| Next changeset 1:a5a2d3cefce1 (2017-01-13) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc |
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locarna.tar.bz2 locarna_multiple.xml macros.xml test-data/archaea-default.stdout test-data/archaea-probabilistic.aln test-data/archaea.fa test-data/archaea.tar.gz test-data/archaea_relplot.scr test-data/haca.snoRNA-default.stdout test-data/haca.snoRNA.fa test-data/haca.snoRNA_anchor.bed test-data/tRNA_2-1.fa test-data/tRNA_2-2.fa test-data/tRNA_2.aln test-data/tRNA_5.fa |
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| diff -r 000000000000 -r 8414fea2a6fd locarna.tar.bz2 |
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| diff -r 000000000000 -r 8414fea2a6fd locarna_multiple.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/locarna_multiple.xml Wed Dec 28 18:52:14 2016 -0500 |
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| b'@@ -0,0 +1,311 @@\n+<tool id="locarna_multiple" name="LocARNA Multiple Aligner (mlocarna)" version="@VERSION@.0">\n+ <description>\n+ Multiple Alignment and Folding of RNAs\n+ </description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ \n+ <expand macro="requirements" />\n+\n+ <expand macro="stdio" />\n+ \n+ <expand macro="version" />\n+ \n+ <command><![CDATA[\n+ mlocarna\n+ \n+ \'$input_data\'\n+ #if \'stockholm\' in str($outputs).split(","):\n+ --stockholm\n+ #end if\n+\n+ --tgtdir mlocarna_results\n+ --width 60\n+ \n+ ## -------------------- alignment mode and specific options\n+\n+ #if str($alignment_mode.alignment_mode_selector) == "global_locarna"\n+ $alignment_mode.free_endgaps\n+ #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"\n+ --sequ-local on\n+ #else if str($alignment_mode.alignment_mode_selector) == "probabilistic"\n+ --probabilistic\n+ $alignment_mode.consistency_transformation\n+ \n+ #if str($alignment_mode.iterate) == "true"\n+ --iterate\n+ --iterations $alignment_mode.iterations\n+ #end if\n+ #else if str($alignment_mode.alignment_mode_selector) == "sparse"\n+ --sparse\n+ #end if\n+ \n+ ## -------------------- scoring parameters\n+ \n+ --indel $Scoring.indel\n+ --indel-opening $Scoring.indel_opening\n+ --struct-weight $Scoring.struct_weight\n+ --tau $Scoring.tau\n+ \n+ #if str($Scoring.sequence_score.sequence_score_selector) == "match"\n+ --match $Scoring.sequence_score.match\n+ --mismatch $Scoring.sequence_score.mismatch\n+ #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"\n+ --use-ribosum true\n+ #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"\n+ --ribofit true\n+ #end if\n+\n+ ## -------------------- folding parameters\n+\n+ #if $Folding.plfold_span>=0\n+ --plfold-span $Folding.plfold_span\n+ --plfold-winsize $Folding.plfold_winsize\n+ #end if\n+ \n+ #if float($Folding.rnafold_temperature) != 37.0\n+ --rnafold-temperature $Folding.rnafold_temperature\n+ #end if\n+\n+ $Folding.alifold_consensus_dp\n+\n+ ## -------------------- heuristic parameters\n+ \n+ -p $Heuristics.min_prob\n+ --max-diff-am $Heuristics.max_diff_am\n+ --max-diff $Heuristics.max_diff\n+ --max-diff-at-am $Heuristics.max_diff_at_am\n+ --max-bps-length-ratio $Heuristics.max_bps_length_ratio\n+ \n+\n+ ## -------------------- other parameters\n+\n+ #if str($Constraint.bed_anchors.bed_anchors_selector) == "yes"\n+ --anchor-constraints $Constraint.bed_anchors.bed_anchors_file\n+ #end if\n+\n+ $Constraint.lonely_pairs\n+\n+ #if $Constraint.maxBPspan != -1\n+ --maxBPspan $Constraint.maxBPspan\n+ #end if\n+\n+ $Constraint.ignore_constraints\n+\n+ $stdout_verbosity\n+\n+ #if str($stdout_verbosity) != "--quiet":\n+ > \'$stdout\'\n+ #end if\n+\n+ #if \'clustal_strict\' in str($outputs).split(",")\n+ && grep -v \'^#\' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln\n+ #end if\n+\n+ ]]></command>\n+\n+ <inputs>\n+ <conditional name="input_data_type">\n+ <param name="input_data_type_selector" type="select" label="Input type">\n+ <option value="fasta">Fasta input (strict)</option>\n+ <option value="text">Fasta-like input with LocARNA constraints</option>\n+ </param>\n+ <when value="fasta">\n+ <param name="input_data" type="data" format="fasta" label="Sequence input"\n+ help="Sequence input in pure fasta format"\n+ />\n+ </when>\n+ <when value="text">\n+ <param name="input_data" type="data" format="text" label="Sequence input"\n+ help="Sequence input in fasta format with locarna-specific extensions"\n+ '..b'/section>\n+\n+ <section name="Constraint" title="Constraint parameters">\n+ <expand macro="bed_anchors" />\n+ <expand macro="constraints" />\n+ </section>\n+ </inputs>\n+ \n+ <outputs>\n+ <expand macro="common_outputs" />\n+ </outputs>\n+ \n+ <tests>\n+ <test>\n+ <param name="input_data" value="archaea.fa" />\n+ <param name="stdout_verbosity" value="" />\n+ <output name="stdout" file="archaea-default.stdout" />\n+ </test>\n+ <test>\n+ <param name="input_data" value="haca.snoRNA.fa" />\n+ <param name="stdout_verbosity" value="" />\n+ <output name="stdout" file="haca.snoRNA-default.stdout" />\n+ </test>\n+ <test>\n+ <param name="input_data" value="archaea.fa" />\n+ <param name="stdout_verbosity" value="" />\n+ <param name="outputs" value="clustal" />\n+ <param name="alignment_mode_selector" value="probabilistic" />\n+ <output name="clustal" file="archaea-probabilistic.aln" />\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[ **MLocARNA -- Multiple alignment of RNAs**\n+\n+MLocARNA is the (general, progressive) multiple RNA alignment tool of\n+the LocARNA suite. It supports several alignment modes and can be\n+adapted to specific needs by a broad range of parameters. Thus, there\n+are parameters for\n+\n+* *scoring* of the alignment, e.g. influencing the cost of\n+ insertions/deletions and the weight of sequence vs. structure\n+ similarity.\n+\n+* *RNA folding*, which control the secondary RNA structure prediciton.\n+\n+* *heuristics*, which trade alignment accuracy vs. computation\n+ speed. The huge complexity of simultaneous alignment and folding\n+ generally requires some heuristics for reasonable computation times.\n+ Some alignment instances and alignment modes will require relaxation\n+ of the default heuristics; in particular, local, constrained, and free end gap\n+ alignment, will often require turning off the "maximal difference for\n+ alignment traces" heuristic.\n+ \n+* *constraints*, which can be applied to include prior knowledge to\n+ improve the quality of results and/or speed of computation.\n+\n+Technically, mlocarna constructs multiple alignments progressively\n+based on pairwise alignments by locarna, locarna-p, or sparse, which\n+perform variants of simultaneous RNA folding and alignment.\n+\n+**Input.**\n+Sequences can be given in plain fasta format like::\n+\n+ >fruA\n+ CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG\n+ >fdhA\n+ CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG\n+ >vhuU\n+ AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU\n+\n+Morover, mlocarna supports structure constraints for folding and anchor\n+constraints for alignment. Both types of constraints can be specified\n+in extension of the standard fasta format via \'constraint\n+lines\'. Fasta-ish input with constraints looks like this::\n+\n+ >A\n+ GACCCUGGGAACAUUAACUACUCUCGUUGGUGAUAAGGAACA\n+ ..((.(....xxxxxx...................))).xxx #S\n+ ..........000000.......................111 #1\n+ ..........123456.......................123 #2\n+ >B\n+ ACGGAGGGAAAGCAAGCCUUCUGCGACA\n+ .(((....xxxxxx.......))).xxx #S\n+ ........000000...........111 #1\n+ ........123456...........123 #2\n+\n+The same anchor constraints (like by the lines tagged #1, #2) can\n+alternatively be specified in bed format by the entries::\n+\n+ A\t10\t16\tfirst_box\n+ B\t8\t14\tfirst_box\n+ A\t39\t42\tACA-box\n+ B\t25\t28\tACA-box\n+\n+where anchor regions (boxes) have arbitrary but matching names\n+and contig/sequence names correspond to the sequence names\n+of the fasta(-like) input.\n+\n+\n+**Output.**\n+\n+The final alignment is reported in standard and/or variants of the\n+clustal and stockholm format. Moreover, an archive with final and\n+intermediary results of the mlocarna run can be returned.\n+\n+ \n+For more information, see \n+.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/\n+ ]]></help>\n+\n+ <expand macro="citations" />\n+ \n+</tool>\n' |
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| diff -r 000000000000 -r 8414fea2a6fd macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 28 18:52:14 2016 -0500 |
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| @@ -0,0 +1,178 @@ +<macros> + <token name="@VERSION@">1.9.0</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">locarna</requirement> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + + <xml name="version"> + <version_command> + <![CDATA[ + mlocarna --version + ]]> + </version_command> + </xml> + + <xml name="bed_anchors"> + <conditional name="bed_anchors"> + <param name="bed_anchors_selector" type="select" label="Anchor constraints" + help="Anchor constraints in bed format specify positions of + named anchor regions per sequence. The sequence names + ('contig' names have to correspond to the fasta input + sequence names. Anchor names must be unique per sequence + and regions of the same name for different sequences + must have the same length. This constrains the alignment + to align all regions of the same name."> + <option value="no">Don't load anchor constraints from bed file</option> + <option value="yes">Load anchor constraints from bed file</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="bed_anchors_file" type="data" format="tabular" + label="Anchor constraint specification in bed format" + /> + </when> + </conditional> + </xml> + + <xml name="common_scoring_parameters"> + <param name="struct_weight" argument="struct-weight" + label="Structure weight" type="integer" + value="200" min="0" max="800" /> + <param name="indel_opening" argument="indel-opening" + label="Indel opening score" type="integer" + value="-500" max="0" min="-1500" /> + <param argument="indel" label="Indel score" type="integer" + value="-350" min="-1000" max="0" /> + <param argument="tau" type="integer" value="50" + min="0" max="200" + label="Sequence contribution at structure match in percent"/> + + <conditional name="sequence_score"> + <param name="sequence_score_selector" type="select" label="Type of sequence score contribution"> + <option value="ribofit">Use ribofit</option> + <option value="ribosum">Use RIBOSUM85_60</option> + <option value="match">Simple match/mismatch costs</option> + </param> + <when value="ribofit" /> + <when value="ribosum" /> + <when value="match"> + <param name="match" type="integer" value="50" + min="0" max="400" + label="Match score" /> + <param name="mismatch" type="integer" value="0" + min="-400" max="0" + label="Mismatch score" /> + </when> + </conditional> + </xml> + + <xml name="plfolding_parameters"> + <param name="plfold_span" argument="--plfold-span" + type="integer" value="150" min="-1" max="400" + label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" /> + + <param name="plfold_winsize" argument="--plfold-winsize" + type="integer" value="300" min="-1" max="800" + label="Window size for local folding" /> + </xml> + + <xml name="common_folding_parameters"> + <param name="rnafold_temperature" argument="rnafold-temperature" + type="float" value="37.0" min="10" max="50" + label="Temperature for RNAfold (RNAfold's -T option)" /> + </xml> + + <xml name="common_heuristic_parameters"> + <param name="min_prob" argument="min-prob" type="float" value="0.0005" + min="0.0" max="0.2" + label="Minimal / cutoff probability" /> + + <param name="max_diff_am" argument="max-diff-am" + type="integer" value="30" + min="-1" max="300" + label="Maximal difference for sizes of matched arcs (-1=off)" /> + + <param name="max_diff" argument="max-diff" type="integer" + value="60" min="-1" max="300" + label="Maximal difference for alignment traces (-1=off)" /> + + <param name="max_diff_at_am" argument="max-diff-am" type="integer" + value="-1" min="-1" max="300" + label="Maximal difference for alignment traces, only at arc match positions" /> + + <param name="max_bps_length_ratio" argument="max-bps-length-ratio" + type="float" value="0.0" min="0.0" max="1.0" + label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" /> + </xml> + + <xml name="alifold_consensus_parameter"> + <param name="alifold_consensus_dp" argument="alifold-consensus-dp" + type="boolean" checked="false" + truevalue="--alifold-consensus-dp" falsevalue="" + label="Compute consensus dot plot by alifold" /> + </xml> + + <xml name="constraints"> + <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" + checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" /> + <param name="maxBPspan" argument="--maxBPspan" + type="integer" value="-1" min="-1" max="400" + label="Maximum basepair span by RNAfold; -1 for arbitrary span" /> + <param name="ignore_constraints" argument="ignore-constraints" + type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue="" + help="Ignore all anchor and structure constraints given + in the fasta(-ish) input." /> + </xml> + + <xml name="common_other_parameters"> + </xml> + + <xml name="common_outputs"> + <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> + <filter>stdout_verbosity != '--quiet'</filter> + </data> + <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln" + label="${tool.name} alignment (annotated clustal) on ${on_string}"> + <filter>'clustal' in outputs</filter> + </data> + <data format="clustal" name="clustal_strict" + from_work_dir="mlocarna_results/results/result.strict-aln" + label="${tool.name} alignment (clustal) on ${on_string}"> + <filter>'clustal_strict' in outputs</filter> + </data> + <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk" + label="${tool.name} alignment (stockholm) on ${on_string}"> + <filter>'stockholm' in outputs</filter> + </data> + <data format="txt" name="pp" + from_work_dir="mlocarna_results/results/result.pp" + label="${tool.name} alignment (PP 2.0) on ${on_string}"> + <filter>'pp' in outputs</filter> + </data> + <data format="tar.gz" name="mlocarna_results_tgz" + label="${tool.name} results archive on ${on_string}"> + <filter>'mlocarna_results' in outputs</filter> + </data> + </xml> + + <xml name="citations"> + <citations> + <citation + type="doi">10.1371/journal.pcbi.0030065</citation> + <citation type="doi">10.1261/rna.029041.111</citation> + </citations> + </xml> + + + +</macros> + |
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| diff -r 000000000000 -r 8414fea2a6fd test-data/archaea-default.stdout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-default.stdout Wed Dec 28 18:52:14 2016 -0500 |
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| @@ -0,0 +1,18 @@ +mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0 +Copyright Sebastian Will + +Compute pair probs ... +Compute pairwise alignments ... +Perform progressive alignment ... + + + +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 ((.(((((((((...(((.................))).))))))))))). (-31.59 = -20.01 + -11.58) |
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| diff -r 000000000000 -r 8414fea2a6fd test-data/archaea-probabilistic.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-probabilistic.aln Wed Dec 28 18:52:14 2016 -0500 |
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| @@ -0,0 +1,11 @@ +CLUSTAL W --- LocARNA 1.9.0 + + + +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 |
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| diff -r 000000000000 -r 8414fea2a6fd test-data/archaea.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea.fa Wed Dec 28 18:52:14 2016 -0500 |
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| @@ -0,0 +1,14 @@ +>fruA +CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG +>fdhA +CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG +>vhuU +AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU +>hdrA +GGCACCACUCGAAGGCUAAGCCAAAGUGGUGCU +>vhuD +GUUCUCUCGGGAACCCGUCAAGGGACCGAGAGAAC +>selD +UUACGAUGUGCCGAACCCUUUAAGGGAGGCACAUCGAAA +>fwdB +AUGUUGGAGGGGAACCCGUAAGGGACCCUCCAAGAU |
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| diff -r 000000000000 -r 8414fea2a6fd test-data/archaea.tar.gz |
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| Binary file test-data/archaea.tar.gz has changed |
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| diff -r 000000000000 -r 8414fea2a6fd test-data/archaea_relplot.scr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea_relplot.scr Wed Dec 28 18:52:14 2016 -0500 |
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| @@ -0,0 +1,137 @@ +pdf("/tmp/tmp5yxSuG/files/000/dataset_2.dat",width=12,height=4,version="1.4") + +rel <- read.table("mlocarna_results/results/result.bmreliability"); +seqrel <- rel[[2]] +strrel <- rel[[3]] + +if ("" != "") { + seq <- "" + seq <- strsplit(seq,split="") + tab <- unlist(seq)!="-" + + seqrel<-seqrel[tab] + strrel<-strrel[tab] +} + +len<-length(seqrel) + +if (0) { + seqrel<-seqrel[len:1] + strrel<-strrel[len:1] +} + + + +if (1) { + seqrel <- seqrel/1.0 +} + + +totalrel <- seqrel+strrel; + +anno_space<-0.075 + +maxy <- max(c(1,totalrel))+anno_space*(0+1); + + +firstpos <- 1 +lastpos <- 1+len-1 + +if (0) { + the_xlim <- c(lastpos,firstpos) +} else { + the_xlim <- c(firstpos,lastpos) +} + +# set margin +# b, l, t, r +par(mar=c(6,2.5,1,1)) + +# open plot (and draw threshold) +plot(c(0),c(0),type="l", + xlab="",ylab="", + xlim=the_xlim,ylim=c(0,maxy), + yaxp=c(0,1,2)) + +## title inside of plot +legend("topleft","",bty="n") + + +# total reliability +polygon(c(firstpos,firstpos:lastpos,lastpos),c(0,totalrel,0),col=rgb(0.8,0.8,0.9,0.5),lwd=2,border=FALSE) +lines(firstpos:lastpos,totalrel,col="blue",lwd=2) + +# plot structure reliability +polygon(c(firstpos,firstpos:lastpos,lastpos),c(0,strrel,0),col=rgb(0.3,0.3,0.5,0.8),lwd=1,border=FALSE) + + +## draw other signals +signals<-c(); +signal_sizes<-c(); + +signal_starts <- 1:0 + +signal_starts[1]<-1; +if (0>1) { + for (i in 2:0) { + signal_starts[i]<-signal_starts[i-1]+signal_sizes[i-1]*2+1; + } +} + +colors <- c( + rgb(0.6,0.1,0.1,0.9), + rgb(0.6,0.6,0.1,0.9), + rgb(0.1,0.6,0.6,0.9), + rgb(0.6,0.1,0.6,0.9) +); +colors<-c(colors,colors); + +if (0>0) { + + for (i in 1:0) { + orientation <- signals[signal_starts[i]+signal_sizes[i]*2]; + sig_y <- maxy-i*anno_space; + + for (j in 0:(signal_sizes[i]-1)) { + + sig_x <- c(signals[signal_starts[i]+j*2],signals[signal_starts[i]+j*2+1]); + + ## draw arrows + if (orientation!=0) { + the_code <- 1+(orientation+1)/2; + arrows(sig_x[1],sig_y,sig_x[2],sig_y,lwd=4,col=colors[i],code=the_code,angle=20,length=0.15); + } else { + lines(sig_x,c(sig_y,sig_y),lwd=4,col=colors[i]); + } + } + } +} + +#draw inferred on-signal +hit_color <- rgb(0.1,0.6,0.1,0.9) + +if (0!=1) { + + on <- c(0,4,33,44,49); + off <- c(3,20,43,48,51); + + if (length(on)>0) { + for (i in 1:length(on)) { + lines(c(1+on[i],1+off[i]-1),c(maxy,maxy),lwd=7,col=hit_color); + } + } + + ### 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) + } +} + + +signal_names<-c(); + +if (length(signal_names)>0 || (0!=1)) { + legend("bottom",c("LocARNA",signal_names),lwd=7,col=c(hit_color,colors),horiz=TRUE,inset=-0.4); + # ,xpd=TRUE +} |
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| diff -r 000000000000 -r 8414fea2a6fd test-data/haca.snoRNA-default.stdout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-default.stdout Wed Dec 28 18:52:14 2016 -0500 |
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| @@ -0,0 +1,33 @@ +mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0 +Copyright Sebastian Will + +Compute pair probs ... +Compute pairwise alignments ... +Perform progressive alignment ... + + + +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGG +ACA30 UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGC +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUGGGUGAC--CCU +#A1 ............................................................ +#A2 ............................................................ + +ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG +ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG +ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG +ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA +#A1 ....AAAAAA.................................................. +#A2 ....123456.................................................. + +ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA +ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA +ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA +ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA +#A1 .............................BBB +#A2 .............................123 + +alifold .((((((((........((((.(((((((......))))))).))))......))..))) + ))).............((((((.....((.....((((((((((((.....))))))))) + )))......)).....)).))))......... (-61.69 = -33.85 + -27.84) |
