| Next changeset 1:8723e3f8e422 (2017-01-21) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0 |
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added:
locarna.tar.bz2 locarna_exparnap.xml macros.xml test-data/archaea-default.stdout test-data/archaea-probabilistic.aln test-data/archaea-ref.aln test-data/archaea-ref_result.aln test-data/archaea.fa test-data/archaea.tar.gz test-data/archaea_relplot.scr test-data/ferritin_human.fa test-data/ferritin_mouse.fa test-data/haca.snoRNA-1.aln test-data/haca.snoRNA-2.aln test-data/haca.snoRNA-c.aln test-data/haca.snoRNA-default.stdout test-data/haca.snoRNA.aln 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_2.amprobs test-data/tRNA_2.bmprobs test-data/tRNA_2.epms test-data/tRNA_5.fa |
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| diff -r 000000000000 -r e91e4f48875e locarna_exparnap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/locarna_exparnap.xml Fri Jan 13 16:49:16 2017 -0500 |
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| b'@@ -0,0 +1,274 @@\n+<tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@VERSION@.0">\n+ <description>\n+ Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)\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+ exparna_p\n+\n+ \'$inputA\'\n+ \'$inputB\'\n+\n+ ## -------------------- scoring parameters\n+ #\n+ $Scoring.no_stacking\n+ --alpha_1 $Scoring.alpha_1\n+ --alpha_2 $Scoring.alpha_2\n+ --alpha_3 $Scoring.alpha_3\n+ --struct-mismatch-score $Scoring.struct_mismatch_score\n+\n+ @HEURISTIC_ARGS@\n+ --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold\n+ --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold\n+\n+ @CONSTRAINT_ARGS@\n+\n+ ## -------------------- other parameters\n+ #\n+ #if str($Other.subopt.subopt_selector) == "on"\n+ --diff-to-opt-score $Other.subopt.diff_to_opt_score\n+ --number-of-EPMs $Other.subopt.number_of_EPMs\n+ #end if\n+\n+ --min-score $Other.min_score\n+\n+ $Other.inexact_struct_match\n+ $Other.add_filter\n+ $Other.no_chaining\n+ --out-min-prob $Other.out_min_prob\n+\n+ ## -------------------- output\n+\n+ #if \'postscript\' in str($outputs).split(",")\n+ --output-ps\n+ --PS_fileA \'$ps_fileA\'\n+ --PS_fileB \'$ps_fileB\'\n+ #end if\n+\n+ #if \'anchors-fasta\' in str($outputs).split(",")\n+ --output-locarna \'$anchors_fasta\'\n+ #end if\n+\n+ #if \'anchors-pp\' in str($outputs).split(",")\n+ --output-anchor-pp anchors_pp\n+ #end if\n+\n+ #if \'clustal\' in str($outputs).split(",")\n+ --output-clustal \'$clustal\'\n+ #end if\n+\n+ #if \'epm_list\' in str($outputs).split(",")\n+ --output-epm-list \'$epm_list\'\n+ #end if\n+\n+ #if \'chained_epm_list\' in str($outputs).split(",")\n+ --output-chained-epm-list \'$chained_epm_list\'\n+ #end if\n+\n+ @STDOUT_ARGS@\n+\n+ ## -------------------- post processing\n+\n+ #if \'anchors-pp\' in str($outputs).split(",")\n+ && mv anchors_pp_A.pp \'$anchors_ppA\'\n+ && mv anchors_pp_B.pp \'$anchors_ppB\'\n+ #end if\n+\n+ ]]></command>\n+\n+ <inputs>\n+ <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"\n+ help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"\n+ />\n+ <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"\n+ help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"\n+ />\n+\n+ <param name="outputs" type="select" display="checkboxes" multiple="True"\n+ label="Output options">\n+ <option value="postscript" selected="False">Best EPM chain\n+ as colored postscript</option>\n+ <option value="anchors-fasta" selected="False">Fasta with anchor\n+ constraints from chaining</option>\n+ <option value="anchors-pp" selected="False">LocARNA PP\n+ files merging input PPs and anchor constraints from\n+ chaining</option>\n+ <option value="clustal" selected="False">Chain as\n+ alignment in Clustal format</option>\n+ <option value="epm_list" selected="False">List of the found EPMs</option>\n+ <option value="chained_epm_list" selected="False">List of\n+ EPMs in the best chain</option>\n+ </param>\n+\n+ <param name="stdout_verbosity" type="select" label="Standard output verbosity">\n+ <option value="--quiet">Don\'t report standard\n+ output</option>\n+ <option value="" selected="True">Non verbose</option>\n+ <option value="--verbose">Verbose</option>\n+ </param>\n+\n+ <section name="Scoring" title="Scoring parameters">\n+ <param argument="alpha_1"\n+ type="integer" value="'..b'er of EPMs" />\n+ </when>\n+ </conditional>\n+\n+ <param name="min_score" argument="min-score"\n+ type="integer" value="30" min="0" max="1000"\n+ label="Minimum score of EPM" />\n+\n+ <param name="inexact_struct_match" argument="inexact-struct-match" type="boolean"\n+ truevalue="--inexact-struct-match" falsevalue=""\n+ label="Allow inexact structure matches"/>\n+\n+ <param name="add_filter" argument="add-filter" type="boolean"\n+ truevalue="--add-filter" falsevalue="" checked="False"\n+ label="Apply an additional filter to enumerate only\n+ EPMs that are maximally extended (only inexact)"/>\n+\n+ <param name="no_chaining" argument="no-chaining" type="boolean"\n+ truevalue="" falsevalue="--no-chaining" checked="True"\n+ label="Find best overall chain by chaining"/>\n+\n+ <param name="out_min_prob" argument="out-min-prob"\n+ type="float" value="0.0005" min="0" max="1"\n+ label="Minimal probability in output (min-prob overrides if smaller)"/>\n+\n+ </section>\n+ </inputs>\n+\n+ <outputs>\n+ <expand macro="standard_outupt" />\n+ <data format="ps" name="ps_fileA"\n+ label="${tool.name} chain in RNA 1 (postscript) on ${on_string}">\n+ <filter>\'postscript\' in outputs</filter>\n+ </data>\n+ <data format="ps" name="ps_fileB"\n+ label="${tool.name} chain in RNA 2 (postscript) on ${on_string}">\n+ <filter>\'postscript\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="anchors_fasta"\n+ label="${tool.name} anchor constraints from chain (fasta) on ${on_string}">\n+ <filter>\'anchors-fasta\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="anchors_ppA"\n+ label="${tool.name} anchors for RNA 1 (pp) on ${on_string}">\n+ <filter>\'anchors-pp\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="anchors_ppB"\n+ label="${tool.name} anchors for RNA 2 (pp) on ${on_string}">\n+ <filter>\'anchors-pp\' in outputs</filter>\n+ </data>\n+ <data format="clustal" name="clustal"\n+ label="${tool.name} chain as alignment (clustal) on ${on_string}">\n+ <filter>\'clustal\' in outputs</filter>\n+ </data>\n+ <data format="tabular" name="epm_list"\n+ label="${tool.name} list of epms on ${on_string}">\n+ <filter>\'epm_list\' in outputs</filter>\n+ </data>\n+ <data format="tabular" name="chained_epm_list"\n+ label="${tool.name} list of epms in chain on ${on_string}">\n+ <filter>\'chained_epm_list\' in outputs</filter>\n+ </data>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="inputA" value="tRNA_2-1.fa" />\n+ <param name="inputB" value="tRNA_2-2.fa" />\n+ <param name="outputs" value="epm_list" />\n+ <output name="epm_list" file="tRNA_2.epms" />\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[ **LocARNA -- Pairwise matching and folding of RNAs (ExpARNA-P)**\n+\n+Pairwise matching and folding tool of the LocARNA suite (ExpARNA-P).\n+\n+**Input.**\n+\n+Input consists of two sequences or alignments, which are specified in\n+fasta, clustal, stockholm, or LocARNA pp format.\n+\n+Optionally, one can specify structure and anchor constraints in these\n+input files.b\n+\n+**Output.**\n+\n+The program enumerates exactly matching local substructures (exact\n+pattern matches = EPMs) and optionally chains them. It returns lists\n+of chained and unchained matches, visualizations of the results and\n+anchor constraints for alignment.\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 e91e4f48875e macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jan 13 16:49:16 2017 -0500 |
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| b'@@ -0,0 +1,322 @@\n+<macros>\n+ <token name="@VERSION@">1.9.0</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">locarna</requirement>\n+ </requirements>\n+ </xml>\n+\n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ </xml>\n+\n+ <xml name="version">\n+ <version_command>\n+ <![CDATA[\n+ mlocarna --version\n+ ]]>\n+ </version_command>\n+ </xml>\n+\n+ <xml name="bed_anchors">\n+ <conditional name="bed_anchors">\n+ <param name="bed_anchors_selector" type="select" label="Anchor constraints"\n+ help="Anchor constraints in bed format specify positions of\n+ named anchor regions per sequence. The sequence names\n+ (\'contig\' names have to correspond to the fasta input\n+ sequence names. Anchor names must be unique per sequence\n+ and regions of the same name for different sequences\n+ must have the same length. This constrains the alignment\n+ to align all regions of the same name.">\n+ <option value="no">Don\'t load anchor constraints from\n+ bed file</option>\n+ <option value="yes">Load anchor constraints from bed\n+ file</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <param name="bed_anchors_file" type="data" format="tabular" \n+ label="Anchor constraint specification in bed format"\n+ />\n+ </when>\n+ </conditional>\n+ </xml>\n+ \n+ <xml name="common_scoring_parameters">\n+ <param name="struct_weight" argument="struct-weight"\n+ label="Structure weight" type="integer" \n+ value="200" min="0" max="800" />\n+ <param name="indel_opening" argument="indel-opening"\n+ label="Indel opening score" type="integer"\n+ value="-500" max="0" min="-1500" />\n+ <param argument="indel" label="Indel score" type="integer" \n+ value="-350" min="-1000" max="0" />\n+ <param argument="tau" type="integer" value="50"\n+ min="0" max="200"\n+ label="Sequence contribution at structure match in percent"/> \n+\n+ <conditional name="sequence_score">\n+ <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">\n+ <option value="ribofit">Use ribofit</option>\n+ <option value="ribosum">Use RIBOSUM85_60</option>\n+ <option value="match">Simple match/mismatch costs</option>\n+ </param>\n+ <when value="ribofit" />\n+ <when value="ribosum" />\n+ <when value="match">\n+ <param name="match" type="integer" value="50" \n+ min="0" max="400"\n+ label="Match score" />\n+ <param name="mismatch" type="integer" value="0" \n+ min="-400" max="0"\n+ label="Mismatch score" />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="plfolding_parameters">\n+ <param name="plfold_span" argument="--plfold-span" \n+ type="integer" value="150" min="-1" max="400" \n+ label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />\n+ \n+ <param name="plfold_winsize" argument="--plfold-winsize"\n+ type="integer" value="300" min="-1" max="800" \n+ label="Window size for local folding" />\n+ </xml>\n+ \n+ <xml name="common_folding_parameters">\n+ <param name="rnafold_temperature" argument="rnafold-temperature"\n+ type="float" value="37.0" min="10" max="50"\n+ '..b'tio \'number considered unpaired bases in loops\' by\n+ \'sequence length\' (default: 0.0; no effect)" />\n+ \n+ <param name="max_bpil_length_ratio" argument="max-bpil-length-ratio"\n+ type="float" value="0.0" min="0.0" max="10.0" \n+ label="Maximal ratio \'number of considered base pairs in loops\'\n+ by \'sequence length\' (default: 0.0; no effect)" />\n+ </xml>\n+\n+ <xml name="exparnap_in_loop_parameters">\n+ <param name="prob_unpaired_in_loop_threshold"\n+ argument="prob_unpaired_in_loop_threshold"\n+ type="float" value="0.01" min="0.0" max="1.0" \n+ label="Probability threshold for unpaired bases in loops" />\n+ <param name="prob_basepair_in_loop_threshold"\n+ argument="prob_basepair_in_loop_threshold"\n+ type="float" value="0.01" min="0.0" max="1.0" \n+ label="Probability threshold for base pairs in loops" />\n+ </xml>\n+\n+ <xml name="alifold_consensus_parameter">\n+ <param name="alifold_consensus_dp" argument="alifold-consensus-dp" \n+ type="boolean" checked="False" \n+ truevalue="--alifold-consensus-dp" falsevalue=""\n+ label="Compute consensus dot plot by alifold" />\n+ </xml>\n+ \n+ <xml name="common_constraint_parameters">\n+ <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" \n+ checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />\n+ <param name="maxBPspan" argument="--maxBPspan" \n+ type="integer" value="-1" min="-1" max="400" \n+ label="Maximum basepair span by RNAfold; -1 for arbitrary span" />\n+ <param name="ignore_constraints" argument="ignore-constraints"\n+ type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""\n+ help="Ignore all anchor and structure constraints given\n+ in the fasta(-ish) input." />\n+ </xml>\n+\n+ <xml name="standard_outupt">\n+ <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">\n+ <filter>stdout_verbosity != \'--quiet\'</filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="mlocarna_outputs">\n+ <expand macro="standard_outupt" />\n+ <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"\n+ label="${tool.name} alignment (annotated clustal) on ${on_string}">\n+ <filter>\'clustal\' in outputs</filter>\n+ </data>\n+ <data format="clustal" name="clustal_strict" \n+ from_work_dir="mlocarna_results/results/result.strict-aln"\n+ label="${tool.name} alignment (clustal) on ${on_string}">\n+ <filter>\'clustal_strict\' in outputs</filter>\n+ </data>\n+ <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"\n+ label="${tool.name} alignment (stockholm) on ${on_string}">\n+ <filter>\'stockholm\' in outputs</filter>\n+ </data>\n+ <data format="txt" name="pp"\n+ from_work_dir="mlocarna_results/results/result.pp"\n+ label="${tool.name} alignment (PP 2.0) on ${on_string}">\n+ <filter>\'pp\' in outputs</filter>\n+ </data>\n+ <data format="tar.gz" name="mlocarna_results_tgz"\n+ label="${tool.name} results archive on ${on_string}">\n+ <filter>\'mlocarna_results\' in outputs</filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation\n+ type="doi">10.1371/journal.pcbi.0030065</citation>\n+ <citation type="doi">10.1261/rna.029041.111</citation>\n+ <citation type="doi">10.1093/bioinformatics/btv185</citation>\n+ <citation type="doi">10.1186/s12859-014-0404-0</citation>\n+ </citations>\n+ </xml>\n+\n+\n+\n+</macros>\n+\n' |
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| diff -r 000000000000 -r e91e4f48875e test-data/archaea-default.stdout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-default.stdout Fri Jan 13 16:49:16 2017 -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 e91e4f48875e test-data/archaea-probabilistic.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-probabilistic.aln Fri Jan 13 16:49:16 2017 -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 e91e4f48875e test-data/archaea-ref.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea-ref.aln Fri Jan 13 16:49:16 2017 -0500 |
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| @@ -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 |
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| @@ -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- |
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| diff -r 000000000000 -r e91e4f48875e test-data/archaea.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea.fa Fri Jan 13 16:49:16 2017 -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 e91e4f48875e test-data/archaea_relplot.scr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/archaea_relplot.scr Fri Jan 13 16:49:16 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 +} |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/ferritin_human.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ferritin_human.fa Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +> human ferritin +CCAGACGUUCUUCGCCGAGAGUCGUCGGGGUUUCCUGCUUCAACAGUGCUUGGACGGAACCCGGCGCUCGUUCCCCACCCCGGCCGGCCGCCCAUAGCCAGCCCUCCGUCACCUCUUCACCGCACCCUCGGACUGCCCCAAGGCCCCCGCCGCCGCUCCAGCGCCGCGCAGCCACCGCCGCCGCCGCCGCCUCUCCUUAGUCGCCGCC |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/ferritin_mouse.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ferritin_mouse.fa Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +> mouse ferritin +CAGACGUUCUCGCCCAGAGUCGCCGCGGUUUCCUGCUUCAACAGUGCUUGAACGGAACCCGGUGCUCGACCCCUCCGACCCCCGCCGGCCGCUUCGAGCCUGAGCCCUUUGCAACUUCGUCGUUCCGCCGCUCCAGCGUCGCCACCGCGCCUCGCCCCGCCGCCACC |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/haca.snoRNA-1.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-1.aln Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/haca.snoRNA-2.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-2.aln Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -0,0 +1,3 @@ +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA +#A1 .............................................................AAAAAA...............................................................................BBB +#A2 .............................................................123456...............................................................................123 |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/haca.snoRNA-c.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-c.aln Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/haca.snoRNA-default.stdout --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA-default.stdout Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -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) |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/haca.snoRNA.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA.aln Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/haca.snoRNA.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA.fa Fri Jan 13 16:49:16 2017 -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 e91e4f48875e test-data/haca.snoRNA_anchor.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/haca.snoRNA_anchor.bed Fri Jan 13 16:49:16 2017 -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 e91e4f48875e test-data/tRNA_2-1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2-1.fa Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>D10744 +GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/tRNA_2-2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2-2.fa Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>AF008220 +GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/tRNA_2.aln --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.aln Fri Jan 13 16:49:16 2017 -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 e91e4f48875e test-data/tRNA_2.amprobs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.amprobs Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/tRNA_2.bmprobs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.bmprobs Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/tRNA_2.epms --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_2.epms Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -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 + |
| b |
| diff -r 000000000000 -r e91e4f48875e test-data/tRNA_5.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tRNA_5.fa Fri Jan 13 16:49:16 2017 -0500 |
| b |
| @@ -0,0 +1,10 @@ +>D10744 +GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG +>AF008220 +GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA +>Z11880 +GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG +>X02172 +GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA +>M68929 +GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC |