb 01 20:51:40 2021 +0000

b'@@ -0,0 +1,5000 @@\n+>asmbl_1\n+AGATAAATTTTCTCTTTCTTTTGAAACATATATATACAGATATAAATAGAGGCAGATACA\n+TGTAACCTAGCCAAAGGAGCATTGGTATCTCAAACAATATTTGCCCTTTCTCTATCTCTC\n+TCTCATCACTATTTGCCATCTCTTTCTCTCTCCCTCTCTTTCAAATGTCAATAAACCAAT\n+ACTCAAGCGATTTCCACTACCATTCTCTCATGTGGCAACAACAGCAGCAACAACAACAAC\n+ACCAAAACGACGTCGTGGAAGAAAAAGAAGCTCTTTTCGAGAAACCCTTAACCCCAAGTG\n+ACGTCGGAAAACTCAACCGCCTCGTCATCCCAAAACAGCACGCCGAGAGATACTTCCCAC\n+TAGCGGCCGCCGCCGCAGACGCCGTGGAGAAAGGACTTCTCCTCTGCTTTGAGGACGAGG\n+AAGGTAAACCATGGAGATTCAGATACTCGTACTGGAACAGTAGCCAGAGTTATGTCTTGA\n+CCAAAGGCTGGAGCAGATACGTCAAGGAGAAGCACCTTGACGCCGGAGACGTCGTTCTCT\n+TCCATCGACACCGTTCAGACGGCGGAAGATTCTTCATTGGCTGGAGAAGACGCGGTGACT\n+CTTCTTCCTCCTCCGACTCTTATCGCCATGTTCAATCCAATGCCTCGCTCCAATATTATC\n+CTCATGCAGGGGCTCAAGCGGTGGAGAGCCAAAGAGGCAACTCGAAGACATTAAGACTGT\n+TCGGAGTGAACATGGAGTGCCAGCTAGATTCGGACTGGTCCGAGCCATCCACACCTGACG\n+GTTCTAACACATATACAACCAATCACGACCAGTTTCATTTCTACCCTCAACAACAACACT\n+ATCCTCCTCCGTACTACATGGACATAAGTTTCACAGGAGATATGAACCGGACGAGCTAGA\n+AGCCCACAAGGATTAAAAAAAAGCTTCACATCTGGTCCTGTTATGTTGTCATAGATGTTG\n+ATTCCTTAATTTTACACAAGCTTCATTTTGCATTATTTAAAGTAAAATCGTATTTTGATT\n+CTTCTTTAAATCTCTCTCAATTTTCACTCTCTTCCTTTTTCTTCTTATGTATTAGATTCT\n+TTTACATAGCTAACACTTGTATAGAGAATTCAAAGTTCTGGCTATTTTCGAAAGTTATCT\n+TTTCTCTTT\n+>asmbl_33\n+TGGGACATGTACAACAAACCTGGTCGAAAGAAACAATGGTGAAGGATGATAGCAGCTGGA\n+TCATCTGAGTAACATCATCTCTCTACAGATTAAGACTTCTTCTTCTCTTTCTCGTCTTAT\n+GATCTCTGCCTTAAATCATTGGAACTTCGGTATAAAAACACATGAGATCCAATAAAACAT\n+TGTCTTCATAAAACTTGGATCTCAAAACTCATTCTACAATCCATATTATCTATAACTCCA\n+AGTTAACACAGTTTTCTTTGTATACCCCTTTATAGTATATGATATTATCCATTTG\n+>asmbl_24\n+TTTCTCCACGCTTCGCTTTCTCCTTCCATTTTCTTCCAAACTCTCTCCGCTTCGTCCTCT\n+CTTTCACACCGCCGCTATGCCTCCTCACGGTCCTAATTCTCAAGGTGGTCGTCGAGGCGG\n+AGGTCATTCCTCCGGTCGTCGTGGTGGACGCGGCGGCGGCGGTCGTGGCGGTGGTGGTGG\n+CGGCCGGGGGGAACAGCGATGGTGGGATCCTGTGTGGAGAGCTGAGCGTTTGCGCCAGCA\n+ACAAGCTGAGATGGAAGTACTTGATGAGAATGAATGGTGGAACAAGATTGAGCAATGGAA\n+AACAGGAGGAGAACAAGAGATGCTAATTAAGCGTAATTTTAGCCGTGGAGATCAGCAAAC\n+ACTTTCTGATATGGCTTTGCAGATGGGTCTTTACTTTCATGCGTACAATAAAGGGAAGGC\n+TCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGG\n+ATCCACTCAGAAAGAGATTAAAATGTCCACAGAGACTGAGAGAAAACTTGGAAGTCTTTT\n+GAAAACAACACAAGAATCAGGGTCCTCTGGTGCCTCTGCTTCAGCTTTTAACGATCAACA\n+GGATCGTACTTCAACTCTTGGCTTGAAAAGACCTGATTCTGCTTCCAAATTGCCGGATTC\n+TCTTGAGAAAGAAAAATTCAGTTTTGCACTCAAGGAAAGGCAGGAAAAGCTTAAGGCAAC\n+TGAGAGTGTAAAAGCACTTAAAGCGTTCAGAGAAAAGCTACCTGCTTTTAAAATGAAAGA\n+GGAGTTTCTTAACTCTGTTTCACAAAACCAGGTATTGGTAGTTTCAGGAGAGACCGGGTG\n+TGGTAAAACAACACAGCTTCCTCAATTTATATTGGAAGAAGAAATATCATCCCTAAGAGG\n+TGCTGATTGCAACATAATTTGCACTCAACCTCGACGTATATCGGCCATATCTGTTGCTTC\n+TCGTATATCTGCTGAAAGAGGTGAATCCATTGGTGAATCTGTGGGTTATCAGATTCGTCT\n+AGAATCAAAGCGTTCTGATCAAACACGATTGCTATTTTGCACTACTGGTGTTTTACTCCG\n+GCGGCTGATTGAGGATCCTAATCTAACTAACGTAAGCCATTTGCTCGTGGATGAGATTCA\n+CGAAAGAGGCATGAATGAAGATTTTCTACTAATCATACTACGCGATCTCCTTCCTCGACG\n+CCCAGATTTGCGTCTTATTCTGATGAGTGCTACGATTAACGCTGACATGTTCTCAACATA\n+CTTTGGGAACTCTCCCACTATGCACATCCCGGGTTTCACATTTCCTGTGGCAGAGTTATT\n+CCTAGAAGATGTATTGGAGAAAAGTCGTTATAATATTAAGTCGTCTGACTCGGGGAATTA\n+TCAAGGTAGTTCGAGAGGTAGAAGAAGAGAATCAGAATCCAAGAAAGATGATCTGACTAC\n+TCTTTTTGAGGATATTGACATCAATTCTCACTATAAAAGTTATAGCTCGGCCACAAGAAA\n+TTCTCTTGAAGCATGGTCTGGTGCACAGATTGATGTGGATCTGGTGGAGGCAACAATTGA\n+ACATATTTGTCGTCTTGAAGGTGGTGGGGCGATTCTTGTCTTCCTTACTGGCTGGGATGA\n+GATTTCAAAACTGCTTGAAAAAATTAACATGAACAACTTTCTTGGAGATTCGAGCAAGTT\n+CTTAGTTCTTCCTTTACATGGTTCAATGCCGACGGTTAATCAACGTGAAATTTTTGACCG\n+TCCACCTCCTAACAAACGGAAAATAGTTTTGGCTACAAACATTGCCGAGAGTAGTATTAC\n+AATTGATGATGTTGTATATGTTGTGGATTGTGGTAAAGCAAAGGAAACTAGCTATGATGC\n+TTTGAACAAGGTGGCATGTCTCTTGCCATCATGGATATCAAAGGCTTCAGCTCACCAGAG\n+ACGAGGTCGTGCTGGACGTGTTCAAGCTGGAGTTTGTTATAGGTTGTATCCAAAAGTTAT\n+CTATGATGCTTTTCCACAGTATCAGTTACCAGAAATCATACGGACTCCATTACAAGAGCT\n+ATGCCTGCATATCAAAAGTTTGCAAGTTGGATCTATAGGCTCATTCTTGGCAAAGGCACT\n+GCAGCCACCAGATGCACTTGCTGTTGAGAATGCTATTGAACTTCTCAAAACAATTGGGGC\n+TTTAAATGACGTGGAAGAGCTTACACCCCTTGGTCGGCATCTTTGCACTCTACCCGTGGA\n+CCCAAATATTGGAAAGATGCTTCTGATTGGAGCTATCTTCCAGTGCGTCAATCCTGCTTT\n+GACAATCGCTGCTGCTCTGGCGTATCGTAGCCCATTTGTCTTACCATTAAATAGGAAAGA\n+GGAAGCTGATGAAGCCAAACGATATTTTGCTGGTG'..b'AGCAATTACCA\n+TGGTGACTCCGAAGCAGATCGATTTCTCTTCCTGTGGTGGTGGTGATAACTCCGACGATA\n+CCCTCTCCCATCGAGAATCTCCACGGAATCCTTCCTCAAAGCGTGCTGCTGCTTCCTTCG\n+CAGCAGAAGCAGGCGAAGAGACTATGAAGAAGAAAAAGAAGAAGAAGAAGAAGAATTTGG\n+GTCCGCCGTTGATCGTCCGGATCTGGAACGAGGAAGATGAGCTCTCTATCTTAAAGGGAT\n+TAGTTGATTACAGAGCTAAGACAGGATTCAATCCCAAAATTGATTGGGATGCGTTTTACA\n+GTTTCCTCGGAAGTTCTATCGTTGCGAAATTCTCCAAGGAGCAGGTTTTGAGTAAGATCA\n+GGAAGTTGAAAAGGAGATTTCATGTTCATTGGGAGAAAATCAGTGAAGGGAATGATCCGA\n+AATTTACTAGGTCTAGTGATTCTGAAGCCTTTGGATTTTCTTCGATGATTTGGGGACAAG\n+GTGAATTTGGTAATGATGATGGTATGGATAAGGAGATGGTGAAGGAGCACGATGTAAACG\n+GAAATGGCGCAGCTGAAAATGGGACTGCTCGAATAGCACAGGAGAACGAGAGTGGGGAGG\n+AGATGTTAAAGGAGCATGAGGAAACGTTAAATGAGAATGGTGCAGAGGAGATAAGAGACA\n+ACGACGAGACTGCTCGGAAAGCACAGCAGCTCGAGAGCGAGAGCGAGGAGGAGATGTTGA\n+AGGAGCATGAGGAACCCTTTAATGAGAATGGTGCAGAGAATATAAGAGACAATAACGGGA\n+CTACTCAAATAGCACAGCAGAGCGAGAGCGAGAGTGAGGAGATGTTGAAGGAGCATGAGG\n+AAGTGGCTAATACTGAACTTGTAAATGAGAATGGGGCAGCGAAAACAACAGAGAACGGGA\n+CTACTGGTGGAAAAGAGAGACATGATGACGATGATGATGATGAGTTATGCGCTGTGCAGG\n+ATGCATTTGAGGCTGTAATGTCGCAAGGTTTAAGTGGTTATCAAAAGAAGTTGCAGCTTG\n+AGAAGCTGATGAACCTTGGAACTGGAAAAAGAAGAGAGTTGAGTGATGAATGGAAAGCGT\n+TATGTGTTGAGGAAAGAAGATTGAATATCAAGAAGCTTAGATTTTCCGCCAAGCTTGCAG\n+AGGCAGCTAATGATAGTTAGATGAAACCAATAAGCCGTTGTAGCATTTGGTGTTAATTAG\n+GTTCTTAGTAAGCCATAAGCTTTAGTCTGTTCAGTGTATATCTTTGGATGTTGTCTTTGT\n+TCTGTTTGGGCAAGTGTTTGTAAGACATTCCAGTTTTAACTGAAGTATCCAGAAGAGCCA\n+TCCATGTCCATTGTTGGATATAATAAATTTCATTACTTTCTTGTTGCACCAATCAGTC\n+>asmbl_213\n+CTTTTCCAGTTGGTCACGGAAATGAAAGCAGAGTATTTTCCTCCCAAAGAAGATGTGATT\n+TTGCAAAATGAAGCCCCAACAGATTTCTACATATTGGTGACCGGAGCTGTTGACATAATT\n+GCACGTGTAAATGGAGTGGAGCAGGTAGTTAGTGAAGCACAGAGAGGACATGTTTTTGGT\n+GAAGTTGGGGTACTATGTTACAGACCGCAGCTGTTTACTGTTCGTACCAAGCGATTGAGT\n+CAGTTGCTTCGTCTGAACCGTACAGTACTCTTAAATCTTGTTCAGGCAAATGTAGGAGAT\n+GGAGCAATAATCATGAATAATCTTCTTCAGCATTTAAAAGACTCAGAAGATCCAGTGATG\n+AAAGGCGTTTTGGCTGATACAGAACACATGTTGGCTCAAGGGAAAATGGATTTACCTCTC\n+AGCTTGTGCTTTGCTGCAGCCAGAGGAGATGATTTATTGCTGCATCAGTTACTAAGACGA\n+GGCTCAAGCCCTAATGAAATGGATAAGGACGGGCGAACTGCGCTGCATATAGCAGCATCA\n+AAGGGAAGCCATTATTGCGTCGTTTTACTTCTCGAACATGGAGCAGATCCTAACATTAGA\n+GATTCCGAAGGCAATGTACCCTTGTGGGAAGCAATCATAGGAAGACATAGAGAAATTGCT\n+AAACTCCTTGCAGAGAATGGAGCAAAGCTAAGCTTAGACTCAGTGAGCTATTTCTCTGGC\n+TTAGCCGTGGAGAAAAACTGCTTAGACGCACTCAAAGACATCATCAAATATGGCGGCGAC\n+GTCACACTCCCTGATGGAAACGGAACCACAGCTTTACACAGAGCAGTGTCAGAAGGACAC\n+TTGGAGATTGTGAAGTTCTTACTAGACCAAGGTGCTGACTTGGACTGGCCGGATTCTTAC\n+GGATGGACTCCTCGTGGTCTTGCCGATCATCAAGGGAATGAAGAAATCAAAACCTTGTTT\n+CATAATCACAGGCCTGTGGAGAAAAAACCGAAACCTATCCCTGGAATACCTCAGAGTCCT\n+GTGACAGGGAAGCCATTAATGAAGTATAGCAGTGAGCCTACAATGCATTCAGGAGAACTC\n+GTCTTAGACGGGGGTCAGGTTGTTGTTTCTCAGAAACGGAAACTCAATAACTTCAGAAAC\n+TCGCTCTTCGGAATCATTTCAGCTGCAAATAGCGCTGATGATGGAGGAGAAGTTCCAAGA\n+AGTCCAGCGGTTCCTGGAGGAGGAGGTAGTATGATTTATCCGGAGAGAGTGACGATAAGT\n+TCGCCGGAAAACGGTGAAACTGGTGGAAAAGTTGTTTTGTTACCAAATTCTATGGAAGAG\n+CTATTGAAAATTGGTGAAAATAAGATGGGATTCGTCCCAACTAAAGTACTTACGAGAGAA\n+GGAGCTGAAATTGACGACATCACTCTTATCAGAGATGGCGATTTTCTCCTTCTATCAAGG\n+GATCCTTGATTCACACGCAACTCTCTTTCGATTTTGAGTAATGAAAACTATTTGTCTTAA\n+CGCAAACTCGCAAACCACCACAGTCAAGCTTTATGGTGGTGATATGATGCTAATATTAGG\n+GGAAACCGTAAGCCCCAATCAACTCCGGGATTGAAATATCTTTTAGGTTTTTTTTTTTTG\n+CTTTTGTGTATATATTCACTGCTTACTATTTTTCACATGTATATATATATATATCCTGTT\n+GACTATTTTCTGTTAAAAGAACTCTCTAACAACCTCATGA\n+>asmbl_236\n+ATTATTCTCTTTAAGGCTCTACTATCACTTTGTTCAGATGAGCTAGTATCAGCAAGAAGT\n+GCCATGGACCTATGCATCAGTCAAATGAAAAACGTATTGAGCTCCAAACAGTTGTCAGAG\n+GGTGCGTCTGTTGAAACAATTGGCCGAGCATATCATGCAACGGAGGCATTTGTGCAGGGT\n+TTGTCGTATGCAAAATCATTGCTGAGAAAGCTTCTAGGTACCACTGAATCGACCAATAAC\n+AATGGTGAAAGAAGTAGAGATGTTGATGATATATCTTCTGATGCTGGCAGCTCCAGTGTT\n+GGCAGTCAGTCAACGGATGAACCATCGGATGTTCTCTCACTTACAGAAATCTGGTTGGGG\n+CGC\n+>asmbl_227\n+AATAAGGATGAAAAATTAACATTTTCTTTTGTCTGTTACAAATATTTCTCCGCTGATTTG\n+AAGCTGAGGAATTTAATTAAGGAATATTTTGGCATATTCTTTGAAAATCTCTCATTCTTT\n+GGTTCTTTCTAAGATAATTTGCTTTTGTTGTATAAAAAAAGAGTAACTAGAATACCAAAA\n+TATTGAAGAAGAAGAAACATCATAACCGTAAAATGCTGAAGACAAGAGCAATGTTTCCTC\n+ACAAAGATCAAGCAATGTCGCTGTCTTTGGATCCACAATCTGATCTTGTCGTCGGTCACA\n+CCAACAACAGACCAATCACTAACCCACTGGCTTTGAGTCTTTTGATTGGTCTGAACAACA\n'

diff -r c6334cb383ff -r d0d4cef4f967 test-data/pasa_genetransmap.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pasa_genetransmap.txt Mon Feb 01 20:51:40 2021 +0000

b'@@ -0,0 +1,859 @@\n+subcluster_id\tasmbl_acc\n+1\tasmbl_1\n+2\tasmbl_2\n+3\tasmbl_3\n+4\tasmbl_4\n+4\tasmbl_5\n+4\tasmbl_6\n+5\tasmbl_7\n+6\tasmbl_8\n+6\tasmbl_9\n+7\tasmbl_10\n+6\tasmbl_11\n+8\tasmbl_12\n+8\tasmbl_13\n+9\tasmbl_14\n+9\tasmbl_15\n+10\tasmbl_16\n+11\tasmbl_17\n+12\tasmbl_18\n+12\tasmbl_19\n+13\tasmbl_20\n+13\tasmbl_21\n+13\tasmbl_22\n+14\tasmbl_23\n+15\tasmbl_24\n+16\tasmbl_25\n+17\tasmbl_26\n+18\tasmbl_27\n+19\tasmbl_28\n+20\tasmbl_29\n+20\tasmbl_30\n+20\tasmbl_31\n+20\tasmbl_32\n+20\tasmbl_33\n+21\tasmbl_34\n+21\tasmbl_35\n+22\tasmbl_36\n+23\tasmbl_37\n+24\tasmbl_38\n+25\tasmbl_39\n+26\tasmbl_40\n+27\tasmbl_41\n+28\tasmbl_42\n+29\tasmbl_43\n+30\tasmbl_44\n+31\tasmbl_45\n+32\tasmbl_46\n+33\tasmbl_47\n+34\tasmbl_48\n+34\tasmbl_49\n+34\tasmbl_50\n+34\tasmbl_51\n+35\tasmbl_52\n+35\tasmbl_53\n+35\tasmbl_54\n+36\tasmbl_55\n+37\tasmbl_56\n+37\tasmbl_57\n+38\tasmbl_58\n+39\tasmbl_59\n+40\tasmbl_60\n+41\tasmbl_61\n+42\tasmbl_62\n+43\tasmbl_63\n+44\tasmbl_64\n+45\tasmbl_65\n+46\tasmbl_66\n+47\tasmbl_67\n+47\tasmbl_68\n+47\tasmbl_69\n+48\tasmbl_70\n+49\tasmbl_71\n+50\tasmbl_72\n+50\tasmbl_73\n+50\tasmbl_74\n+51\tasmbl_75\n+52\tasmbl_76\n+52\tasmbl_77\n+53\tasmbl_78\n+54\tasmbl_79\n+55\tasmbl_80\n+56\tasmbl_81\n+57\tasmbl_82\n+58\tasmbl_83\n+59\tasmbl_84\n+59\tasmbl_85\n+60\tasmbl_86\n+61\tasmbl_87\n+62\tasmbl_88\n+63\tasmbl_89\n+63\tasmbl_90\n+64\tasmbl_91\n+64\tasmbl_92\n+65\tasmbl_93\n+66\tasmbl_94\n+67\tasmbl_95\n+68\tasmbl_96\n+69\tasmbl_97\n+69\tasmbl_98\n+70\tasmbl_99\n+71\tasmbl_100\n+72\tasmbl_101\n+73\tasmbl_102\n+74\tasmbl_103\n+75\tasmbl_104\n+75\tasmbl_105\n+76\tasmbl_106\n+77\tasmbl_107\n+78\tasmbl_108\n+79\tasmbl_109\n+79\tasmbl_110\n+80\tasmbl_111\n+81\tasmbl_112\n+82\tasmbl_113\n+83\tasmbl_114\n+84\tasmbl_115\n+84\tasmbl_116\n+85\tasmbl_117\n+86\tasmbl_118\n+87\tasmbl_119\n+88\tasmbl_120\n+89\tasmbl_121\n+89\tasmbl_122\n+90\tasmbl_123\n+91\tasmbl_124\n+91\tasmbl_125\n+92\tasmbl_126\n+93\tasmbl_127\n+94\tasmbl_128\n+95\tasmbl_129\n+96\tasmbl_130\n+97\tasmbl_131\n+98\tasmbl_132\n+97\tasmbl_133\n+97\tasmbl_134\n+99\tasmbl_135\n+100\tasmbl_136\n+101\tasmbl_137\n+102\tasmbl_138\n+103\tasmbl_139\n+104\tasmbl_140\n+105\tasmbl_141\n+106\tasmbl_142\n+107\tasmbl_143\n+108\tasmbl_144\n+109\tasmbl_145\n+109\tasmbl_146\n+110\tasmbl_147\n+111\tasmbl_148\n+112\tasmbl_149\n+112\tasmbl_150\n+112\tasmbl_151\n+112\tasmbl_152\n+113\tasmbl_153\n+114\tasmbl_154\n+115\tasmbl_155\n+116\tasmbl_156\n+117\tasmbl_157\n+117\tasmbl_158\n+118\tasmbl_159\n+119\tasmbl_160\n+120\tasmbl_161\n+121\tasmbl_162\n+121\tasmbl_163\n+122\tasmbl_164\n+122\tasmbl_165\n+123\tasmbl_166\n+123\tasmbl_167\n+124\tasmbl_168\n+125\tasmbl_169\n+126\tasmbl_170\n+127\tasmbl_171\n+127\tasmbl_172\n+127\tasmbl_173\n+128\tasmbl_174\n+129\tasmbl_175\n+130\tasmbl_176\n+131\tasmbl_177\n+132\tasmbl_178\n+133\tasmbl_179\n+134\tasmbl_180\n+135\tasmbl_181\n+136\tasmbl_182\n+137\tasmbl_183\n+138\tasmbl_184\n+139\tasmbl_185\n+140\tasmbl_186\n+141\tasmbl_187\n+142\tasmbl_188\n+143\tasmbl_189\n+144\tasmbl_190\n+145\tasmbl_191\n+146\tasmbl_192\n+147\tasmbl_193\n+148\tasmbl_194\n+149\tasmbl_195\n+150\tasmbl_196\n+150\tasmbl_197\n+151\tasmbl_198\n+151\tasmbl_199\n+151\tasmbl_200\n+151\tasmbl_201\n+152\tasmbl_202\n+153\tasmbl_203\n+154\tasmbl_204\n+155\tasmbl_205\n+156\tasmbl_206\n+156\tasmbl_207\n+157\tasmbl_208\n+158\tasmbl_209\n+159\tasmbl_210\n+160\tasmbl_211\n+161\tasmbl_212\n+162\tasmbl_213\n+163\tasmbl_214\n+163\tasmbl_215\n+164\tasmbl_216\n+165\tasmbl_217\n+165\tasmbl_218\n+166\tasmbl_219\n+167\tasmbl_220\n+167\tasmbl_221\n+168\tasmbl_222\n+169\tasmbl_223\n+170\tasmbl_224\n+170\tasmbl_225\n+171\tasmbl_226\n+172\tasmbl_227\n+172\tasmbl_228\n+173\tasmbl_229\n+174\tasmbl_230\n+174\tasmbl_231\n+174\tasmbl_232\n+175\tasmbl_233\n+176\tasmbl_234\n+176\tasmbl_235\n+177\tasmbl_236\n+178\tasmbl_237\n+179\tasmbl_238\n+180\tasmbl_239\n+181\tasmbl_240\n+182\tasmbl_241\n+183\tasmbl_242\n+184\tasmbl_243\n+185\tasmbl_244\n+186\tasmbl_245\n+187\tasmbl_246\n+188\tasmbl_247\n+186\tasmbl_248\n+189\tasmbl_249\n+190\tasmbl_250\n+191\tasmbl_251\n+192\tasmbl_252\n+193\tasmbl_253\n+194\tasmbl_254\n+195\tasmbl_255\n+196\tasmbl_256\n+197\tasmbl_257\n+198\tasmbl_258\n+198\tasmbl_259\n+198\tasmbl_260\n+199\tasmbl_261\n+200\tasmbl_262\n+201\tasmbl_263\n+202\tasmbl_264\n+203\tasmbl_265\n+204\tasmbl_266\n+205\tasmbl_267\n+206\tasmbl_268\n+207\tasmbl_269\n+208\tasmbl_270\n+209\tasmbl_271\n+210\tasmbl_272\n+211\tasmbl_273\n+212\tasmbl_274\n+213\tasmbl_275\n+214\tasmbl_276\n+215\tasmbl_277\n+216\tasmbl_278\n+217\tasmbl_279\n+216\tasmbl_280\n+218\tasmbl_281'..b'smbl_592\n+460\tasmbl_593\n+460\tasmbl_594\n+460\tasmbl_595\n+461\tasmbl_596\n+462\tasmbl_597\n+463\tasmbl_598\n+464\tasmbl_599\n+465\tasmbl_600\n+466\tasmbl_601\n+467\tasmbl_602\n+468\tasmbl_603\n+469\tasmbl_604\n+470\tasmbl_605\n+471\tasmbl_606\n+472\tasmbl_607\n+473\tasmbl_608\n+474\tasmbl_609\n+475\tasmbl_610\n+476\tasmbl_611\n+477\tasmbl_612\n+478\tasmbl_613\n+479\tasmbl_614\n+480\tasmbl_615\n+481\tasmbl_616\n+481\tasmbl_617\n+481\tasmbl_618\n+482\tasmbl_619\n+483\tasmbl_620\n+484\tasmbl_621\n+485\tasmbl_622\n+486\tasmbl_623\n+487\tasmbl_624\n+487\tasmbl_625\n+488\tasmbl_626\n+488\tasmbl_627\n+489\tasmbl_628\n+489\tasmbl_629\n+490\tasmbl_630\n+491\tasmbl_631\n+492\tasmbl_632\n+493\tasmbl_633\n+493\tasmbl_634\n+494\tasmbl_635\n+495\tasmbl_636\n+496\tasmbl_637\n+497\tasmbl_638\n+498\tasmbl_639\n+498\tasmbl_640\n+499\tasmbl_641\n+500\tasmbl_642\n+501\tasmbl_643\n+501\tasmbl_644\n+501\tasmbl_645\n+502\tasmbl_646\n+503\tasmbl_647\n+503\tasmbl_648\n+504\tasmbl_649\n+505\tasmbl_650\n+505\tasmbl_651\n+506\tasmbl_652\n+507\tasmbl_653\n+508\tasmbl_654\n+508\tasmbl_655\n+509\tasmbl_656\n+510\tasmbl_657\n+510\tasmbl_658\n+511\tasmbl_659\n+512\tasmbl_660\n+512\tasmbl_661\n+513\tasmbl_662\n+514\tasmbl_663\n+515\tasmbl_664\n+516\tasmbl_665\n+517\tasmbl_666\n+518\tasmbl_667\n+519\tasmbl_668\n+519\tasmbl_669\n+520\tasmbl_670\n+521\tasmbl_671\n+522\tasmbl_672\n+523\tasmbl_673\n+524\tasmbl_674\n+525\tasmbl_675\n+526\tasmbl_676\n+527\tasmbl_677\n+528\tasmbl_678\n+529\tasmbl_679\n+530\tasmbl_680\n+531\tasmbl_681\n+532\tasmbl_682\n+533\tasmbl_683\n+534\tasmbl_684\n+535\tasmbl_685\n+536\tasmbl_686\n+535\tasmbl_687\n+537\tasmbl_688\n+537\tasmbl_689\n+538\tasmbl_690\n+539\tasmbl_691\n+540\tasmbl_692\n+541\tasmbl_693\n+542\tasmbl_694\n+541\tasmbl_695\n+543\tasmbl_696\n+544\tasmbl_697\n+545\tasmbl_698\n+546\tasmbl_699\n+547\tasmbl_700\n+548\tasmbl_701\n+549\tasmbl_702\n+550\tasmbl_703\n+551\tasmbl_704\n+552\tasmbl_705\n+553\tasmbl_706\n+554\tasmbl_707\n+555\tasmbl_708\n+556\tasmbl_709\n+557\tasmbl_710\n+558\tasmbl_711\n+559\tasmbl_712\n+560\tasmbl_713\n+560\tasmbl_714\n+560\tasmbl_715\n+561\tasmbl_716\n+562\tasmbl_717\n+563\tasmbl_718\n+564\tasmbl_719\n+565\tasmbl_720\n+566\tasmbl_721\n+567\tasmbl_722\n+568\tasmbl_723\n+569\tasmbl_724\n+569\tasmbl_725\n+570\tasmbl_726\n+571\tasmbl_727\n+572\tasmbl_728\n+573\tasmbl_729\n+574\tasmbl_730\n+574\tasmbl_731\n+574\tasmbl_732\n+574\tasmbl_733\n+575\tasmbl_734\n+576\tasmbl_735\n+577\tasmbl_736\n+578\tasmbl_737\n+579\tasmbl_738\n+580\tasmbl_739\n+581\tasmbl_740\n+581\tasmbl_741\n+582\tasmbl_742\n+583\tasmbl_743\n+583\tasmbl_744\n+584\tasmbl_745\n+584\tasmbl_746\n+585\tasmbl_747\n+586\tasmbl_748\n+587\tasmbl_749\n+588\tasmbl_750\n+588\tasmbl_751\n+589\tasmbl_752\n+590\tasmbl_753\n+590\tasmbl_754\n+590\tasmbl_755\n+590\tasmbl_756\n+590\tasmbl_757\n+590\tasmbl_758\n+591\tasmbl_759\n+592\tasmbl_760\n+593\tasmbl_761\n+594\tasmbl_762\n+595\tasmbl_763\n+596\tasmbl_764\n+597\tasmbl_765\n+597\tasmbl_766\n+598\tasmbl_767\n+599\tasmbl_768\n+600\tasmbl_769\n+601\tasmbl_770\n+601\tasmbl_771\n+602\tasmbl_772\n+602\tasmbl_773\n+603\tasmbl_774\n+604\tasmbl_775\n+605\tasmbl_776\n+606\tasmbl_777\n+607\tasmbl_778\n+608\tasmbl_779\n+609\tasmbl_780\n+610\tasmbl_781\n+611\tasmbl_782\n+612\tasmbl_783\n+613\tasmbl_784\n+614\tasmbl_785\n+615\tasmbl_786\n+615\tasmbl_787\n+616\tasmbl_788\n+617\tasmbl_789\n+618\tasmbl_790\n+619\tasmbl_791\n+620\tasmbl_792\n+620\tasmbl_793\n+621\tasmbl_794\n+622\tasmbl_795\n+623\tasmbl_796\n+624\tasmbl_797\n+625\tasmbl_798\n+626\tasmbl_799\n+627\tasmbl_800\n+628\tasmbl_801\n+629\tasmbl_802\n+630\tasmbl_803\n+631\tasmbl_804\n+631\tasmbl_805\n+632\tasmbl_806\n+633\tasmbl_807\n+634\tasmbl_808\n+635\tasmbl_809\n+635\tasmbl_810\n+636\tasmbl_811\n+637\tasmbl_812\n+638\tasmbl_813\n+639\tasmbl_814\n+640\tasmbl_815\n+641\tasmbl_816\n+642\tasmbl_817\n+643\tasmbl_818\n+643\tasmbl_819\n+644\tasmbl_820\n+645\tasmbl_821\n+646\tasmbl_822\n+647\tasmbl_823\n+648\tasmbl_824\n+649\tasmbl_825\n+650\tasmbl_826\n+651\tasmbl_827\n+652\tasmbl_828\n+653\tasmbl_829\n+653\tasmbl_830\n+654\tasmbl_831\n+655\tasmbl_832\n+656\tasmbl_833\n+656\tasmbl_834\n+656\tasmbl_835\n+657\tasmbl_836\n+658\tasmbl_837\n+658\tasmbl_838\n+658\tasmbl_839\n+659\tasmbl_840\n+660\tasmbl_841\n+661\tasmbl_842\n+662\tasmbl_843\n+663\tasmbl_844\n+664\tasmbl_845\n+665\tasmbl_846\n+666\tasmbl_847\n+667\tasmbl_848\n+668\tasmbl_849\n+669\tasmbl_850\n+670\tasmbl_851\n+671\tasmbl_852\n+672\tasmbl_853\n+673\tasmbl_854\n+674\tasmbl_855\n+675\tasmbl_856\n+676\tasmbl_857\n+677\tasmbl_858\n'

diff -r c6334cb383ff -r d0d4cef4f967 test-data/pfam.domtblout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pfam.domtblout Mon Feb 01 20:51:40 2021 +0000

[

b'@@ -0,0 +1,252 @@\n+# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord\n+# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target\n+#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------\n+Fe-ADH PF00465.18 364 CUFF.50.1.p1 - 423 8.2e-127 415.8 1.9 1 1 1.6e-128 9.4e-127 415.6 1.9 1 364 52 414 52 414 0.96 Iron-containing alcohol dehydrogenase\n+Fe-ADH_2 PF13685.5 250 CUFF.50.1.p1 - 423 9e-23 74.1 4.0 1 2 4.9e-22 2.9e-20 65.9 2.6 2 245 57 320 56 323 0.89 Iron-containing alcohol dehydrogenase\n+Fe-ADH_2 PF13685.5 250 CUFF.50.1.p1 - 423 9e-23 74.1 4.0 2 2 0.8 47 -3.6 0.0 27 60 355 388 350 399 0.70 Iron-containing alcohol dehydrogenase\n+Pantoate_ligase PF02569.14 266 CUFF.50.1.p2 - 284 1.6e-104 341.7 0.0 1 1 4.4e-106 1.7e-104 341.6 0.0 4 265 5 278 2 279 0.91 Pantoate-beta-alanine ligase\n+FAD_syn PF06574.11 158 CUFF.50.1.p2 - 284 0.00024 14.0 0.0 1 2 2e-05 0.00081 12.2 0.0 18 82 33 92 22 109 0.84 FAD synthetase\n+FAD_syn PF06574.11 158 CUFF.50.1.p2 - 284 0.00024 14.0 0.0 2 2 0.31 12 -1.4 0.0 112 145 141 174 125 188 0.77 FAD synthetase\n+CTP_transf_like PF01467.25 143 CUFF.50.1.p2 - 284 0.00046 13.3 0.0 1 1 2.2e-05 0.00086 12.4 0.0 9 43 33 66 29 73 0.88 Cytidylyltransferase-like\n+Pantoate_transf PF02548.14 259 CUFF.50.1.p3 - 268 1.5e-104 341.9 0.0 1 1 2.8e-106 1.7e-104 341.7 0.0 2 258 6 261 5 262 0.99 Ketopantoate hydroxymethyltransferase\n+Asp_Glu_race PF01177.21 224 CUFF.50.1.p3 - 268 4.5e-06 19.6 0.0 1 1 1.4e-07 8.5e-06 18.6 0.0 49 98 157 205 141 212 0.87 Asp/Glu/Hydantoin racemase\n+Chitin_synth_1 PF01644.16 163 CUFF.60.2.p1 - 844 2.4e-83 270.9 0.2 1 1 2.1e-84 4.2e-83 270.1 0.2 1 163 196 358 196 358 1.00 Chitin synthase\n+Chitin_synth_1N PF08407.10 73 CUFF.60.2.p1 - 844 6.2e-29 92.8 0.1 1 1 7.6e-30 1.5e-28 91.6 0.1 2 73 124 195 123 195 0.96 Chitin synthase N-terminal\n+Chitin_synth_2 PF03142.14 527 CUFF.60.2.p1 - 844 5.4e-24 77.5 9.9 1 4 1 20 -3.5 0.0 27 49 190 212 180 222 0.78 Chitin synthase\n+Chitin_synth_2 PF03142.14 527 CUFF.60.2.p1 - 844 5.4e-24 77.5 9.9 2 4 0.81 16 -3.2 0.0 236 264 242 270 225 278 0.78 Chitin synthase\n+Chitin_synth_2 PF03142.14 527 CUFF.60.2.p1 - 844 5.4e-24 77.5 9.9 3 4 1.7e-22 3.4e-21 68.3 0.0 203 433 335 576 320 600 0.76 Chitin synthase\n+Chitin_synth_2 PF03142.14 527 CUFF.60.2.p1 - 844 5.4e-24 77.5 9.9 4 4 1.7e-05 0.00033 12.2 3.7 434 491 665 722 612 732 0.87 Chitin synthase\n+Glyco_trans_2_3 PF13632.5 197 CUFF.60.2.p1 - 844 3.4e-11 36.3 7.3 1 1 9.7e-12 1.9e-10 33.9 7.3 3 191 338 564 336 713 0.80 Glycosyl transferase family group 2\n+Glyco_tranf_2_3 PF13641.5 230 CUFF.60.2.p1 - 844 '..b' 298 271 301 0.83 Winged helix-turn helix\n+DsrD PF08679.10 64 CUFF.17.1.p1 - 352 0.00099 12.3 0.0 1 2 4 1.2e+02 -4.1 0.0 21 33 102 114 97 116 0.82 Dissimilatory sulfite reductase D (DsrD)\n+DsrD PF08679.10 64 CUFF.17.1.p1 - 352 0.00099 12.3 0.0 2 2 9.6e-05 0.0028 10.9 0.0 2 58 132 188 131 192 0.80 Dissimilatory sulfite reductase D (DsrD)\n+HTH_psq PF05225.15 45 CUFF.17.1.p1 - 352 0.0012 11.5 0.3 1 3 0.01 0.31 3.8 0.0 24 33 81 90 80 93 0.91 helix-turn-helix, Psq domain\n+HTH_psq PF05225.15 45 CUFF.17.1.p1 - 352 0.0012 11.5 0.3 2 3 0.66 19 -1.9 0.0 7 16 169 179 165 180 0.80 helix-turn-helix, Psq domain\n+HTH_psq PF05225.15 45 CUFF.17.1.p1 - 352 0.0012 11.5 0.3 3 3 0.0086 0.25 4.1 0.0 21 33 285 297 281 304 0.87 helix-turn-helix, Psq domain\n+Glyco_hydro_cc PF11790.7 239 CUFF.59.1.p1 - 531 3.6e-61 199.6 0.0 1 1 4.5e-63 5.3e-61 199.1 0.0 1 239 298 528 298 528 0.92 Glycosyl hydrolase catalytic core\n+Oxidored_FMN PF00724.19 341 CUFF.52.1.p1 - 393 3.9e-138 453.2 0.0 1 1 3.8e-140 4.5e-138 453.0 0.0 1 341 12 360 12 360 0.99 NADH:flavin oxidoreductase / NADH oxidase family\n+Glyco_transf_34 PF05637.11 239 CUFF.52.1.p2 - 330 3.5e-86 281.7 0.0 1 1 1.1e-87 4.2e-86 281.4 0.0 2 239 84 318 83 318 0.98 galactosyl transferase GMA12/MNN10 family\n+DUF705 PF05152.11 304 CUFF.52.1.p2 - 330 0.00054 12.4 0.0 1 1 2.4e-05 0.00095 11.6 0.0 225 270 70 116 58 152 0.73 Protein of unknown function (DUF705)\n+Fig1 PF12351.7 188 CUFF.52.1.p2 - 330 0.00096 12.0 0.1 1 1 3.7e-05 0.0015 11.4 0.1 73 147 7 79 2 95 0.75 Ca2+ regulator and membrane fusion protein Fig1\n+Pantoate_transf PF02548.14 259 CUFF.52.1.p3 - 240 9e-98 319.6 0.0 1 1 1.7e-99 1e-97 319.5 0.0 2 235 6 238 5 240 0.98 Ketopantoate hydroxymethyltransferase\n+Asp_Glu_race PF01177.21 224 CUFF.52.1.p3 - 240 3.8e-06 19.8 0.0 1 1 1.2e-07 7.2e-06 18.9 0.0 49 98 157 205 141 211 0.87 Asp/Glu/Hydantoin racemase\n+MIP PF00230.19 227 CUFF.20.1.p1 - 599 2.2e-51 167.6 6.0 1 1 4.9e-53 2.9e-51 167.2 6.0 6 227 308 548 303 548 0.91 Major intrinsic protein\n+MDM31_MDM32 PF08118.10 525 CUFF.20.1.p1 - 599 0.0012 10.4 0.1 1 1 3.3e-05 0.002 9.7 0.1 365 448 134 218 124 228 0.68 Yeast mitochondrial distribution and morphology (MDM) proteins\n+Dak1 PF02733.16 307 CUFF.20.1.p2 - 204 1.7e-52 171.0 1.0 1 1 3.5e-54 2.1e-52 170.8 1.0 2 125 75 202 74 204 0.95 Dak1 domain\n+Usher PF00577.19 551 CUFF.20.1.p2 - 204 0.0007 11.4 0.0 1 1 1.4e-05 0.00085 11.1 0.0 35 132 17 114 2 116 0.77 Outer membrane usher protein\n+#\n+# Program: hmmscan\n+# Version: 3.3.1 (Jul 2020)\n+# Pipeline mode: SCAN\n+# Query file: transcripts.fasta.transdecoder_dir/longest_orfs.pep\n+# Target file: mini_Pfam-A.hmm\n+# Option settings: hmmscan --domtblout pfam.domtblout mini_Pfam-A.hmm transcripts.fasta.transdecoder_dir/longest_orfs.pep \n+# Current dir: /home/stephan/Projects/git/TransDecoder/sample_data/cufflinks_example\n+# Date: Mon Jan 25 19:01:22 2021\n+# [ok]\n'

diff -r c6334cb383ff -r d0d4cef4f967 test-data/transcripts.fasta
--- a/test-data/transcripts.fasta Thu Oct 08 12:33:46 2020 +0000
+++ b/test-data/transcripts.fasta Mon Feb 01 20:51:40 2021 +0000

[

b'@@ -1,10000 +1,128 @@\n->comp0_c0_seq1 len=796 path=[175:0-795]\n-AATTTTTCTATGTACAATATTGTAAGCAACATAACTGATCGGAACAGGAAAAGTAGATGA\n-GAAGAGGGAAACGGTTAGGATAGCGTGAAATTCAAGATCAATGCGAAAGAAATAAATTAT\n-AAGGGTTAAATAAGGCATAAATTAAGGAAGTCATCGAAACAAAACCTAAGAAAAAAACAC\n-AAGACAGCAGGGGAAAACAGTCATAGAGACCTAAGGGCCTCCAAGAACACCAACTTATTA\n-CGAAAGGTAAAACGAGGCAGTTGTTCTACATTAAGAATGGGATGATGGCACGACGGTTTG\n-CTGGATACTTCGGAAACTTTTTACAGTACCATTGATGGGCTTTTAATGCTCTTGGAAGCA\n-TCAACAGAATCTCTGACAGGAAGAACCACCAAAAAGGTTCGGCAGAAGGACCGGCTGCCA\n-AGTAGCATCCAAACCATTCAATCCATTCGCAAAAGTAATTGGGACACGAAACATACTGGA\n-AAAGCCCTCCATAGGGAATTCGATAATACGAATTCTCAGATTGTACGGTGTCAAGATTAT\n-CGGGATCCTTTTTTTTATTAGATGATCTTCTTAGGTCGTATAAGATGTTGTCGTGATACA\n-TATTTCCCAACCAACCCATTAACCAAAGAAACATACCAATGTATCGACGAATGATAGACA\n-CTGGATGATGCTGGACGCTAGCTTGAACCAAGTACAGACCTATTGACATACCGTTCAAAA\n-AGTTAAACAATACCGCAGAAACAAACACCGTCCAATGCATGGGTGAAACTTGTGGTGCCA\n-TCAAAAGAGGACTCAC\n->comp3_c0_seq1 len=226 path=[84:0-225]\n-ACATCCATCCCCTTGGAGCAAGGGAGAGGGAGAGGGAAAGAGAAAGTGGGAGTCAGCAAC\n-ATTTCCTAATACTTTCCTTATTGAATGATTGTAAAGCGGGGAGAGATTAAGATGATAGAT\n-TCACAATAGTTAGGGGAGAAAAGTAGAAAGAAACAAATGATACTCTCAACCACTTTTTTT\n-CCTTTCCAACAGAGAATAAGAGAAAACAAGAGAAATTGAATATGAA\n->comp5_c0_seq1 len=429 path=[73:0-428]\n-ATTCGGTTCAAGTGACTACAATACAATAACCACTATTTGCGAGATTAAACATACTATTAC\n-AGTAACCAACACATTTGAAATGTAAAAAATTGCCATAGTTGAAGCTATTCAGCGTCAGCG\n-AACATCTTCGGAGAGCTCAAATAATCTTAGCTCTTAAGATGGGGGTTTTTTCTGCCGAAT\n-ACTGTATCTGTTTGACTTTTATTTTTAATACGTTGGAGTAACCGCTGTATTCTTGTGCAA\n-CTTGGTGTTTTTGAAATTAACAATGGCACTGTTGATGAACGAAAGTGAATTATAATACAT\n-TTTTTGACAGTACCAATCTTATGGAAGTGCCTTGAAATCCTGTTACGTTACGTTTTAGCA\n-AGATCGCTTCTCTTATGATTTTCTTGTTTCAATGGTTTTCTACCCATAATCAATGAAATA\n-TGTTTACAA\n->comp6_c0_seq1 len=584 path=[1:0-583]\n-GCGTTAAGTACCGCTTCTAGTAATCGACTCATAGATTTAAAAAATGACGAAGTTCCTATT\n-TTTCGCATTCCTTTAAGTGATTATGAAACAGATGACATGGATGACGGTACACCTCTCCAA\n-CGCCATGTTGCGACCCTGAACCAATATCAAAGTCCCATTTTTAATTTAGGCCCGGACATT\n-TTAGAAGATGAACCATCTTACTCTTCAAGAGCTTCCAGATCCCGTCAATCATCTCTCTCT\n-TCTCGATTATCTGAGTTACCTTCTAAACGCGCCAGCCTTGAGATTTTAAGGCGCGAAAAT\n-ACTTTCCCAGCCGATCCAATTCAGGAATTTGGTGAAAAAGCATACAATGAAAGAGAATTG\n-ATGGAAGAAATCTCAAATTTTGAACCCTTACTAGATGATAACTTGCTTGAAAATGCCAAC\n-GAAGCTGTCAATTCCCCAGTAGTAGACGCACCAATGGATGCTGATTCTGCTTTAGAAATA\n-CCCAATGATGAAGATAATGGGGAAATTCTAAATAAACTAAAAGATTCTCCGTTTAAAAAA\n-CCTAAAAGAAGATATTCCAAATCTTCAACACTTGTGCTACCGGT\n->comp8_c0_seq1 len=439 path=[1:0-438]\n-ATTTATCTATAGCAGATGTAAAAGTTATATAATTTGATTAAGTTTTTAAATGAGGAAGTT\n-GCAATATTATCTGATTCCAAAGGTTTTCTGTAGCTGCAAAAGTTAAGCAGTAATGCTTTG\n-CTAACAATTGCCATTCTTCCAACTCATCAAGCATTTCTATGCTCATCGTTCTTTTCTTTT\n-CTTCTATGGGTATCCAGGTTTCTTCAATAGTTAAAAAATCTTCTGCAATTACTTCCGAGT\n-ATCCATAATCAAGAAACCTCATCCTTTGCTGCTCAGTTGTCTCATAACAATCGAGTGTTT\n-TAAGAATCACTCCTCTTGCCTAAATTTTGTTAGTTCTTAATCTGTGAAATGATATGCAAG\n-CATCGTACAGAAAGATTAGCCTTCATCATTTTTCCAAAGTTATCCATCCCCTGAATAGGT\n-TCATAAACAACAATGCCAG\n->comp12_c0_seq1 len=447 path=[1:0-446]\n-TTTTGAACACTTTCAATGTCGTTGCTTTCATAATCAACCCAGCAGTGAGGATGAAAGAAA\n-GAAGCATCATTGAAGGGTATAACTTTTTCAAAGCTCATTTGTTCCAGCGGTCCGTTTATC\n-GCCATAGAATTGATAGCCACGTCTAGTAAAATCCATATGTCGCGTTTATGCAATTCTTGT\n-ATTAGCTCCATAAATTCTTCCTTTGTTCCAAAGTGGTGATTAAGCTCATAGAGGTTGGTT\n-GTCCAATATCCGTGATAGGACGAACCGTCAATATCATTTCCTTCAACATTTTCAAAGATT\n-GGTGAGATCCATATCTATCATTATGTTAATCAAGTATTTGGGTAAAAATACATACTGCGT\n-CAAATCCCATGCCTTGGATGTAATCTAGATGATTTCGAATTCCATTCCAAGTTCCCCCGC\n-AGTACATAAATCGAACGGGATCGCATG\n->comp18_c0_seq1 len=402 path=[1:0-401]\n-ACATTTATAACCTTCGAATAAGCTTACGATAGAGTTTGTTTTAGATTTCTGTACTTGTTA\n-CTAATCTATGTAAGTTTTCTATGAATAAACCAATTTATATTTTAGCAAATCTATTTTTGT\n-AGAGCGATGCTTTCTCTCGTTTACCCAGGTTTCCCCAAATAGTCAAGTGAGCTTAAAGAG\n-ACGACGATCTACATGAAACTAGAAAACAACAAATGAACGTGACAATAAGATTAAATCATA\n-AATAAAAACAATGTTATTTCTGGAAATTAAACGAAAAATCATCACATTTAGGCAATATGC\n-AGAAGATTTTGTCAGATCACTGGATTTAAGTCGTAAATTTTGTTCCTTTCTTCTTTAGTC\n-AATCTTCCTATCTAGTGCGGGTTTTCTTATTAGTCTATGTAA\n->comp19_c0_seq1 len=269 path=[155:0-268]\n-TGGCTTCTGCGCGAATCCCGATCACTGTGTACCTCCACGATCAACGAGAAGTAAAAGCAG\n-AATTTGGAGCGATAGACAGTAGTGAGTCAAAGTTGGCAGTTTCCAATCTACAAACCGATT\n-GGGGCGTTATTAACAGAGCGGTGATACGAACAGGAGACGTCGTGGGCATCGAATACAATT\n-TGGTGCAGGAAGAAGGAGAACTTTGATG'..b'TCGGAAATTTTCGTGGTATAATATAATTGGATATCGAAAGACTCATAGTTTACTTTATGAGGGTAATCTATCCTCGTTTTCGGTTGCATCTTCTGTATTTTGCGCCTGATTTGCTGAAGTTTCCACGGCACTTGCTTCTGCTTCATTAGATACTTGATTGCTAGTAGAAACTAAAGTCGTATACGAGGAAGCCCTTGTGGTAGTAGGGGTTTGCGAGTTCGCTGGTCGAGTAGAAGTATCGGTTTGGGAAGATTCAGAAGTGGATGGCTTTCCAGGGCTGGTTTGGGTAGGATTGGGAGAGAATTTTACATGAAAAATGCAAGTTGGAAGATTAGGGCATTGAGCTATGACCTGCGCTGAGTACCCAAATGTATATACTACTCCCCGAATAAACCCACTTGGGAAATAAAAATACTAAAAAGAAACGATTAGGTAAAAATATACGAAGG\n+>CUFF.20.1 CUFF.20\n+ACCTCTTTTTTTGCCTACAGAAACATCATCTCCTACGGCAACAAGCTCAACGTTCATTCCAGCTGCCTTGGCTCTCTCAGCTGCCAGGCCAAAATGAATAATATCGCCTGTATAATTCTTGACAATAATTAAAGTTCCCTTAGGAGAAGCAACAGCTTTGAGGGCAGAGTAAATTTGTTTAGTAGAGGGAGAAGCAAAAATGTCTCCACAAGCTACAGCGTCCAAGGCTCCATCACCAACAAAACCTGCATGTGTAGGCTCGTGCCCACTACCACCACCAGACACTAAAGTTACTTTAGGAAGATCACCAGAACCCGGGGCAGAAGCTGTCCTGTAAATCACACGATCATGTTCAATAACAGTAAGACCAGGGTTACTTCTAGCAAGTCCAAGCAAGTATGGGCGTACTATATGTCCGTCAGATACAAATTGTTTTACAGACATTTTTAATTGAAAAGAAACGTTCCCTTCCTGCTTTTTTATCTCATTCTTTACATTACTACTACCCCGCGCGCGGTGCGTTCTAAGATTTGCAAATATCCGGCATACCCGCCTAGCTGACCAATTGTTGATTACGGTTGAAGCGGCAGTTATGCGAGTGTGCAAACGCATTGTATAAACTTGTCCAATTCAGGGAAATTTATAACACATATTCTTAATATTCTGTAGATAAATTGATTTGCGCTTAAGATTCGTCACCAAATTTGTGCCGCCACTACACGTTGTCATCGACGGTTGCTTAACTTCGGTTATCTGGACCACTTGCATGAGTATATAATGCACTGTTTTACTCCACCTTATTCCCAAAGCTATTTCAAACCTTAATTTTGGTATTCCCGCCAGTACCCGCGTGCATTCAAAAAATTTCCATAAAAGCCAAGATTTGTCCCGTCTAATTCACTACTAAATGAGCGTCCCTTTACGCTTCTCGACACCATCATCATCTCCTTCAGCCTCAGATAATGAGAGCGTGCATGATGATGGTCCCACAACTGAATTAGACACTTTCAATACGACGGACGTGCCAAGAAGAGTCAATACCACTAAAGCTCGACAAATGCGTCCCAAAAATACCCTAAAAGTTGCGTTCTCTTCACCCAACCTCAAAGGCCTGGACAACACTGCCGACTCGGATTCTCAACCCTGGCTTGGTGGGTACCTTGCTGGAAGACTTGAAGATATATCCGGACAATCGCGTCGAAATTATGTTGATCCTTATTACGAAGAATTGAATGCTGGGAGGAGACCCAACAAACCGGTGTGGAGTTTGAATGGACCATTGCCACATGTTCTTGGTAACTCTGTGGTAGAAAAAATATCTCAAAAGAATCAGGAAGCTCGTTCTAGAGCAAATTCCAGGGTGAATTCCAGAGCAAATTCCAGAGCAAACTCCTCGGTCTCTTTGGCTGGTATGGATGGATCGCCCAATTGGAAACGGAAAATGAAGAGTGCTGTTTTTGGATCAAGAGTCAAGCTTAATGATGAAGAAGCTCAATTGCCGCGCAATAAATCTTCCGTTTCCATAGCGGAACAAGCCGCTTCAAGACCCAAAGTTAGTTTCTCGCTTCAAAGCAGCCGTCAACCATCCATTGCTGAGGAGCAACCCCAAACCCAGCGTAAGTCTTCCGCGATAACGGTAGAGCATGCGGAAAATGCTGAACCAGAGACCCCAAGAAATAATGTTAGTTTCTCTAGGAAACCGTCAATAGCTGAACAAGATTCATCTCAAGATATTACTATGCCTCCTAATGAAATTATTGCTGAAGAAAGTTTAGACTCGGGAAGCGATACTGAAACCCTGTATCTCAACTATTGGTGCAAGATTAGACACTTTTTTCGTGAGGGTTTTGCTGAGTTCCTGGGCACTTTGGTTTTGGTTGTGTTTGGTGTAGGCAGTAATTTGCAAGCTACCGTCACTAATGGAGCAGGTGGAAGCTTCGAATCCCTTTCTTTTGCTTGGGGATTTGGTTGCATGCTTGGCGTTTATATAGCTGGTGGAATCAGTGGTGGTCATGTCAATCCCGCTGTGACTATCTCATTAGCCATATTTCGCAAATTTCCTTGGTATAAAGTGCCAATCTACATTTTTTTCCAAATCTGGGGTGCATTCTTTGGAGGTGCACTTGCCTATGGTTACCATTGGAGTTCAATTACTGAATTTGAAGGAGGCAAAGATATTAGAACACCGGCAACAGGTGGTTGTTTGTACACCAATCCAAAACCATACGTCACTTGGAGAAACGCATTTTTCGATGAGTTTATTGGAACAGCCGTTTTGGTAGGATGTTTATTCGCCATTCTAGATGATACCAACTCTCCACCAACCCAGGGCATGACTGCTTTTATCGTTGGTTTGCTTATTGCAGCTATTGGTATGGCTCTTGGATATCAAACAAGTTTCACTCTGAATCCAGCTCGTGACTTGGGACCTCGTATGTTTGCATGGTGGATTGGCTATGGACCACATTCATTTCACCTGTATCATTGGTGGTGGACTTGGGGTGCTTGGGGCGGTACCATAGGAGGTGGTATTGCTGGAGGACTTATTTATGATTTAGTAATATTTACGGGCCCAGAGTCTCCACTTAATTATCCAGATAACGGGTTTATCGATAAAAAAGTGCATCAGATTACCGCAAAATTTGAGAAGGAAGAAGAGGTTGAAAACTTGGAAAAAACAGATTCTCCGATTGAGAATAATTGAACTCTTAATAATCTTTCATGTCACAAAATGCAGAAGATTGAAACCATTTACTTTTTATTTATTTATTCTTATTATTGTGGAGCAGCTTTTCTCTTTATACTAAGCATATATTAGCTTTTATATTATCTTTTGAGATGGACAAAGAGCTATGTCTTCCCCATTTTTTTTGTTTAATTTAAGCACTAGGGTTTTGTTGTGTTACTCTTTGTTGCTGTAAAAATTTTCAGCTTCTTAATGCTTGGGACGCCCTTATGTTGTTGCAATAGCGGCAGCTTCAATTAAAATTGATTTCATATCAAAAAAGACGATTTTCCCATTATATTGCGGTGTCTCGAATTTATTACTTCTTCCCTCAACTTACTTTGAAACCTAATTTTTGGATTCCTGTTGACTTCTTTTTTACGTTTTTGCGTATTACCGATTTTTCTTCCGCTTTGCGTAACACAATTTTCTTGCTCTCTTCTTTACTCTATGTACTGCGAAAGTAGTACGATTACCTTGTATGATTACTTATATTGCCCAACCCCCTTTTCAAGTTCAACTTTGACCGAAATTTTCTCTTCTCTTTTTTGCTATTTATTCATATATCTACCTGTAATTTTTAGTCCTTAAAACATTTGGTTTTTCAAAACAACAGATATTAAAAATGGCCGATATGACCATTACGTCATGAAATACTTGCTTCTCTATTTGGTTAACATACTTAGGATTTAGCTAAATTAGTTAAGATATCAAAAAAGTTTTAACTCATATCTAAAGATTTTTTTATTTAGAATAATTGGACGTTATGTTATGATATATAATTTTATGATTCACTTTTGTC\n'

diff -r c6334cb383ff -r d0d4cef4f967 transdecoder.xml
--- a/transdecoder.xml Thu Oct 08 12:33:46 2020 +0000
+++ b/transdecoder.xml Mon Feb 01 20:51:40 2021 +0000

[

b'@@ -2,10 +2,11 @@\n <description>finds coding regions within transcripts</description>\n <macros>\n <token name="@TOOL_VERSION@">5.5.0</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>\n+ <requirement type="package" version="3.0">zip</requirement>\n </requirements>\n <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep \'TransDecoder.LongOrfs\' | cut -f 2 -d \' \']]></version_command>\n <command detect_errors="exit_code"><![CDATA[\n@@ -52,6 +53,7 @@\n #if \'log\' in $oo.out\n |& tee \'$out_log\'\n #end if\n+&& if ls \'output/\'*\'.pdf\' >/dev/null 2>&1; then zip \'seqlogo.zip\' \'output/\'*\'.pdf\' -q -j; fi\n ]]></command>\n <inputs>\n <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/>\n@@ -84,7 +86,7 @@\n <section name="lo" title="LongOrfs options" expanded="true">\n <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Select gene-to-transcript identifier mapping file" help="gene_id<tab>trans_id<return>"/>\n <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/>\n- <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand."/>\n+ <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand?"/>\n </section>\n <section name="po" title="Predict options" expanded="true">\n \n <output name="out_lo_cds">\n <assert_contents>\n- <has_n_lines n="772"/>\n- <has_text_matching expression=">comp874\\_c0\\_seq1.+"/>\n+ <has_n_lines n="534"/>\n+ <has_text_matching expression=">asmbl\\_236\\.p1.+"/>\n </assert_contents>\n </output>\n <output name="out_lo_gff3">\n <assert_contents>\n- <has_n_lines n="2486"/>\n- <has_text_matching expression="comp874\\_c0\\_seq1.+"/>\n+ <has_n_lines n="1742"/>\n+ <has_text_matching expression="asmbl\\_236.+"/>\n </assert_contents>\n </output>\n <output name="out_lo_pep">\n <assert_contents>\n- <has_n_lines n="772"/>\n- <has_text_matching expression=">comp874\\_c0\\_seq1.+"/>\n+ <has_n_lines n="534"/>\n+ <has_text_matching expression=">asmbl\\_236\\.p1.+"/>\n </assert_contents>\n </output>\n \n <output name="out_bed">\n <assert_contents>\n- <has_n_lines n="337"/>\n- <has_text_matching expression="comp98\\_c0\\_seq1.+"/>\n+ <has_n_lines n="204"/>\n+ <has_text_matching expression="asmbl\\_99.+"/>\n </assert_contents>\n </output>\n <output name="out_cds">\n <assert_contents>\n- <has_n_lines n="6959"/>\n- <has_text_matching expression=">comp98\\_c0\\_seq1.+"/>\n+ <has_n_lines n="3560"/>\n+ <has_text_matching expression=">asmbl\\_99\\.p1.+"/>\n </assert_contents>\n </output>\n <output name="out_gff3">\n <assert_contents>\n- <has_n_lines n="2165"/>\n- <has_text_matching expression="comp98\\_c0\\_seq1.+"/>\n+ <has_n_lines n="1337"/>\n+ <has_text_matching expression="asmbl\\_99.+"/>\n </assert_contents>\n </output>\n <output name="out_pep">\n <assert_contents>\n- <has_n_lines n="2644"/>\n- <has_text_matching expression=">comp98\\_c0\\_seq1.+"/>\n+ <has_n_lines n="1391"/>\n+ <has_text_matching expression=">asmbl\\_99\\.p1.+"/>\n+ </assert_contents>\n+ </output>\n+ <output name="out_plot">\n+ <assert_contents>\n+ <has_size value="714868" delta="1000"/>\n </assert_contents>\n </output>\n \n@@ -347,10 +358,10 @@\n </conditional>\n </section>\n \n- <output name="out_lo_pep">\n+ <output name="out_pep">\n <assert_contents>\n- <has_n_lines n="772"/>\n- <has_text_matching expression="c"/>\n+ <has_n_lines n="190"/>\n+ <has_text_matching expression="CUFF\\.9\\.1.+"/>\n </assert_contents>\n </output>\n </test>\n@@ -403,6 +414,7 @@\n - Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs\n - Results (GFF3): positions within the target transcripts of the final selected ORFs\n - Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV\n+- Plots: sequence logos and scores (compressed PDF)\n \n *Other*\n \n'