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| diff -r 000000000000 -r 8414fea2a6fd test-data/haca.snoRNA.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA.fa Wed Dec 28 18:52:14 2016 -0500 |
| b |
| @@ -0,0 +1,21 @@ +>ACA59 +GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA +.............................................................xxxxxx...............................................................................xxx #S +.............................................................AAAAAA...............................................................................BBB #1 +.............................................................123456...............................................................................123 #2 + +>ACA7 +ACCUCCUGGGAUCGCAUCUGGAGAGUGCCUAGUAUUCUGCCAGCUUCGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA +...........................................................xxxxxx...................................................................xxx #S +...........................................................AAAAAA...................................................................BBB #1 +...........................................................123456...................................................................123 #2 +>ACA5 +UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAAGGCUGCCACAGAAACACUGUGACUCAUGGGCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA +..............................................................xxxxxx............................................................xxx #S +..............................................................AAAAAA............................................................BBB #1 +..............................................................123456............................................................123 #2 +>ACA30 +UGGCACUUUCACAGUUCCUUCCCCAGGCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACCCUUGAUUGUAUUCUUGCCCUGGGAUUAUACCAGUGGCAACUGUCACUCAAUGGGACA +..........................................................xxxxxx..........................................................xxx #S +..........................................................AAAAAA..........................................................BBB #1 +..........................................................123456..........................................................123 #2 |
| b |
| diff -r 000000000000 -r 8414fea2a6fd test-data/haca.snoRNA_anchor.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA_anchor.bed Wed Dec 28 18:52:14 2016 -0500 |
| b |
| @@ -0,0 +1,8 @@ +ACA59 61 67 ANANNA +ACA7 59 65 ANANNA +ACA5 62 68 ANANNA +ACA30 58 64 ANANNA +ACA59 146 149 ACA +ACA7 132 135 ACA +ACA5 128 131 ACA +ACA30 122 125 ACA |
| b |
| diff -r 000000000000 -r 8414fea2a6fd test-data/tRNA_2-1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2-1.fa Wed Dec 28 18:52:14 2016 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>D10744 +GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG |
| b |
| diff -r 000000000000 -r 8414fea2a6fd test-data/tRNA_2-2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2-2.fa Wed Dec 28 18:52:14 2016 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>AF008220 +GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA |
| b |
| diff -r 000000000000 -r 8414fea2a6fd test-data/tRNA_2.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.aln Wed Dec 28 18:52:14 2016 -0500 |
| b |
| @@ -0,0 +1,7 @@ +CLUSTAL W --- LocARNA 1.9.0 --- Score: 2875 + +D10744 GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGG +AF008220 GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCG + +D10744 UGAGUUCGAAUCUCACAUUUUCCG +AF008220 GCGGUUCGAGCCCGUCAUCCUCCA |
| b |
| diff -r 000000000000 -r 8414fea2a6fd test-data/tRNA_5.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_5.fa Wed Dec 28 18:52:14 2016 -0500 |
| b |
| @@ -0,0 +1,10 @@ +>D10744 +GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG +>AF008220 +GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA +>Z11880 +GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG +>X02172 +GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA +>M68929 +GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC |