# HG changeset patch # User rnateam # Date 1540660899 14400 # Node ID c05c83b3ef0f937d6cdb72b3db70502f3759e2c1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92 diff -r 000000000000 -r c05c83b3ef0f align_cluster.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align_cluster.xml Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,224 @@ + +structural alignment and conservation analysis of predicted clusters + + graphclust-wrappers + perl-array-utils + scikit-learn + locarna + rnaz + infernal + viennarna + graphicsmagick + rscape + unzip + evofold2 + biopython + pandas + + + alignment.rnaz.out && + #if str($genomic_cons_opts.genomic_cons_opts_selector) != "no": + clustal_to_alma.py '$alignment_clustal' $cluster_all && + EvoFoldV2.sh -o alignment.evofold.out '${alignment_clustal}.ama' + #if str($genomic_cons_opts.genomic_cons_opts_selector) == "hg38_100way": + '$__tool_directory__/hg38.100way.nh' + #elif str($genomic_cons_opts.genomic_cons_opts_selector) == "hg38_20way": + '$__tool_directory__/hg38.20way.nh' + #else + '$alignment_clustal'.ama '$genomic_cons_opts.phylo_tree' + #end if + && + #else + touch alignment.evofold.out && + #end if + + extract_conservation_metrics.py + '$alignment_clustal' alignment.rnaz.out RESULTS/result.aln.sum alignment.evofold.out + '$cluster_all' + #if str($bed_opts.bed_opts_selector) == "yes": + '$bed_opts.transcript_loci_fasta' + '$bed_opts.transcript_loci_bed' + '$bed_opts.genome_version' + #else + '' '' '' + #end if + conservation_metrics.tsv + +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ^\S+\s+[0-9]+\s+[0-9]+\s+\S+\s+\S+\s+[-+]\s*$ + + + ^[a-zA-Z]+[0-9]+$ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.5281/zenodo.597695 + + diff -r 000000000000 -r c05c83b3ef0f hg38.100way.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hg38.100way.nh Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,100 @@ +((((((((((((((((((hg38:0.00655, + panTro4:0.00684):0.00422, + gorGor3:0.008964):0.009693, + ponAbe2:0.01894):0.003471, + nomLeu3:0.02227):0.01204, + (((rheMac3:0.004991, + macFas5:0.004991):0.003, + papAnu2:0.008042):0.01061, + chlSab2:0.027000):0.025000):0.021830, + (calJac3:0.03, + saiBol1:0.010350):0.019650):0.072610, + otoGar3:0.13992):0.013494, + tupChi1:0.174937):0.002, + (((speTri2:0.125468, + (jacJac1:0.1, + ((micOch1:0.08, + (criGri1:0.04, + mesAur1:0.040000):0.040000):0.060000, + (mm10:0.084509, + rn6:0.091589):0.047773):0.060150):0.100000):0.022992, + (hetGla2:0.1, + (cavPor3:0.065629, + (chiLan1:0.06, + octDeg1:0.100000):0.060000):0.050000):0.060150):0.025746, + (oryCun2:0.114227, + ochPri3:0.201069):0.101463):0.015313):0.020593, + (((susScr3:0.12, + ((vicPac2:0.047275, + camFer1:0.04):0.04, + ((turTru2:0.034688, + orcOrc1:0.039688):0.03, + (panHod1:0.1, + (bosTau8:0.1, + (oviAri3:0.05, + capHir1:0.050000):0.050000):0.010000):0.013592):0.025153):0.020335):0.020000, + (((equCab2:0.059397, + cerSim1:0.025):0.05, + (felCat8:0.098612, + (canFam3:0.052458, + (musFur1:0.05, + (ailMel1:0.02, + (odoRosDiv1:0.02, + lepWed1:0.020000):0.020000):0.030000):0.030000):0.020000):0.049845):0.006219, + ((pteAle1:0.05, + pteVam1:0.063399):0.05, + (eptFus1:0.02, + (myoDav1:0.04, + myoLuc2:0.042540):0.050000):0.060000):0.033706):0.004508):0.011671, + (eriEur2:0.221785, + (sorAra2:0.169562, + conCri1:0.100000):0.100000):0.056393):0.021227):0.023664, + (((((loxAfr3:0.002242, + eleEdw1:0.05):0.04699, + triMan1:0.1):0.049697, + (chrAsi1:0.03, + echTel2:0.235936):0.010000):0.030000, + oryAfe1:0.03):0.02, + dasNov3:0.169809):0.006717):0.234728, + (monDom5:0.125686, + (sarHar1:0.1, + macEug2:0.072008):0.050000):0.215100):0.071664, + ornAna1:0.456592):0.109504, + (((((colLiv1:0.1, + ((falChe1:0.1, + falPer1:0.1):0.03, + (((ficAlb2:0.04, + ((zonAlb1:0.034457, + geoFor1:0.041261):0.015, + taeGut2:0.060000):0.010000):0.052066, + pseHum1:0.06):0.025, + (melUnd1:0.046985, + (amaVit1:0.026, + araMac1:0.026000):0.010000):0.040000):0.064703):0.060000):0.050000, + (anaPla1:0.1, + (galGal4:0.041254, + melGal1:0.085718):0.031045):0.090000):0.220000, + allMis1:0.25):0.045143, + ((cheMyd1:0.1, + chrPic2:0.1):0.05, + (pelSin1:0.1, + apaSpi1:0.100000):0.050000):0.040000):0.010000, + anoCar2:0.447000):0.122000):0.050000, + xenTro7:0.977944):0.1, + latCha1:0.977944):0.111354, + (((((((tetNig2:0.124159, + (fr3:0.103847, + takFla1:0.100000):0.100000):0.097590, + (oreNil2:0.1, + (neoBri1:0.05, + (hapBur1:0.05, + (mayZeb1:0.05, + punNye1:0.050000):0.050000):0.050000):0.100000):0.100000):0.097590, + (oryLat2:0.38197, + xipMac1:0.400000):0.100000):0.015000, + gasAcu1:0.246413):0.045, + gadMor1:0.25):0.22564, + (danRer10:0.430752, + astMex1:0.400000):0.300000):0.143632, + lepOcu1:0.400000):0.326688):0.200000, +petMar2:0.975747); diff -r 000000000000 -r c05c83b3ef0f hg38.20way.nh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hg38.20way.nh Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,20 @@ +((((((((((((hg38:0.00988692, + panTro4:0.00346722):0.00188147, + panPan1:0.00264326):0.00531373, + gorGor3:0.00893149):0.00925601, + ponAbe2:0.0188981):0.0034213, + nomLeu3:0.0230926):0.011557, + ((((rheMac3:0.00340845, + macFas5:0.00235962):0.00535291, + papAnu2:0.00850951):0.0040808, + chlSab2:0.0129507):0.00594416, + (nasLar1:0.00691583, + rhiRox1:0.00647931):0.0119022):0.0216071):0.0217539, + (calJac3:0.0352577, + saiBol1:0.0327629):0.0373501):0.0612174, + tarSyr2:0.142005):0.0118853, + (micMur1:0.092909, + otoGar3:0.128695):0.0342627):0.0166216, + tupBel1:0.184214):0.0152928, + mm10:0.330771):0.0876596, +canFam3:0.0876596); diff -r 000000000000 -r c05c83b3ef0f test-data/alignment1.clustal --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment1.clustal Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,9 @@ +CLUSTAL W --- LocARNA 1.8.10 + + + +SEQ47_2_50_+ AGGUAU-UAGAAAAAC-CAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC +SEQ42_1_50_+ GUAAAUAUAGUUUAAC-CAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC +SEQ41_1_50_+ ACUCUUUUAGUAUAAA-UAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC +SEQ39_1_50_+ GUUCUUGUAGUUGAAA-UACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU +SEQ34_1_51_+ CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU diff -r 000000000000 -r c05c83b3ef0f test-data/alignment1.cons.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment1.cons.tsv Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,2 @@ + Background model Columns Combinations/Pair Consensus MFE Covariance contribution Decision model Energy contribution G+C content Mean pairwise identity Mean single sequence MFE Mean z-score Prediction Reading direction SVM RNA-class probability SVM decision value Sequences Shannon entropy Structure conservation index alignment multihit per_species num_human_seqs_all num_seqs num_seqs_all rscape_#target_E-val rscape_Found rscape_MSA rscape_PPV rscape_SEN rscape_TP rscape_True rscape_alen rscape_avgid rscape_method rscape_nseq rscape_out cluster_bed cluster_human_ids cluster_human_loc +0 dinucleotide 51 2.890 -7.640 -4.520 structural RNA alignment quality -3.120 0.320 44.050 -5.080 0.220 RNA forward 1.000 3.530 5.000 1.035 1.500 cluster.aln 0 0 5 12 0.050 5 result.aln_1 100.000 55.560 5 9 50 44.730 GTp 5 RESULTS/result.aln.sum diff -r 000000000000 -r c05c83b3ef0f test-data/alignment1.evofold.out diff -r 000000000000 -r c05c83b3ef0f test-data/alignment1.png Binary file test-data/alignment1.png has changed diff -r 000000000000 -r c05c83b3ef0f test-data/alignment1.ps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment1.ps Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,184 @@ +%!PS-Adobe-3.0 EPSF-3.0 +%%BoundingBox: 0 0 444 91 +%%EndComments +% draws Vienna RNA like colored boxes +/box { % x1 y1 x2 y2 hue saturation + gsave + dup 0.3 mul 1 exch sub sethsbcolor + exch 3 index sub 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1.03471 + G+C content: 0.31965 + Mean single sequence MFE: -5.08 + Consensus MFE: -7.64 + Energy contribution: -3.12 + Covariance contribution: -4.52 + Combinations/Pair: 2.89 + Mean z-score: 0.22 + Structure conservation index: 1.50 + Background model: dinucleotide + Decision model: structural RNA alignment quality + SVM decision value: 3.53 + SVM RNA-class probability: 0.999916 + Prediction: RNA + +###################################################################### + +>SEQ47_2_50_+ +AGGUAU-UAGAAAAAC-CAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC +.(((..-.......))-)......((((((.....)))))).......... ( -4.20, z-score = 0.02, S) +>SEQ42_1_50_+ +GUAAAUAUAGUUUAAC-CAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC +.........((((...-..)))).((((((.....)))))).......... ( -5.90, z-score = -0.43, R) +>SEQ41_1_50_+ +ACUCUUUUAGUAUAAA-UAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC +.........((((...-..)))).(((((.......))))).......... ( -1.80, z-score = 1.22, R) +>SEQ39_1_50_+ +GUUCUUGUAGUUGAAA-UACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU +....(((((.......-)))))(((((((.......)))))))........ ( -7.30, z-score = -0.10, R) +>SEQ34_1_51_+ +CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU +..............((((...((((((((.......))))).)))..)))) ( -6.20, z-score = 0.37, R) +>consensus +AUGAAUAUAGUUUAAA_UAGAACAUUAGAUUUUCAAACUAAUAGUAGAGGC +.........((((......)))).(((((.......))))).......... ( -7.64 = -3.12 + -4.52) diff -r 000000000000 -r c05c83b3ef0f test-data/alignment1.sth --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment1.sth Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,9 @@ +# STOCKHOLM 1.0 + +SEQ39_1_50_+ GUUCUUGUAGUUGAAA-UACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU +SEQ42_1_50_+ GUAAAUAUAGUUUAAC-CAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC +SEQ47_2_50_+ AGGUAU-UAGAAAAAC-CAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC +SEQ41_1_50_+ ACUCUUUUAGUAUAAA-UAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC +SEQ34_1_51_+ CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU +#=GC SS_cons .........<<<<......>>>>.<<<<<.......>>>>>.......... +// \ No newline at end of file diff -r 000000000000 -r c05c83b3ef0f test-data/alignment1_R2R.sto.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment1_R2R.sto.pdf Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,618 @@ +%PDF-1.0 +5 0 obj +<< +/Type /Font +/Subtype /Type1 +/Name /FH +/BaseFont /Helvetica +/Encoding /WinAnsiEncoding +>> +endobj +4 0 obj 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+0000009544 00000 n +0000009667 00000 n +0000009609 00000 n +0000000116 00000 n +0000000009 00000 n +0000000152 00000 n +0000000269 00000 n +0000009524 00000 n +0000009286 00000 n +0000009174 00000 n +trailer +<< +/Size 11 +/Root 1 0 R +>> +startxref +9713 +%%EOF diff -r 000000000000 -r c05c83b3ef0f test-data/alignment2.clustal --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment2.clustal Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,9 @@ +CLUSTAL W --- LocARNA 1.8.10 + + + +SEQ4_526_595_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +SEQ5_526_595_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +SEQ16_526_595_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +SEQ19_523_592_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +SEQ14_529_598_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUUCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC diff -r 000000000000 -r c05c83b3ef0f test-data/alignment2.cons.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment2.cons.tsv Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,2 @@ + Background model Columns Combinations/Pair Consensus MFE Covariance contribution Decision model Energy contribution G+C content Mean pairwise identity Mean single sequence MFE Mean z-score Prediction Reading direction SVM RNA-class probability SVM decision value Sequences Shannon entropy Structure conservation index alignment multihit per_species num_human_seqs_all num_seqs num_seqs_all # seqId basePairCount beginPos bgCykProb bgProb cykScore endPos fold posScore score strCykProb strPostProb strProb rscape_#target_E-val rscape_Found rscape_MSA rscape_PPV rscape_SEN rscape_TP rscape_True rscape_alen rscape_avgid rscape_method rscape_nseq rscape_out cluster_bed cluster_human_ids cluster_human_loc +0 dinucleotide 70 1.000 -14.410 0.000 structural RNA alignment quality -14.410 0.497 99.430 -14.750 -0.200 OTHER forward 0.014 -1.570 5.000 0.010 0.980 cluster.aln 0 0 5 19 0.050 result.aln_1 70 99.430 5 RESULTS/result.aln.sum diff -r 000000000000 -r c05c83b3ef0f test-data/alignment2.evofold.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment2.evofold.out Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,1 @@ +# seqId beginPos endPos basePairCount strCykProb bgCykProb strProb bgProb cykScore score strPostProb fold posScore diff -r 000000000000 -r c05c83b3ef0f test-data/alignment2.png Binary file test-data/alignment2.png has changed diff -r 000000000000 -r c05c83b3ef0f test-data/alignment2.rnaz.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment2.rnaz.out Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,42 @@ + +############################ RNAz 2.1 ############################## + + Sequences: 5 + Columns: 70 + Reading direction: forward + Mean pairwise identity: 99.43 + Shannon entropy: 0.01031 + G+C content: 0.49714 + Mean single sequence MFE: -14.75 + Consensus MFE: -14.41 + Energy contribution: -14.41 + Covariance contribution: 0.00 + Combinations/Pair: 1.00 + Mean z-score: -0.20 + Structure conservation index: 0.98 + Background model: dinucleotide + Decision model: structural RNA alignment quality + SVM decision value: -1.57 + SVM RNA-class probability: 0.014380 + Prediction: OTHER + +###################################################################### + +>SEQ4_526_595_+ +CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +(((((((...((((((((((....))))).......))))))))))))............((....)).. ( -14.41, z-score = -0.08, R) +>SEQ5_526_595_+ +CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +(((((((...((((((((((....))))).......))))))))))))............((....)).. ( -14.41, z-score = -0.08, R) +>SEQ16_526_595_+ +CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +(((((((...((((((((((....))))).......))))))))))))............((....)).. ( -14.41, z-score = -0.08, R) +>SEQ19_523_592_+ +CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +(((((((...((((((((((....))))).......))))))))))))............((....)).. ( -14.41, z-score = -0.08, R) +>SEQ14_529_598_+ +CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUUCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +(((((((.((((..((((((....)))))).....))))..)))))))............((....)).. ( -16.10, z-score = -0.67, R) +>consensus +CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +(((((((...((((((((((....))))).......))))))))))))............((....)).. (-14.41 = -14.41 + 0.00) diff -r 000000000000 -r c05c83b3ef0f test-data/alignment2.sth --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment2.sth Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,9 @@ +# STOCKHOLM 1.0 + +SEQ5_526_595_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +SEQ4_526_595_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +SEQ14_529_598_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUUCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +SEQ19_523_592_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +SEQ16_526_595_+ CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC +#=GC SS_cons <<<<<<<...<<<<<<<<<<....>>>>>.......>>>>>>>>>>>>............<<<....>>> +// \ No newline at end of file diff -r 000000000000 -r c05c83b3ef0f test-data/alignment2b-transcript.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment2b-transcript.fa Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,73 @@ +>hg38_chr7_27162434_27166719_- Hoxa9-Xtend5UTR +GTTCCGGAGCTGCGGGGTCTCTTAGGCGAGGCTGCCTTTTCCCAAACCGAACTTGCCTTC +CATTCATGCCACTTGTAGTTTTTTCCCCAGCTGGGATTCACGGAGCGCAACCAGGCTTGC +AGCGCTCATGGTTAGAGCCTCTGAGGCTGGAGCACAGGGCTGGGTCGCCAGCCGCCTGCG +CCTGGGAATCCTGATTGCCAGCTGATGAGAAAGGCGGGCTGGGCGCGCGTGTGCGTGGGG +TCGAGGGCCGGGGACCGAGCGCGCCGCACAACCAACCAGGCCCTCAAAACCTTCGCCCTG +GTGGCGGCTGGCCGCTCCCTCCTGGCCAGCTCCTCCGTGGGGTCCTCGTAGCAAAGGCGA +ATTTAAGGGTTGCCCGGGCGCCCCTCGCTCCAGGCGGGTAGCTGTGGGGACCTACACCCG +CGGTACTCCCTGAGCGGCCGGTCCCTGCCTGGAGTGCCCTGGTAGGGCCGGCGGCGGCTC +CGTTTGGGACGGATCCTGCGTTGAATTTGACTTTTCGAGGGCGGCCGCGGGTAAACTCGC +CTCTCCCGGGGACCGCAGGGATTATTTACAGGGAGCTCGCCAACCAAACACAACAGTCTA +ACCTTTCCAAGTCCTCGTAAATTTTTACAGCTGGGAGCCACGGCGAGGCAAACGAATCTG +TTGGTCGTTTCCGACTTCCCGCCAGCCTGTGTGGCTTCTGAAACAATAACTCCTTATGAA +ATATCATAAATATAGATTTAAATACAGTAGAGCGACAATGCGATTTGGCTGCTTTTTTAT +GGCTTCAATTATTGTCTAATTTTATGTGAGGGGCTCCGCTGGCCGCACTCGCACGCGGGA +CCCGCGCCTTCTTGATGGCGTGATTAATTGTGATATAAAATAGTCCGCTTAAGAAGTGTG +TGTATGGGGGGGGAGACGGGAGAGTACAGAGACAAGGCTAGATTTGATCTTTTAATCGTC +GTTGGCCACAATTAAAACAAACCCCATCGTAGAGCGGCACGATCCCTTTACATAAAAACA +TATGGCTTTTGCTATAAAAATTATGACTGCAAAACATCGGACCATTAATAGCGTGCGGAG +TGATTTACGCGTTATTGTTCTGCTGGACGGGCACGTGACGCGCACGGCCAATGGGGGCGC +GGGCGCCGGCAACTTATTAGGTGACTGTACTTCCCCCCCGGTGCCACCAAGTTGTTACAT +GAAATCTGCAGTTTCATAATTTCCGTGGGTCGGGCCGGGCGGGCCAGGCGCTGGGCACGG +TGATGGCCACCACTGGGGCCCTGGGCAACTACTACGTGGACTCGTTCCTGCTGGGCGCCG +ACGCCGCGGATGAGCTGAGCGTTGGCCGCTATGCGCCGGGGACCCTGGGCCAGCCTCCCC +GGCAGGCGGCGACGCTGGCCGAGCACCCCGACTTCAGCCCGTGCAGCTTCCAGTCCAAGG +CGACGGTGTTTGGCGCCTCGTGGAACCCAGTGCACGCGGCGGGCGCCAACGCTGTACCCG +CTGCGGTGTaccaccaccatcaccaccacccctacgtgcacccccaggcgcccgtggcgg +cggcggcgccggacggcAGGTACATGCGCTCCTGGCTGGAGCCCACGCCCGGTGCGCTCT +CCTTCGCGGGCTTGCCCTCCAGCCGGCCTTATGGCATTAAACCTGAACCGCTGTCGGCCA +GAAGGGGTGACTGTCCCACGCTTGACACTCACACTTTGTCCCTGACTGACTATGCTTGTG +GTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGCCTTCTCTGAAAACAATG +CTGAGAATGAGAGCGGCGGAGACAAGCCCCCCATCGATCCCAGTAAGTGTCTCCTCCCTT +CAAATCCGCCGCCGCCTCCACGCCGGCCTCCCGGATCTGCTGGCCCGCCAGGTTTCTCTC +GAGCCTGCCTTCGTCCTCGCTGGAAGCCTCTCGAGTTGGGGCCAGGAGCCAGAAGTTGGT +GTTTGGGACGCCTCAGATAGGGCCCCAAGTCTGGAGAGCAGTGAAGAGCGGCCCGCAGGG +CTACGGGAGAGGAGGCGGCTGCTGCAGCGAGAGGGGGCGGGGCGGGCACTTCGGGACGAG +CCAAGACTGGCCGCCCCTCTCCTTGGCTGCCCAGGCCCAGGACCGAGATACTTTGGGCCG +TTCTTCGAAAGCAGTGCAGCCCAGAGAGCCTTTTGTACAACTAGATTGTCCGTGAGCGGC +GGCAGCCAGGGCAGCCGGAGCTGGGACGCTGGGGGAGACGGCCGATTCCTTCCACTTCTT +GCCTTCGGCCAGTGGCGGCGTAAATCCTGCCAAGATGAGGCTGCGGGCGACCCGGGCCAC +AAGGGTCCCCATGACAGATTATTCAAATAAGCCACAGACGTGATCAGCGGCCTTAGGGCG +CCCTGACGGCTTGCCCAGCTCCGAAGGCCTTCCAGGAAGGTTAAATAAGGAGTGGGGGGC +GTAGAGGGACAGGTTGGGAAAGAAAGACGAAGTCAGTGAACGGGACAGAGGAATCCTAAT +CTTGCTACAGAACACAAGGCAGCATGCTTTCCCTCTGCGTGGCAAGGAGACCTGTTTCCA +AATTTCATTCTATACAGCGTTTTGAGAGTGGGAGGAAGGAGAAGGGGGACAAGAGGACAG +AGTAGGAGAAAGGAAGGTCTCGGAGGGGAGGGCGAGCCAAAGTTTTACTGCGTGCAATTT +TAAGTGACTGTCTGTGCGTCTGTCTGCCAGGGTTCCATTGTGTCCGAGGCCTGACTGCCT +TTCCTAACCAGTTCAGCAGAGTTCTGCACTTCGGCCAGAGACCCCATGCAGGAGGCTCAT +TTGCCCCAGCGGGATGTGCGTCTTCTGCTCCTAAACCCAGTGTTTCTCTTCCCCGCAGAT +AACCCAGCAGCCAACTGGCTTCATGCGCGCTCCACTCGGAAAAAGCGGTGCCCCTATACA +AAACACCAGACCCTGGAACTGGAGAAAGAGTTTCTGTTCAACATGTACCTCACCAGGGAC +CGCAGGTACGAGGTGGCTCGACTGCTCAACCTCACCGAGAGGCAGGTCAAGATCTGGTTC +CAGAACCGCAGGATGAAAATGAAGAAAATCAACAAAGACCGAGCAAAAGACGAGTGATGC +CATTTGGGCTTATTTAGAAAAAAGGGTAAGCTAGAGAGAAAAAGAAAGAACTGTCCGTCC +CCCTTCCGCCTTCTCCCTTCTCTCACCCCCACCCTAGCCTCCACCATCCCCGCACAAAGC +GGCTCTAAACCTCAGGCCACATCTTTTCCAAGGCAAACCCTGTTCAGGCTGGCTCGTAGG +CCTGCCGCTTTGATGGAGGAGGTATTGTAAGCTTTCCATTTTCTATAAGAAAAAGGAAAA +GTTGAGGGGGGGGCATTAGTGCTGATAGCTGTGTGTGTTAGCTTGTATATATATTTTTAA +AAATCTACCTGTTCCTGACTTAAAACAAAAGGAAAGAAACTACCTTTTTATAATGCACAA +CTGTTGATGGTAGGCTGTATAGTTTTTAGTCTGTGTAGTTAATTTAATTTGCAGTTTGTG +CGGCAGATTGCTCTGCCAAGATACTTGAACACTGTGTTTTATTGTGGTAATTATGTTTTG +TGATTCAAACTTCTGTGTACTGGGTGATGCACCCATTGTGATTGTGGAAGATAGAATTCA +ATTTGAACTCAGGTTGTTTATGAGGGGAAAAAAACAGTTGCATAGAGTATAGCTCTGTAG +TGGAATATGTCTTCTGTATAACTAGGCTGTTAACCTATGATTGTAAAGTAGCTGTAAGAA +TTTCCCAGTGAAATAAAAAAAAATTTTAAGTGTTCTCGGGGATGCATAGATTCATCATTT +TCTCCACCTTAAAAATGCGGGCATTTAAGTCTGTCCATTATCTATATAGTCCTGTCTTGT +CTATTGTATATATAATCTATATGATTAAAGAAAATATGCATAATCAGACAAGCTTGAATA +TTGTTTTTGCACCAGACGAACAGTGAGGAAATTCGGAGCTATACATATGTGCAGAAGGTT +ACTACCTAGGGTTTATGCTTAATTTTAATTGGAGGAAATGAATGCTGATTGTAACGGAGT +TAATTTTATTGATAATAAATTATACACTATGAAACCGCCATTGGGCTACTGTAGATTTGT +ATCCTTGATGAATCTGGGGTTTCCATCAGACTGAACTTACACTGTATATTTTGCAATAGT +TACCTCAAGGCCTACTGACCAAATTGTTGTGTTGAGATGATATTTAACTTTTTGCCAAAT +AAAATATATTGATTCTTTTCTATTTT \ No newline at end of file diff -r 000000000000 -r c05c83b3ef0f test-data/alignment2b.cons.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignment2b.cons.tsv Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,2 @@ + Background model Columns Combinations/Pair Consensus MFE Covariance contribution Decision model Energy contribution G+C content Mean pairwise identity Mean single sequence MFE Mean z-score Prediction Reading direction SVM RNA-class probability SVM decision value Sequences Shannon entropy Structure conservation index alignment multihit per_species num_human_seqs_all num_seqs num_seqs_all # seqId basePairCount beginPos bgCykProb bgProb cykScore endPos fold posScore score strCykProb strPostProb strProb rscape_#target_E-val rscape_Found rscape_MSA rscape_PPV rscape_SEN rscape_TP rscape_True rscape_alen rscape_avgid rscape_method rscape_nseq rscape_out cluster_bed cluster_human_ids cluster_human_loc +0 dinucleotide 70 1.000 -14.410 0.000 structural RNA alignment quality -14.410 0.497 99.430 -14.750 -0.200 OTHER forward 0.014 -1.570 5.000 0.010 0.980 cluster.aln 0 1 5 19 0.050 result.aln_1 70 99.430 5 RESULTS/result.aln.sum diff -r 000000000000 -r c05c83b3ef0f test-data/cluster1.all --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster1.all Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,12 @@ +SEQ44#1#51#+ RESULT 2 CM_SCORE 43.7 MODEL 1.3 ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005_rep.46 +SEQ8#1#48#+ RESULT 2 CM_SCORE 39.1 MODEL 1.3 ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13 +SEQ47#2#50#+ RESULT 2 CM_SCORE 38.0 MODEL 1.3 ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6 +SEQ48#1#52#+ RESULT 2 CM_SCORE 37.9 MODEL 1.3 ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005_rep.7 +SEQ43#1#52#+ RESULT 2 CM_SCORE 35.3 MODEL 1.3 ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45 +SEQ39#1#50#+ RESULT 2 CM_SCORE 28.6 MODEL 1.3 ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41 +SEQ34#1#51#+ RESULT 2 CM_SCORE 22.2 MODEL 1.3 ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005_rep.37 +SEQ42#1#50#+ RESULT 2 CM_SCORE 45.6 CMSEARCH 1.3 ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44 +SEQ38#1#50#+ RESULT 2 CM_SCORE 45.2 CMSEARCH 1.3 ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40 +SEQ6#1#51#+ RESULT 2 CM_SCORE 43.6 CMSEARCH 1.3 ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11 +SEQ41#1#50#+ RESULT 2 CM_SCORE 40.6 CMSEARCH 1.3 ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005_rep.43 +SEQ49#1#50#+ RESULT 2 CM_SCORE 35.7 CMSEARCH 1.3 ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005_rep.8 diff -r 000000000000 -r c05c83b3ef0f test-data/cluster1.all.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster1.all.fa Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,24 @@ +>SEQ34_1_51_+ RESULT 2 SCORE 22.2 EVALUE 1.9e-06 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005_rep.37 +CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU +>SEQ41_1_50_+ RESULT 2 SCORE 40.6 EVALUE 3.3e-14 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005_rep.43 +ACUCUUUUAGUAUAAAUAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC +>SEQ47_2_50_+ RESULT 2 SCORE 38.0 EVALUE 4e-13 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6 +AGGUAUUAGAAAAACCAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC +>SEQ42_1_50_+ RESULT 2 SCORE 45.6 EVALUE 2.6e-16 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44 +GUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC +>SEQ39_1_50_+ RESULT 2 SCORE 28.6 EVALUE 3.7e-09 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41 +GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU +>SEQ43_1_52_+ RESULT 2 SCORE 35.3 EVALUE 5.8e-12 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45 +GUUUAUGUAGCUUACCUCCUCAAAGCAAUACACUGAAAAUGUUUAGACGGGC +>SEQ49_1_50_+ RESULT 2 SCORE 35.7 EVALUE 3.9e-12 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005_rep.8 +AGAAAUUUAGGUUAAAUACAGACCAAGAGCCUUCAAAGCCCUCAGUAAGU +>SEQ44_1_51_+ RESULT 2 SCORE 43.7 EVALUE 1.7e-15 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005_rep.46 +CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAAC +>SEQ8_1_48_+ RESULT 2 SCORE 39.1 EVALUE 1.4e-13 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13 +CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAG +>SEQ6_1_51_+ RESULT 2 SCORE 43.6 EVALUE 1.7e-15 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11 +GUCCUUGUAGUAUAAACUAAUACACCAGUCUUGUAAACCGGAGAUGAAAAC +>SEQ38_1_50_+ RESULT 2 SCORE 45.2 EVALUE 3.9e-16 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40 +UGGUAUAUAGUUUAAACAAAACGAAUGAUUUCGACUCAUUAAAUUAUGAU +>SEQ48_1_52_+ RESULT 2 SCORE 37.9 EVALUE 4.5e-13 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005_rep.7 +ACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGCCCCAAAAAUUUUGGU diff -r 000000000000 -r c05c83b3ef0f test-data/cluster2.all --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster2.all Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,19 @@ +SEQ4#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID gorGor3_4 ORIGHEAD gorGor3 +SEQ5#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID ponAbe2_5 ORIGHEAD ponAbe2 +SEQ1#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID hg38_1 ORIGHEAD hg38 +SEQ3#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID panPan1_3 ORIGHEAD panPan1 +SEQ8#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID macFas5_8 ORIGHEAD macFas5 +SEQ10#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID chlSab2_10 ORIGHEAD chlSab2 +SEQ11#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID nasLar1_11 ORIGHEAD nasLar1 +SEQ2#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID panTro4_2 ORIGHEAD panTro4 +SEQ12#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID rhiRox1_12 ORIGHEAD rhiRox1 +SEQ7#526#595#+ RESULT 1 CM_SCORE 136.4 MODEL 1.1 ORIGID rheMac3_7 ORIGHEAD rheMac3 +SEQ14#529#598#+ RESULT 1 CM_SCORE 129.7 MODEL 1.1 ORIGID saiBol1_14 ORIGHEAD saiBol1 +SEQ18#527#596#+ RESULT 1 CM_SCORE 129.7 MODEL 1.1 ORIGID tupBel1_18 ORIGHEAD tupBel1 +SEQ15#529#598#+ RESULT 1 CM_SCORE 128.6 MODEL 1.1 ORIGID tarSyr2_15 ORIGHEAD tarSyr2 +SEQ16#526#595#+ RESULT 1 CM_SCORE 136.4 CMSEARCH 1.1 ORIGID micMur1_16 ORIGHEAD micMur1 +SEQ19#523#592#+ RESULT 1 CM_SCORE 136.4 CMSEARCH 1.1 ORIGID mm10_19 ORIGHEAD mm10 +SEQ17#526#595#+ RESULT 1 CM_SCORE 136.4 CMSEARCH 1.1 ORIGID otoGar3_17 ORIGHEAD otoGar3 +SEQ9#444#513#+ RESULT 1 CM_SCORE 136.4 CMSEARCH 1.1 ORIGID papAnu2_9 ORIGHEAD papAnu2 +SEQ6#526#595#+ RESULT 1 CM_SCORE 132.7 CMSEARCH 1.1 ORIGID nomLeu3_6 ORIGHEAD nomLeu3 +SEQ20#525#594#+ RESULT 1 CM_SCORE 129.1 CMSEARCH 1.1 ORIGID canFam3_20 ORIGHEAD canFam3 diff -r 000000000000 -r c05c83b3ef0f test-data/cluster2.all.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cluster2.all.fa Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,38 @@ +>SEQ4_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID gorGor3_4 ORIGHEAD gorGor3 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ5_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID ponAbe2_5 ORIGHEAD ponAbe2 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ16_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID micMur1_16 ORIGHEAD micMur1 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ19_523_592_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID mm10_19 ORIGHEAD mm10 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ14_529_598_+ RESULT 1 SCORE 129.7 EVALUE 3.3e-33 CLUSTER 1.1 LOC MISS ORIGID saiBol1_14 ORIGHEAD saiBol1 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTTCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ17_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID otoGar3_17 ORIGHEAD otoGar3 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ1_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID hg38_1 ORIGHEAD hg38 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ3_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID panPan1_3 ORIGHEAD panPan1 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ8_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID macFas5_8 ORIGHEAD macFas5 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ10_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID chlSab2_10 ORIGHEAD chlSab2 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ11_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID nasLar1_11 ORIGHEAD nasLar1 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ20_525_594_+ RESULT 1 SCORE 129.1 EVALUE 4.5e-33 CLUSTER 1.1 LOC MISS ORIGID canFam3_20 ORIGHEAD canFam3 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAGCCCAGCGAAGGCGC +>SEQ15_529_598_+ RESULT 1 SCORE 128.6 EVALUE 6.3e-33 CLUSTER 1.1 LOC MISS ORIGID tarSyr2_15 ORIGHEAD tarSyr2 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACCACCCAGCGAAGGCGC +>SEQ2_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID panTro4_2 ORIGHEAD panTro4 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ18_527_596_+ RESULT 1 SCORE 129.7 EVALUE 3.3e-33 CLUSTER 1.1 LOC MISS ORIGID tupBel1_18 ORIGHEAD tupBel1 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAGCAATCCAGCGAAGGCGC +>SEQ12_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID rhiRox1_12 ORIGHEAD rhiRox1 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ9_444_513_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID papAnu2_9 ORIGHEAD papAnu2 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ7_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID rheMac3_7 ORIGHEAD rheMac3 +CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC +>SEQ6_526_595_+ RESULT 1 SCORE 132.7 EVALUE 6.4e-34 CLUSTER 1.1 LOC MISS ORIGID nomLeu3_6 ORIGHEAD nomLeu3 +CTTTGTCTCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC diff -r 000000000000 -r c05c83b3ef0f test-data/structure.png diff -r 000000000000 -r c05c83b3ef0f test-data/structure.ps diff -r 000000000000 -r c05c83b3ef0f test-data/structure1.png Binary file test-data/structure1.png has changed diff -r 000000000000 -r c05c83b3ef0f test-data/structure1.ps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/structure1.ps Sat Oct 27 13:21:39 2018 -0400 @@ -0,0 +1,352 @@ +%!PS-Adobe-3.0 EPSF-3.0 +%%Creator: ViennaRNA-2.2.10 +%%CreationDate: Sat Oct 27 14:38:56 2018 +%%Title: RNA Secondary Structure Plot +%%BoundingBox: 66 210 518 662 +%%DocumentFonts: Helvetica +%%Pages: 1 +%%EndComments + +%Options: --noLP +% to switch off outline pairs of sequence comment or +% delete the appropriate line near the end of the file + +%%BeginProlog +/RNAplot 100 dict def +RNAplot begin +/fsize 14 def +/outlinecolor {0.2 setgray} bind def +/paircolor {0.2 setgray} bind def +/seqcolor {0 setgray} bind def +/cshow { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def +/min { 2 copy gt { exch } if pop } bind def +/max { 2 copy lt { exch } if pop } bind def +/arccoords { % i j arccoords + % puts optimal x1 y1 x2 y2 coordinates used in bezier curves from i to j + % onto the stack + dup 3 -1 roll dup 4 -1 roll lt dup dup 5 2 roll {exch} if + dup 3 -1 roll dup 3 -1 roll exch sub 1 sub dup + 4 -2 roll 5 -1 roll {exch} if 4 2 roll + sequence length dup 2 div exch 3 1 roll lt + {exch 5 -1 roll pop 4 -2 roll exch 4 2 roll} + { 4 2 roll 5 -1 roll dup 6 1 roll {exch} if + 4 -2 roll exch pop dup 3 -1 roll dup 4 1 roll + exch add 4 -1 roll dup 5 1 roll sub 1 sub + 5 -1 roll not {4 -2 roll exch 4 2 roll} if + }ifelse + % compute the scalingfactor and prepare (1-sf) and sf*r + 2 mul exch cpr 3 1 roll div dup + 3 -1 roll mul exch 1 exch sub exch + % compute the coordinates + 3 -1 roll 1 sub coor exch get aload pop % get coord for i + 4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate y1 + 4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate x1 + 5 -1 roll 1 sub coor exch get aload pop % get coord for j + % duplicate j coord + dup 3 -1 roll dup 4 1 roll exch 8 2 roll + 6 -1 roll dup 7 1 roll mul 5 -1 roll dup 6 1 roll add exch % calculate y2 + 6 -1 roll mul 5 -1 roll add exch % calculate x2 + 6 -2 roll % reorder +} bind def +/drawoutline { + gsave outlinecolor newpath + coor 0 get aload pop 0.8 0 360 arc % draw 5' circle of 1st sequence + currentdict /cutpoint known % check if cutpoint is defined + {coor 0 cutpoint getinterval + {aload pop lineto} forall % draw outline of 1st sequence + coor cutpoint 1 add get aload pop + 2 copy moveto 0.8 0 360 arc % draw 5' circle of 2nd sequence + coor cutpoint 1 add coor length cutpoint 1 add sub getinterval + {aload pop lineto} forall} % draw outline of 2nd sequence + {coor {aload pop lineto} forall} % draw outline as a whole + ifelse + stroke grestore +} bind def +/drawpairs { + paircolor + 0.7 setlinewidth + [9 3.01] 9 setdash + newpath + pairs {aload pop + currentdict (cpr) known + { exch dup + coor exch 1 sub get aload pop moveto + exch arccoords curveto + } + { coor exch 1 sub get aload pop moveto + coor exch 1 sub get aload pop lineto + }ifelse + } forall + stroke +} bind def +% draw bases +/drawbases { + [] 0 setdash + seqcolor + 0 + coor { + aload pop moveto + dup sequence exch 1 getinterval cshow + 1 add + } forall + pop +} bind def + +/init { + /Helvetica findfont fsize scalefont setfont + 1 setlinejoin + 1 setlinecap + 0.8 setlinewidth + 72 216 translate + % find the coordinate range + /xmax -1000 def /xmin 10000 def + /ymax -1000 def /ymin 10000 def + coor { + aload pop + dup ymin lt {dup /ymin exch def} if + dup ymax gt {/ymax exch def} {pop} ifelse + dup xmin lt {dup /xmin exch def} if + dup xmax gt {/xmax exch def} {pop} ifelse + } forall + /size {xmax xmin sub ymax ymin sub max} bind def + 72 6 mul size div dup scale + size xmin sub xmax sub 2 div size ymin sub ymax sub 2 div + translate +} bind def +end +RNAplot begin +% extra definitions for standard anotations +/min { 2 copy gt { exch } if pop } bind def +/BLACK { 0 0 0 } def +/RED { 1 0 0 } def +/GREEN { 0 1 0 } def +/BLUE { 0 0 1 } def +/WHITE { 1 1 1 } def +/LabelFont { % font size LabelFont + exch findfont exch fsize mul scalefont setfont +} bind def +/Label { % i dx dy (text) Label + % write text at base i plus offset dx, dy + 4 3 roll 1 sub coor exch get aload pop moveto + 3 1 roll fsize mul exch fsize mul exch rmoveto + show +} bind def +/cmark { % i cmark draw circle around base i + newpath 1 sub coor exch get aload pop + fsize 2 div 0 360 arc stroke +} bind def +/gmark { % i j c gmark + % draw basepair i,j with c counter examples in gray + gsave + 3 min [0 0.33 0.66 0.9] exch get setgray + 1 sub dup coor exch get aload pop moveto + sequence exch 1 getinterval cshow + 1 sub dup coor exch get aload pop moveto + sequence exch 1 getinterval cshow + grestore +} bind def +/segmark { % f i j lw r g b segmark + % mark segment [i,j] with outline width lw and color rgb + % use omark and Fomark instead + gsave + setrgbcolor setlinewidth + newpath + 1 sub exch 1 sub dup + coor exch get aload pop moveto + currentdict (cpr) known + { + 3 -1 roll dup 4 1 roll dup + { + 3 1 roll dup 3 -1 roll dup + 4 1 roll exch 5 2 roll exch + } + { + 3 1 roll exch + } ifelse + 1 exch { coor exch get aload pop lineto } for + { + dup 3 1 roll 1 add exch 1 add arccoords pop pop + 4 2 roll 5 -1 roll coor exch get aload pop curveto + } if + } + { + exch 1 exch { + coor exch get aload pop lineto + } for + } ifelse + { closepath fill } if stroke + grestore +} bind def +/omark { % i j lw r g b omark + % stroke segment [i..j] with linewidth lw, color rgb + false 7 1 roll segmark +} bind def +/Fomark { % i j r g b Fomark + % fill segment [i..j] with color rgb + % should precede drawbases + 1 4 1 roll true 7 1 roll segmark +} bind def +/BFmark{ % i j k l r g b BFmark + % fill block between pairs (i,j) and (k,l) with color rgb + % should precede drawbases + gsave + setrgbcolor + newpath + currentdict (cpr) known + { + dup 1 sub coor exch get aload pop moveto % move to l + dup 1 sub 4 -1 roll dup 5 1 roll 1 sub 1 exch + { coor exch get aload pop lineto } for % lines from l to j + 3 -1 roll 4 -1 roll dup 5 1 roll arccoords curveto % curve from j to i + exch dup 4 -1 roll 1 sub exch 1 sub 1 exch + { coor exch get aload pop lineto } for % lines from i to k + exch arccoords curveto% curve from k to l + } + { exch 4 3 roll exch 1 sub exch 1 sub dup + coor exch get aload pop moveto + exch 1 exch { coor exch get aload pop lineto } for + exch 1 sub exch 1 sub dup + coor exch get aload pop lineto + exch 1 exch { coor exch get aload pop lineto } for + } ifelse + closepath fill stroke + grestore +} bind def +/hsb { + dup 0.3 mul 1 exch sub sethsbcolor +} bind def +/colorpair { % i j hue sat colorpair + % draw basepair i,j in color + % 1 index 0.00 ne { + gsave + newpath + hsb + fsize setlinewidth + currentdict (cpr) known + { + exch dup + coor exch 1 sub get aload pop moveto + exch arccoords curveto + } + { 1 sub coor exch get aload pop moveto + 1 sub coor exch get aload pop lineto + } ifelse + stroke + grestore + % } if +} bind def +end + +%%EndProlog +RNAplot begin +% data start here +/sequence (\ +AUGAAUAUAGUUUAAA_UAGAACAUUAGAUUUUCAAACUAAUAGUAGAGGC\ +) def +/coor [ +[95.00124359 138.88397217] +[87.89935303 137.28974915] +[81.21456146 134.41014099] +[75.17730713 130.34443665] +[69.99568176 125.23274994] +[65.84830475 119.25129700] +[62.87813568 112.60626221] +[61.18754959 105.52667999] +[60.83482361 98.25659943] +[61.83211517 91.04661560] +[48.15361786 84.89042664] +[34.47511673 78.73423004] +[20.79662132 72.57804108] +[6.11008787 78.41596222] +[-8.36961174 72.08241272] +[-14.05193043 57.33497620] +[-7.56564760 42.92304993] +[7.24103928 37.39696503] +[21.58358574 44.03525925] +[26.95281219 58.89954376] +[40.63130951 65.05573273] +[54.30980682 71.21192932] +[67.98830414 77.36811829] +[94.10119629 61.24235916] +[123.82917786 68.86929321] +[135.05683899 58.92245483] +[146.28450012 48.97561264] +[157.51216125 39.02877426] +[168.73982239 29.08193398] +[168.13914490 13.45589161] +[177.76402283 1.13129318] +[193.06988525 -2.07256317] +[206.82977295 5.35708570] +[212.54667664 19.91218758] +[207.52125549 34.72026825] +[194.12637329 42.78940201] +[178.68666077 40.30959702] +[167.45899963 50.25643539] +[156.23133850 60.20327377] +[145.00367737 70.15011597] +[133.77601624 80.09695435] +[136.87315369 86.68378448] +[138.69926453 93.72961426] +[139.19142151 100.99159241] +[138.33265686 108.21938324] +[136.15257263 115.16385651] +[132.72630310 121.58563232] +[128.17196655 127.26335907] +[122.64655304 132.00131226] +[116.34051514 135.63619995] +[109.47121429 138.04269409] +] def +/pairs [ +[10 23] +[11 22] +[12 21] +[13 20] +[25 41] +[26 40] +[27 39] +[28 38] +[29 37] +] def + +init + +% Start Annotations +10 23 0.16 1 colorpair +11 22 0.16 1 colorpair +12 21 0.16 1 colorpair +13 20 0.48 1 colorpair +25 41 0.32 1 colorpair +26 40 0.32 1 colorpair +27 39 0.32 1 colorpair +28 38 0.48 1 colorpair +29 37 0.32 1 colorpair + +% End Annotations +% switch off outline pairs or bases by removing these lines +drawoutline +drawpairs +drawbases +% Start Annotations +23 cmark +11 cmark +22 cmark +12 cmark +21 cmark +13 cmark +20 cmark +25 cmark +41 cmark +26 cmark +40 cmark +27 cmark +39 cmark +28 cmark +38 cmark +29 cmark +37 cmark + +% End Annotations +% show it +showpage +end +%%EOF diff -r 000000000000 -r c05c83b3ef0f test-data/structure2.png Binary file test-data/structure2.png has changed