diff -r 7554c0df9139 -r 6e20ad2c8752 macros.xml --- a/macros.xml Mon Dec 05 14:28:49 2022 +0000 +++ b/macros.xml Mon Aug 19 18:52:41 2024 +0000 @@ -1,7 +1,7 @@ - 1.9.2.3 - 1 - 21.09 + 2.0.1 + 0 + 23.0 diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/archaea-default.stdout --- a/test-data/archaea-default.stdout Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/archaea-default.stdout Mon Aug 19 18:52:41 2024 +0000 @@ -1,9 +1,13 @@ -mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0 -Copyright Sebastian Will - -Compute pair probs ... -Compute pairwise alignments ... -Perform progressive alignment ... +mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 2.0.1 +vhuU AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU- +fwdB AU-GUUGGAGGGGAACCC-GU------------AAGGGACCCUCCAAGAU- +selD UUACGAUGUGCCGAACCCUUU------------AAGGGAGGCACAUCGAAA +hdrA GG--CACCACUCGAAGGC--U------------AAGCCAAAGUGGUG-CU- +vhuD GU--UCUCUCGGGAACCCGUC------------AAGGGACCGAGAGA-AC- +fruA ---CCUCGAGGGGAACCC-GA------------AAGGGACCCGAGAGG--- +fdhA CG-CCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGGCG- + alifold ((.(((((((((...(((.................))).))))))))))). (-31.36 = -20.01 + -11.34) +Results written to target directory /tmp/tmpstsz4a83/job_working_directory/000/2/working/mlocarna_results. diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/archaea-probabilistic.aln --- a/test-data/archaea-probabilistic.aln Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/archaea-probabilistic.aln Mon Aug 19 18:52:41 2024 +0000 @@ -1,11 +1,10 @@ -CLUSTAL W --- LocARNA 1.9.0 - +CLUSTAL W --- LocARNA 2.0.1 -selD UUACGAUGUGCCGAACCCUU------------UAAGGGAGGCACAUCGAAA -vhuU AGC-UCACAACCGAACCCAU-------------UUGGGAGGUUGUGAG-CU -fwdB AUG-UUGGAGGGGAACCCGU-------------AAGGGACCCUCCAAG-AU -hdrA GGC-ACC-ACUCGAAGGCU--------------AAGCCAAAGU-GGUG-CU -vhuD GUU-CUC-UCGGGAACCCGU------------CAAGGGACCGA-GAGA-AC -fdhA CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGG-CG -fruA CC-UCG--AGGGGAACCCGA-------------AAGGGACCC--GAGA-GG +vhuU AGC-UCACAACCGAACCCA-----U---U-----UGGGAGGUUGUGA-GCU +fwdB AUG-UUGGAGGGGAACCCG-----U---A-----AGGGACCCUCCAA-GAU +selD UUACGAUGUGCCGAACCCU-----U--UA-----AGGGAGGCACAUCGAAA +hdrA GGC-ACC-ACUCGAAGGCU---------A-----AGCCAAAGU-GGU-GCU +vhuD GUU-CUC-UCGGGAACCCG-----U--CA-----AGGGACCGA-GAG-AAC +fruA CC-UCGA--GGGGAACCCG-----A---A-----AGGGACCC--GAGA-GG +fdhA CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUG-GCG diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/archaea-ref_result.aln --- a/test-data/archaea-ref_result.aln Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/archaea-ref_result.aln Mon Aug 19 18:52:41 2024 +0000 @@ -1,5 +1,4 @@ -CLUSTAL W --- LocARNA 1.9.0 - +CLUSTAL W --- LocARNA 2.0.1 vhuU AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU- diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/archaea_relplot.scr --- a/test-data/archaea_relplot.scr Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/archaea_relplot.scr Mon Aug 19 18:52:41 2024 +0000 @@ -1,4 +1,4 @@ -pdf("/tmp/tmp5yxSuG/files/000/dataset_2.dat",width=12,height=4,version="1.4") +pdf("/tmp/tmpewnb251n/job_working_directory/000/2/outputs/dataset_a612ea0e-aca2-4d90-987a-39141bc61f36.dat",width=12,height=4,version="1.4") rel <- read.table("mlocarna_results/results/result.bmreliability"); seqrel <- rel[[2]] @@ -112,8 +112,8 @@ if (0!=1) { - on <- c(0,4,33,44,49); - off <- c(3,20,43,48,51); + on <- c(0,33); + off <- c(20,51); if (length(on)>0) { for (i in 1:length(on)) { @@ -123,8 +123,8 @@ ### draw on/off values if (0) { - lines(c(1,1+len),c(0.0355791,0.0355791),lty=2,lwd=1) - lines(c(1,1+len),c(0.702675,0.702675),lty=2,lwd=1) + lines(c(1,1+len),c(0.0139513,0.0139513),lty=2,lwd=1) + lines(c(1,1+len),c(0.656017,0.656017),lty=2,lwd=1) } } diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/haca.snoRNA-c.aln --- a/test-data/haca.snoRNA-c.aln Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/haca.snoRNA-c.aln Mon Aug 19 18:52:41 2024 +0000 @@ -1,4 +1,4 @@ -CLUSTAL W --- LocARNA 1.9.2.3 +CLUSTAL W --- LocARNA 2.0.1 ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/haca.snoRNA-default.stdout --- a/test-data/haca.snoRNA-default.stdout Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/haca.snoRNA-default.stdout Mon Aug 19 18:52:41 2024 +0000 @@ -1,10 +1,20 @@ -mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0 -Copyright Sebastian Will - -Compute pair probs ... -Compute pairwise alignments ... -Perform progressive alignment ... +mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 2.0.1 -alifold .((((((((........((((.(((((((......))))))).))))......))..)))))).............(((((((...((......((((((((((((.....))))))))) - ))).........)).))).))))......... (-62.29 = -34.50 + -27.79) +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG +ACA30 UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGCUGCCACAGAAACAC--UGUGAC-----UCAUG-GGCCCUGUUCCUGUGUCCCAGGCUCAG +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG--CCCAUGGGUGA-CCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA +#A1 ................................................................AAAAAA.................................................. +#A2 ................................................................123456.................................................. + +ACA7 AUUGGA-----AGACACU-CUGCG-----ACA +ACA30 CAACUG-----UCACUCA-AUGGG-----ACA +ACA5 GGAUAA-----AUUUGGU-UACAG-----ACA +ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA +#A1 .............................BBB +#A2 .............................123 + +alifold .((((((..........((((..(((((........)))))..))))..........)))))).............((((((.............((((((((..........)))).)) + ))..............)).))))......... (-53.08 = -26.63 + -26.46) +Results written to target directory /tmp/tmpstsz4a83/job_working_directory/000/4/working/mlocarna_results. diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/haca.snoRNA.aln --- a/test-data/haca.snoRNA.aln Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/haca.snoRNA.aln Mon Aug 19 18:52:41 2024 +0000 @@ -1,4 +1,4 @@ -CLUSTAL W --- LocARNA 1.9.2.3 +CLUSTAL W --- LocARNA 2.0.1 ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/tRNA_2.aln --- a/test-data/tRNA_2.aln Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/tRNA_2.aln Mon Aug 19 18:52:41 2024 +0000 @@ -1,4 +1,4 @@ -CLUSTAL W --- LocARNA 1.9.2.3 --- Score: 2587 +CLUSTAL W --- LocARNA 2.0.1 --- Score: 2587 D10744 GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG AF008220 GGAGGAUUAGC--UCAGCUGGGAGAGCAUCUGCCUUA-------CAAGCAGAGGGUCGGCG-GUUCGAGCCCGUCAUCCUCCA diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/tRNA_2.amprobs --- a/test-data/tRNA_2.amprobs Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/tRNA_2.amprobs Mon Aug 19 18:52:41 2024 +0000 @@ -1,108 +1,185 @@ -64 69 54 59 0.079977 -63 70 53 60 0.0158884 -63 71 53 61 0.0915855 -62 72 52 62 0.203921 -61 73 51 63 0.202155 -60 74 50 64 0.175676 -59 75 49 65 0.0815626 -39 44 33 38 0.0114647 -39 46 33 37 0.0168669 -38 47 33 38 0.0303705 -37 48 32 39 0.0111801 -37 48 31 39 0.0434528 -36 42 34 38 0.0105213 -36 42 33 37 0.0442772 -36 42 33 38 0.0150469 -36 49 30 40 0.0445378 -35 40 33 37 0.0438048 -35 40 33 38 0.0131652 -35 43 33 37 0.0482007 -35 43 33 38 0.0524118 -35 43 32 39 0.0124841 -35 44 33 38 0.0456243 -35 44 32 39 0.0111628 -35 46 33 37 0.0220704 -35 50 29 41 0.016731 -34 44 33 38 0.0275446 -34 44 32 39 0.0318614 -34 44 31 39 0.0265932 -34 45 32 39 0.0344691 -33 42 31 39 0.123358 -33 47 31 39 0.0238501 -33 48 31 39 0.207448 -33 48 30 40 0.0278532 -33 49 32 39 0.0279853 -33 49 30 40 0.0365409 -32 36 33 37 0.0659838 -32 37 33 38 0.0229925 -32 40 31 39 0.01072 -32 43 30 40 0.102105 -32 45 31 39 0.0127413 -32 45 30 40 0.0472967 -32 46 30 40 0.0814206 -32 50 29 41 0.012395 -31 38 32 39 0.0108954 -31 44 29 41 0.0212986 -31 46 29 41 0.0101171 -31 50 30 40 0.105751 -31 50 29 41 0.490312 -31 50 28 42 0.0414615 -30 38 31 39 0.10883 -30 51 29 41 0.110433 -30 51 28 42 0.628654 -30 51 27 43 0.0377824 -29 39 30 40 0.119173 -29 52 28 42 0.130101 -29 52 27 43 0.657133 -28 40 29 41 0.103713 -28 53 27 43 0.113664 -28 53 25 45 0.0385623 -27 41 28 42 0.114432 -27 54 25 45 0.651098 -26 42 27 43 0.107977 -26 55 25 45 0.119566 -26 55 23 47 0.0239947 -26 56 25 46 0.011099 -26 56 24 47 0.147548 -26 56 23 47 0.0142523 -25 57 24 47 0.0172058 -25 57 22 48 0.0238997 -24 49 25 45 0.0155194 -24 57 23 47 0.0913467 -24 57 22 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0.011409 +12 16 11 15 0.0197214 +12 17 13 18 0.0110198 +12 21 13 22 0.0246713 +12 21 11 20 0.0113061 +12 61 13 57 0.0221517 +12 63 13 57 0.0118578 +12 67 13 57 0.0206475 +11 17 10 16 0.027035 +11 22 12 23 0.0289103 +11 22 11 20 0.0100156 +11 62 12 58 0.0238073 +11 63 12 58 0.020677 +11 68 12 58 0.0231266 +11 69 11 59 0.126668 +10 14 11 15 0.0664008 +10 23 11 24 0.0292855 +10 64 11 59 0.0182822 +10 65 11 59 0.0270649 +10 70 11 59 0.013269 +10 70 10 60 0.111863 +10 72 11 63 0.0111665 +10 72 10 61 0.0197501 +10 72 10 62 0.0851968 +9 15 10 16 0.0281596 +9 18 9 17 0.0412594 +9 66 10 60 0.0160834 +9 71 10 61 0.0165719 +9 73 9 64 0.0380848 +9 73 8 63 0.028412 +9 75 9 64 0.0125148 +8 16 9 17 0.0193588 +8 19 8 18 0.0410658 +8 74 9 64 0.109379 +8 74 8 63 0.029173 +8 76 8 66 0.0732703 +8 76 7 66 0.0172466 +7 76 8 66 0.0398486 +7 76 7 66 0.552277 +6 77 6 67 0.695078 +5 78 5 68 0.823761 +4 79 4 69 0.829247 +3 80 3 70 0.718496 +2 81 2 71 0.630949 +1 82 1 72 0.630758 diff -r 7554c0df9139 -r 6e20ad2c8752 test-data/tRNA_2.bmprobs --- a/test-data/tRNA_2.bmprobs Mon Dec 05 14:28:49 2022 +0000 +++ b/test-data/tRNA_2.bmprobs Mon Aug 19 18:52:41 2024 +0000 @@ -1,172 +1,204 @@ -1 1 0.247253 -2 2 0.247252 -3 3 0.127121 -4 4 0.0367335 -5 5 0.0369676 -6 6 0.129988 -7 7 0.156077 -8 8 0.835935 -8 9 0.012729 -9 8 0.010632 -9 9 0.727258 -9 10 0.0549287 -10 9 0.04195 -10 10 0.0853335 -10 11 0.0115868 -11 10 0.0364601 -11 11 0.112239 -12 10 0.011935 -12 11 0.0436248 -12 12 0.0614308 -13 11 0.0645154 -13 12 0.028434 -14 12 0.133445 -14 13 0.0169358 -15 13 0.260167 -15 14 0.0172799 -15 16 0.0124747 -16 14 0.271834 -16 15 0.0178714 -16 17 0.0141486 -17 15 0.185722 -17 16 0.0202801 -17 18 0.0184277 -18 16 0.300704 -18 17 0.0355582 -18 19 0.0165149 -19 17 0.700705 -19 18 0.0610097 -19 20 0.0138794 -20 18 0.193762 -20 19 0.11731 -20 21 0.012503 -21 19 0.633061 -21 20 0.119843 -22 20 0.625797 -22 21 0.127468 -23 20 0.0117929 -23 21 0.621337 -23 22 0.0118595 -23 24 0.0104834 -24 21 0.0184503 -24 22 0.0481581 -24 23 0.0441549 -24 25 0.0420745 -25 23 0.68405 -25 24 0.0269372 -25 26 0.0420693 -26 24 0.53624 -27 25 0.0346266 -27 26 0.120675 -28 26 0.681355 -28 27 0.0199945 -28 29 0.0196255 -29 27 0.0227404 -30 28 0.0396584 -30 29 0.0227396 -30 31 0.0165441 -31 29 0.121498 -31 32 0.114327 -32 30 0.351807 -32 31 0.0703916 -32 33 0.0332191 -33 31 0.0980398 -33 32 0.0266787 -33 34 0.0331979 -34 31 0.0122885 -34 32 0.400684 -34 33 0.0116529 -34 35 0.0331958 -35 32 0.0101403 -35 33 0.22599 -35 36 0.0332106 -36 33 0.0136772 -36 34 0.156117 -36 37 0.0332566 -37 34 0.0427905 -37 35 0.113127 -37 38 0.0933967 -38 35 0.0723242 -38 36 0.0618818 -39 34 0.0149807 -39 36 0.0997152 -39 37 0.0299675 -40 34 0.0108419 -40 35 0.01547 -40 37 0.111326 -40 38 0.0203761 -40 41 0.0196142 -41 35 0.0159003 -41 36 0.0127203 -41 38 0.149756 -42 34 0.0119499 -42 36 0.0189085 -42 37 0.010129 -42 39 0.0145996 -43 34 0.010789 -43 35 0.013731 -43 37 0.0170711 -43 38 0.0146016 -43 44 0.0354944 -44 35 0.0181452 -44 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