Mercurial > repos > rnateam > locarna_pairwise_p
changeset 0:c5f150d2686f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/locarna_pairwise_p.xml Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,212 @@ +<tool id="locarna_pairwise_p" name="LocARNA Pairwise Probability Aligner" version="@VERSION@.0"> + <description> + Partition Function and Probabilities from Pairwise Simultaneous Alignment and Folding of RNAs (LocARNA-P) + </description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements" /> + + <expand macro="stdio" /> + + <expand macro="version" /> + + <command><![CDATA[ + locarna_p + + '$inputA' + '$inputB' + + --width 60 + + @SCORING_ARGS@ + + @FOLDING_ARGS@ + + @HEURISTIC_ARGS@ + #if float($Heuristics.pf_scale) != 1.0 + --pf-scale $Heuristics.pf_scale + #end if + + ## -------------------- other parameters + + #if $Constraints.maxBPspan != -1 + --maxBPspan $Constraints.maxBPspan + #end if + + $Constraints.ignore_constraints + + ## -------------------- probability parameters + $Probabilities.include_am_in_bm + #if float($Probabilities.min_bm_prob) != 0.0005 + --min-bm-prob $Probabilities.min_bm_prob + #end if + #if float($Probabilities.min_am_prob) != 0.0005 + --min-am-prob $Probabilities.min_am_prob + #end if + + ## -------------------- output + + #if not $arc_match_probs is None + --write-arcmatch-probs=$arc_match_probs + #end if + + #if not $base_match_probs is None + --write-basematch-probs=$base_match_probs + #end if + + @STDOUT_ARGS@ + + ]]></command> + + <inputs> + <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" + help="First sequence in fasta, clustal, dp_ps, or PP2.0 format" + /> + <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" + help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format" + /> + + <param name="outputs" type="select" display="checkboxes" multiple="True" + label="Output options"> + <option value="base_match_probs" selected="True"> + Output base match probabilities</option> + <option value="arc_match_probs" selected="True"> + Output arc match probabilities</option> + </param> + + <param name="stdout_verbosity" type="select" label="Standard output verbosity"> + <option value="--quiet">Don't report standard + output</option> + <option value="">Non verbose</option> + <option value="--verbose">Verbose</option> + </param> + + <section name="Probabilities" title="Probability parameters"> + <param name="include_am_in_bm" argument="include-am-in-bm" + type="boolean" + truevalue="--include-am-in-bm" falsevalue="" + label="Include arc match cases in computation of base match probabilities" /> + <param name="min_bm_prob" argument="min-bm-prob" + type="float" + value="0.0005" min="0.0" max="1.0" + label="Minimal base match probability" + /> + <param name="min_am_prob" argument="min-am-prob" + type="float" + value="0.0005" min="0.0" max="1.0" + label="Minimal arc match probability" + /> + </section> + + <section name="Scoring" title="Scoring parameters"> + <expand macro="common_scoring_parameters" /> + </section> + + <section name="Folding" title="RNA folding parameters"> + <expand macro="common_folding_parameters" /> + <expand macro="alifold_consensus_parameter" /> + <param name="consensus_structure" type="select" label="Consensus structure type" + help="Type of consensus structures written to screen and stockholm output" + > + <!-- <option value="mea">mea</option>--> + <option value="none">none</option> + <option value="alifold">alifold</option> + </param> + </section> + + <section name="Heuristics" title="Heuristic parameters"> + <expand macro="common_heuristic_parameters" /> + <expand macro="max_diff_parameters_aln" /> + <param name="pf_scale" argument="pf-scale" + type="float" value="1.0" + label="Scaling of the partition function." + help="Use (only) if standard scaling overflows." /> + </section> + + <section name="Constraints" title="Constraint parameters"> + <expand macro="common_constraint_parameters" /> + </section> + + </inputs> + + <outputs> + <expand macro="standard_outupt" /> + <data format="table" name="base_match_probs" label="${tool.name} base match probabilties on ${on_string}"> + <filter>'base_match_probs' in outputs</filter> + </data> + <data format="table" name="arc_match_probs" label="${tool.name} arc match probabilties on ${on_string}"> + <filter>'arc_match_probs' in outputs</filter> + </data> + </outputs> + + <tests> + <test> + <param name="inputA" value="tRNA_2-1.fa" /> + <param name="inputB" value="tRNA_2-2.fa" /> + <param name="outputs" value="arc_match_probs,base_match_probs"/> + <param name="min_bm_prob" value="0.01" /> + <param name="min_am_prob" value="0.01" /> + <output name="base_match_probs" file="tRNA_2.bmprobs" /> + <output name="arc_match_probs" file="tRNA_2.amprobs" /> + </test> + </tests> + + <help><![CDATA[ **LocARNA -- Pairwise probability alignment of RNAs** + +Pairwise probability alignment tool of the LocARNA suite. This tool +computes base and arc match probabilities from simultaneous RNA +folding and alignment. It can be adapted to specific needs by a broad +range of parameters: + +* *scoring* of the alignment, e.g. influencing the cost of + insertions/deletions and the weight of sequence vs. structure + similarity. + +* *RNA folding*, which control the secondary RNA structure prediciton. + +* *heuristics*, which trade alignment accuracy vs. computation + speed. The huge complexity of simultaneous alignment and folding + generally requires some heuristics for reasonable computation times. + Some alignment instances and alignment modes will require relaxation + of the default heuristics; in particular, local, constrained, and free end gap + alignment, will often require turning off the "maximal difference for + alignment traces" heuristic. + +* *constraints*, which can be applied to include prior knowledge to + improve the quality of results and/or speed of computation. + +**Input.** + +Input consists of two sequences or alignments, which are specified in +fasta, clustal, stockholm, or LocARNA pp format. + +Optionally, one can specify structure and anchor constraints in these +input files. + +**Output.** + +The tool writes two tables of base match and arc match probabilities, respectively. Rows +in the base match probabilities table consist of + + i j p + +where p is the probability of matching position i in the first sequence to position j in the second sequence. + +For arc matchs, the table contains rows + + i j k l p + +where p is the probability of matching the base pair (i,j) of sequence one to (k,l) of sequence two. + +Moreover, the partition function and further information can be written to standard out. + +For more information, see +.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/ + ]]></help> + + <expand macro="citations" /> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,322 @@ +<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> + + <token name="@SCORING_ARGS@"> + ## -------------------- scoring parameters + --indel $Scoring.indel + --indel-opening $Scoring.indel_opening + --struct-weight $Scoring.struct_weight + --tau $Scoring.tau + + #if str($Scoring.sequence_score.sequence_score_selector) == "match" + --match $Scoring.sequence_score.match + --mismatch $Scoring.sequence_score.mismatch + #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum" + --use-ribosum true + #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit" + --ribofit true + #end if + </token> + + <token name="@FOLDING_ARGS@"> + ## -------------------- folding parameters + #if float($Folding.rnafold_temperature) != 37.0 + --rnafold-temperature $Folding.rnafold_temperature + #end if + </token> + + <token name="@HEURISTIC_ARGS@"> + ## -------------------- heuristic parameters + -p $Heuristics.min_prob + + #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off" + --max-diff -1 + #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff" + --max-diff $Heuristics.max_diff_mode.max_diff + #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am" + --max-diff -1 + --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am + #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln" + --max-diff $Heuristics.max_diff_mode.max_diff + --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln' + $Heuristics.max_diff_mode.max_diff_relax + #end if + + --max-diff-am $Heuristics.max_diff_am + + #if float($Heuristics.max_bps_length_ratio) > 0.0 + --max-bps-length-ratio $Heuristics.max_bps_length_ratio + #end if + </token> + + <token name="@CONSTRAINT_ARGS@"> + ## -------------------- constraint parameters + $Constraints.lonely_pairs + + #if $Constraints.maxBPspan != -1 + --maxBPspan $Constraints.maxBPspan + #end if + + $Constraints.ignore_constraints + </token> + + <token name="@STDOUT_ARGS@"> + $stdout_verbosity + + #if str($stdout_verbosity) != "--quiet": + > '$stdout' + #end if + </token> + + <xml name="max_diff_parameters_selector"> + <param name="max_diff_mode_selector" type="select" + label="Restrict alignable positions by maximum difference" + help="(max-diff*)"> + <option value="off">Off</option> + <option value="max-diff" selected="True">Maximal difference of aligned positions</option> + <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option> + <yield /> + </param> + </xml> + + <xml name="max_diff_parameters_standard_cases"> + <when value="off" /> + <when value="max-diff"> + <param name="max_diff" argument="max-diff" type="integer" + value="60" min="-1" max="300" + label="Maximal difference of aligned positions" /> + </when> + <when value="max-diff-at-am"> + <param name="max_diff_at_am" argument="max-diff-at-am" type="integer" + value="60" min="-1" max="300" + label="Maximal difference of aligned positions, + only at arc match positions" /> + </when> + </xml> + + <xml name="max_diff_parameters"> + <conditional name="max_diff_mode"> + <expand macro="max_diff_parameters_selector" /> + <expand macro="max_diff_parameters_standard_cases" /> + </conditional> + </xml> + + <xml name="max_diff_parameters_aln"> + <conditional name="max_diff_mode"> + <expand macro="max_diff_parameters_selector"> + <option value="max-diff-aln">Maximal difference to a reference alignment</option> + </expand> + <expand macro="max_diff_parameters_standard_cases" /> + <when value="max-diff-aln"> + <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal" + label="Reference alignment" + /> + <param name="max_diff" argument="max-diff" type="integer" + value="60" min="-1" max="300" + label="Maximal difference of aligned positions" /> + <param name="max_diff_relax" argument="max-diff-relax" type="boolean" + truevalue="--max-diff-relax" falsevalue="" + checked="False" + label="Relax deviation constraints in multiple + aligmnent." + /> + </when> + </conditional> + </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_bps_length_ratio" argument="max-bps-length-ratio" + type="float" value="0.0" min="0.0" max="10.0" + label="Maximal ratio 'number of considered base pairs' by + 'sequence length' (default: 0.0 = no effect)" /> + </xml> + + <xml name="in_loop_ratio_parameters"> + <param name="max_uil_length_ratio" argument="max-uil-length-ratio" + type="float" value="0.0" min="0.0" max="10.0" + label="Maximal ratio 'number considered unpaired bases in loops' by + 'sequence length' (default: 0.0; no effect)" /> + + <param name="max_bpil_length_ratio" argument="max-bpil-length-ratio" + type="float" value="0.0" min="0.0" max="10.0" + label="Maximal ratio 'number of considered base pairs in loops' + by 'sequence length' (default: 0.0; no effect)" /> + </xml> + + <xml name="exparnap_in_loop_parameters"> + <param name="prob_unpaired_in_loop_threshold" + argument="prob_unpaired_in_loop_threshold" + type="float" value="0.01" min="0.0" max="1.0" + label="Probability threshold for unpaired bases in loops" /> + <param name="prob_basepair_in_loop_threshold" + argument="prob_basepair_in_loop_threshold" + type="float" value="0.01" min="0.0" max="1.0" + label="Probability threshold for base pairs in loops" /> + </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="common_constraint_parameters"> + <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="standard_outupt"> + <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> + <filter>stdout_verbosity != '--quiet'</filter> + </data> + </xml> + + <xml name="mlocarna_outputs"> + <expand macro="standard_outupt" /> + <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln" + label="${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> + <citation type="doi">10.1093/bioinformatics/btv185</citation> + <citation type="doi">10.1186/s12859-014-0404-0</citation> + </citations> + </xml> + + + +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-default.stdout Fri Jan 13 16:48:31 2017 -0500 @@ -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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-probabilistic.aln Fri Jan 13 16:48:31 2017 -0500 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-ref.aln Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,9 @@ +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-ref_result.aln Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,11 @@ +CLUSTAL W --- LocARNA 1.9.0 + + + +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-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea.fa Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,14 @@ +>fruA +CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG +>fdhA +CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG +>vhuU +AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU +>hdrA +GGCACCACUCGAAGGCUAAGCCAAAGUGGUGCU +>vhuD +GUUCUCUCGGGAACCCGUCAAGGGACCGAGAGAAC +>selD +UUACGAUGUGCCGAACCCUUUAAGGGAGGCACAUCGAAA +>fwdB +AUGUUGGAGGGGAACCCGUAAGGGACCCUCCAAGAU
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea_relplot.scr Fri Jan 13 16:48:31 2017 -0500 @@ -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 +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ferritin_human.fa Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,2 @@ +> human ferritin +CCAGACGUUCUUCGCCGAGAGUCGUCGGGGUUUCCUGCUUCAACAGUGCUUGGACGGAACCCGGCGCUCGUUCCCCACCCCGGCCGGCCGCCCAUAGCCAGCCCUCCGUCACCUCUUCACCGCACCCUCGGACUGCCCCAAGGCCCCCGCCGCCGCUCCAGCGCCGCGCAGCCACCGCCGCCGCCGCCGCCUCUCCUUAGUCGCCGCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ferritin_mouse.fa Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,2 @@ +> mouse ferritin +CAGACGUUCUCGCCCAGAGUCGCCGCGGUUUCCUGCUUCAACAGUGCUUGAACGGAACCCGGUGCUCGACCCCUCCGACCCCCGCCGGCCGCUUCGAGCCUGAGCCCUUUGCAACUUCGUCGUUCCGCCGCUCCAGCGUCGCCACCGCGCCUCGCCCCGCCGCCACC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-1.aln Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,5 @@ +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA +ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGGCAACUGUCACUCAAUGGGACA +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA +#A1 ................................................................AAAAAA...................................................................BBB +#A2 ................................................................123456...................................................................123
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-2.aln Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,3 @@ +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA +#A1 .............................................................AAAAAA...............................................................................BBB +#A2 .............................................................123456...............................................................................123
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-c.aln Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,22 @@ +CLUSTAL W --- LocARNA 1.9.0 + +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG +ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-default.stdout Fri Jan 13 16:48:31 2017 -0500 @@ -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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA.aln Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,16 @@ +CLUSTAL W --- LocARNA 1.9.0 + +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG +ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU + +ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG +ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG +ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG +ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA + +ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA +ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA +ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA +ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA.fa Fri Jan 13 16:48:31 2017 -0500 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA_anchor.bed Fri Jan 13 16:48:31 2017 -0500 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2-1.fa Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,2 @@ +>D10744 +GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2-2.fa Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,2 @@ +>AF008220 +GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.aln Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,7 @@ +CLUSTAL W --- LocARNA 1.9.0 --- Score: 2875 + +D10744 GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGG +AF008220 GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCG + +D10744 UGAGUUCGAAUCUCACAUUUUCCG +AF008220 GCGGUUCGAGCCCGUCAUCCUCCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.amprobs Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,108 @@ +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 48 0.640114 +23 58 22 48 0.121828 +21 60 19 51 0.071982 +20 60 18 51 0.512044 +18 63 16 53 0.410891 +17 56 18 51 0.0172516 +17 64 15 54 0.505795 +17 65 15 55 0.0373483 +16 57 17 52 0.025034 +16 65 14 55 0.456198 +15 58 16 53 0.0181784 +15 67 13 57 0.463917 +14 19 13 18 0.0159303 +14 59 15 54 0.0239939 +14 68 12 58 0.536735 +13 60 14 55 0.0191717 +12 16 11 15 0.0116456 +12 21 13 22 0.0351601 +11 17 10 16 0.0359852 +11 22 12 23 0.0512024 +11 69 11 59 0.534042 +10 14 11 15 0.0213866 +10 23 11 24 0.0659783 +10 70 10 60 0.389747 +10 72 10 62 0.247777 +9 18 9 17 0.0444132 +9 73 8 63 0.0119982 +8 19 8 18 0.0421045 +8 74 9 64 0.0471423 +8 76 8 66 0.0271918 +7 76 7 66 0.821868 +6 77 6 67 0.869036 +5 78 5 68 0.962952 +4 79 4 69 0.963261 +3 80 3 70 0.872876 +2 81 2 71 0.752745 +1 82 1 72 0.752744
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.bmprobs Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,172 @@ +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 36 0.0122707 +44 38 0.0248855 +44 39 0.0183418 +44 45 0.0336616 +45 36 0.0423026 +45 39 0.0300877 +45 40 0.013096 +45 46 0.0286025 +46 37 0.0702926 +46 38 0.0130327 +46 40 0.0113529 +47 38 0.119444 +48 39 0.0264015 +48 40 0.0166626 +49 39 0.0133557 +49 40 0.309884 +50 41 0.109972 +51 41 0.0223073 +51 42 0.0365047 +52 43 0.0228365 +53 43 0.02009 +53 44 0.683193 +54 44 0.121387 +54 45 0.035521 +55 46 0.681952 +56 46 0.0343041 +56 47 0.536468 +56 48 0.0112514 +57 47 0.0531432 +57 48 0.0486503 +58 48 0.0521922 +58 49 0.632028 +59 49 0.117956 +59 50 0.628217 +60 50 0.0252284 +60 51 0.104879 +61 51 0.0460576 +61 52 0.573747 +62 52 0.165836 +62 53 0.0472354 +63 53 0.382375 +64 54 0.2672 +65 55 0.320519 +66 56 0.818192 +67 57 0.355528 +68 58 0.282881 +69 59 0.27801 +70 60 0.464549 +71 61 0.857675 +72 62 0.497193 +73 63 0.7313 +74 64 0.734773 +75 65 0.881053 +76 66 0.139472 +77 67 0.130956 +78 68 0.0370464 +79 69 0.0367371 +80 70 0.127122 +81 71 0.247251 +82 72 0.247251 +83 73 0.999955
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.epms Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,4 @@ +epm_id score structure positions +0 3583 ((())) 1:4 2:5 3:6 80:67 81:68 82:69 +1 3593 ((())) 1:1 2:2 3:3 80:70 81:71 82:72 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_5.fa Fri Jan 13 16:48:31 2017 -0500 @@ -0,0 +1,10 @@ +>D10744 +GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG +>AF008220 +GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA +>Z11880 +GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG +>X02172 +GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA +>M68929 +GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC