Mercurial > repos > rnateam > graphclust_postprocessing
changeset 17:f93c868203cc draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92
| author | rnateam |
|---|---|
| date | Sat, 27 Oct 2018 13:23:06 -0400 |
| parents | 79df97a1bc0f |
| children | |
| files | evaluation.py glob_report.xml glob_report.xml.orig test-data/1.cluster.all test-data/1.cluster.all.fa test-data/1.cluster.top5.alirna.ps test-data/1.cluster.top5.aln.ps test-data/1.cluster.top5.result.aln_1.R2R.sto.pdf test-data/2.cluster.all test-data/2.cluster.top5.alirna.ps test-data/2.cluster.top5.aln.ps test-data/RESULTS.zip test-data/combined_cm_out test-data/evaluation1.txt |
| diffstat | 14 files changed, 2010 insertions(+), 62 deletions(-) [+] |
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--- a/evaluation.py Fri Feb 23 10:46:41 2018 -0500 +++ b/evaluation.py Sat Oct 27 13:23:06 2018 -0400 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2 +#!/usr/bin/env python import glob from os import system import re @@ -12,7 +12,7 @@ fasta_dir = sys.argv[1] results_dir = sys.argv[2] -dataNames = fasta_dir+"/data.names" +dataNames = os.path.join(fasta_dir,"data.names") listOfClusters = [] listOfHeaders = [] @@ -54,7 +54,7 @@ numberOfClusters += 1 # 1 cluster for all unassigned seqs ignoreBlackList = False with open(dataNames, "r") as names: - for line in names.readlines(): + for line in names: splits = line.split() fullUniqeId = splits[3] fullHeader = '' @@ -72,9 +72,9 @@ toWrite = "" for i in range(len(listOfClusters)): - toWrite += listOfHeaders[i] + "\t" + listOfClusters[i] + '\n' - -with open(results_dir+"/fullTab.tabular", "w") as full: + toWrite += "%s\t%s\n" % (listOfHeaders[i], listOfClusters[i]) + +with open(os.path.join(results_dir,"fullTab.tabular"), "w") as full: full.write(toWrite) @@ -88,7 +88,11 @@ adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfHeaders, listOfClusters) v_measure_score = metrics.v_measure_score(listOfHeaders, listOfClusters) - toWrite = "completeness_score : " + str(completeness_score) + "\n" + "homogeneity_score : " + str(homogeneity_score) + "\n" + "adjusted_rand_score : " +str(adjusted_rand_score) + "\n" + "adjusted_mutual_info_score : " + str(adjusted_mutual_info_score)+ "\n" + "v_measure_score : " + str(v_measure_score) + toWrite = "completeness_score : {}\n".format(completeness_score) + toWrite += "homogeneity_score : {}\n".format(homogeneity_score) + toWrite += "adjusted_rand_score : {}\n".format(adjusted_rand_score) + toWrite += "adjusted_mutual_info_score : {}\n".format(adjusted_mutual_info_score) + toWrite += "v_measure_score : {}\n".format(v_measure_score) else:
--- a/glob_report.xml Fri Feb 23 10:46:41 2018 -0500 +++ b/glob_report.xml Sat Oct 27 13:23:06 2018 -0400 @@ -1,46 +1,32 @@ -<tool id="glob_report" name="cluster_collection_report" version="0.4" > +<tool id="glob_report" name="cluster_collection_report" version="0.5" > <requirements> - <requirement type="package" version="0.5.2">graphclust-wrappers</requirement> + <requirement type="package" version="0.6.0">graphclust-wrappers</requirement> <requirement type="package" version='0.5'>perl-array-utils</requirement> <requirement type="package" version='0.18.1'>scikit-learn</requirement> <requirement type="package" version='1.8.10'>locarna</requirement> <requirement type="package" version='2.1'>rnaz</requirement> <requirement type="package" version="1.1.2">infernal</requirement> <requirement type="package" version='2.2.10'>viennarna</requirement> - <requirement type="package" version='1.3.26'>graphicsmagick</requirement> + <requirement type="package" version='1.3.30'>graphicsmagick</requirement> <requirement type="package" version='0.6.1'>rscape</requirement> <requirement type="package" version='6.0'>unzip</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ + <command detect_errors="exit_code"> + <![CDATA[ unzip $FASTA &> /dev/null && - - mkdir ./CMSEARCH && - mkdir ./MODEL && - - #set $inputFiles = "" - + mkdir ./CMSEARCH && + mkdir ./MODEL && + #import re #for $cms_res in $cmsearch_results: - ###set $inputFiles += str($cms_res.element_identifier)+',' - ln -f -s '$cms_res' ./CMSEARCH/$cms_res.element_identifier && + #set $safename_cm = re.sub('[^\w\-_\.]', '_', $cms_res.element_identifier) + ln -f -s '$cms_res' ./CMSEARCH/$safename_cm && #end for - #set $inputFiles = $inputFiles[:-1] - - #set $inputFilesTrees = "" - #for $mods in $model_tree_files: - ###set $inputFilesTrees += str($mods.element_identifier)+',' - ln -f -s '$mods' ./MODEL/$mods.element_identifier && + #set $safename_tr = re.sub('[^\w\-_\.]', '_', $mods.element_identifier) + ln -f -s '$mods' ./MODEL/$safename_tr && #end for - #set $inputFilesTrees = $inputFilesTrees[:-1] - 'glob_res.pl' - ##'$inputFiles' $merge_cluster_ol $merge_overlap $min_cluster_size @@ -49,7 +35,6 @@ $cm_bitscore_sig $partition_type '' $cut_type - ##'$inputFilesTrees' $results_top_num #if $iteration_num.iteration_num_selector: $iteration_num.CI @@ -157,7 +142,10 @@ <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" /> <collection name="clusters" type="list" label="CLUSTERS"> - <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> + <discover_datasets format="txt" pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> + </collection> + <collection name="allFasta" type="list" label="sequences.fa"> + <discover_datasets format="fasta" pattern="(?P<name>^.*\.all.fa$)" directory="RESULTS" /> </collection> <collection name="partitions" type="list" label="Partitions"> <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" /> @@ -178,7 +166,6 @@ <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> <param name="cmsearch_results" value="1.1.tree,1.2.tree"/> <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> - <param name="combined_cm_out" value="combined_cm_out"/> <param name="partition_type" value="0"/> <param name="cut_type" value="0"/> <conditional name="iteration_num"> @@ -190,11 +177,13 @@ <param name="cm_min_bitscore" value="20"/> <param name="cm_max_eval" value="0.001"/> <param name="cm_bitscore_sig" value="0"/> + <param name="results_top_num" value="5"/> <output name="final_stats" file="RESULTS/cluster.final.stats" /> + <output name="combined_cm_out" file="combined_cm_out"/> + <output name="evaluation" file="evaluation1.txt"/> <output_collection name="clusters" type="list"> <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> - <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> - + <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> </output_collection> <output_collection name="partitions"> <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> @@ -215,7 +204,6 @@ <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/> </output_collection> - <param name="results_top_num" value="5"/> <output_collection name="topSecondaryStruct" type="list"> <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> @@ -247,14 +235,6 @@ ]]> </help> <citations> - <citation type="bibtex">@inproceedings{costa2010fast, - title={Fast neighborhood subgraph pairwise distance kernel}, - author={Costa, Fabrizio and De Grave, Kurt}, - booktitle={Proceedings of the 26th International Conference on Machine Learning}, - pages={255--262}, - year={2010}, - organization={Omnipress} - } - </citation> + <citation type="doi">10.5281/zenodo.597695</citation> </citations> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glob_report.xml.orig Sat Oct 27 13:23:06 2018 -0400 @@ -0,0 +1,268 @@ +<<<<<<< HEAD +<tool id="glob_report" name="cluster_collection_report" version="0.4" > +======= +<tool id="glob_report" name="cluster_collection_report" version="0.3" > +>>>>>>> edc317491e1fdf1233bd9b45376dc05abf6eabd5 + <requirements> + <requirement type="package" version="0.5.2">graphclust-wrappers</requirement> + <requirement type="package" version='0.5'>perl-array-utils</requirement> + <requirement type="package" version='0.18.1'>scikit-learn</requirement> + <requirement type="package" version='1.8.10'>locarna</requirement> + <requirement type="package" version='2.1'>rnaz</requirement> + <requirement type="package" version="1.1.2">infernal</requirement> + <requirement type="package" version='2.2.10'>viennarna</requirement> + <requirement type="package" version='1.3.26'>graphicsmagick</requirement> + <requirement type="package" version='0.6.1'>rscape</requirement> + <requirement type="package" version='6.0'>unzip</requirement> + + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + unzip $FASTA &> /dev/null && + + mkdir ./CMSEARCH && + mkdir ./MODEL && + + #set $inputFiles = "" + + #for $cms_res in $cmsearch_results: + ###set $inputFiles += str($cms_res.element_identifier)+',' + ln -f -s '$cms_res' ./CMSEARCH/$cms_res.element_identifier && + #end for + #set $inputFiles = $inputFiles[:-1] + + #set $inputFilesTrees = "" + + #for $mods in $model_tree_files: + ###set $inputFilesTrees += str($mods.element_identifier)+',' + ln -f -s '$mods' ./MODEL/$mods.element_identifier && + #end for + #set $inputFilesTrees = $inputFilesTrees[:-1] + + + 'glob_res.pl' + ##'$inputFiles' + $merge_cluster_ol + $merge_overlap + $min_cluster_size + $cm_min_bitscore + $cm_max_eval + $cm_bitscore_sig + $partition_type '' + $cut_type + ##'$inputFilesTrees' + $results_top_num + #if $iteration_num.iteration_num_selector: + $iteration_num.CI + $final_partition_soft + $final_partition_used_cmsearch + '$combined_cm' + + #end if + + #if str($advanced_opts.advanced_opts_selector) == "show": + #if str($advanced_opts.param_type.param_type_selector) == "gclust": + $advanced_opts.param_type.p + $advanced_opts.param_type.max_diff_am + $advanced_opts.param_type.max_diff + $advanced_opts.param_type.tau + $advanced_opts.param_type.struct_weight + $advanced_opts.param_type.indel_opening + $advanced_opts.param_type.indel + $advanced_opts.param_type.alifold_consensus_dp + #end if + #end if + + && +<<<<<<< HEAD + python '$__tool_directory__/evaluation.py' FASTA/ RESULTS/ +======= + python '$__tool_directory__/evaluation.py' +>>>>>>> edc317491e1fdf1233bd9b45376dc05abf6eabd5 + + #if $cdhit: + && + python '$__tool_directory__/addCdhitseqs.py' '$cdhit' + #end if +]]> + </command> + <inputs> + <param type="data" name="FASTA" format="zip" /> + <param type="data" name="cmsearch_results" format="tabular" multiple="True"/> + <param type="data" name="model_tree_files" format="txt" multiple="True"/> + <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/> + <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/> + <param type="data" name="cdhit" format="txt" optional="true"/> + <conditional name="iteration_num"> + <param name="iteration_num_selector" type="boolean" checked="no" label="Multiple iterations" help="for single iteration- NO, for multiple-YES"/> + <when value="true"> + <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/> + <param type="data" name="final_partition_soft" format="txt" /> + <param type="data" name="final_partition_used_cmsearch" format="txt" /> + <param type="data" name="combined_cm" format="txt" /> + </when> + <when value="false" ></when> + </conditional> + <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/> + <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/> + <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/> + <param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/> + <param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/> + <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/> + <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/> + + <conditional name="advanced_opts"> + <param name="advanced_opts_selector" type="select" label="Advanced Options"> + <option value="hide" selected="True">Hide</option> + <option value="show">Show</option> + </param> + <when value="hide"></when> + <when value="show"> + + <conditional name="param_type"> + <param name="param_type_selector" type="select" label="Choose the type of parameters"> + <option value="locarna">LocARNA defaults</option> + <option value="gclust" selected="True">GrapClust defaults(changeable)</option> + </param> + <when value="gclust"> + + <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/> + <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/> + <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/> + <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/> + + <param name="struct_weight" argument="struct-weight" + label="Structure weight" type="integer" + value="180" min="0" max="800" /> + <param name="indel_opening" argument="indel-opening" + label="Indel opening score" type="integer" + value="-400" max="0" min="-1500" /> + <param argument="indel" label="Indel score" type="integer" + value="-200" min="-1000" max="0" /> + + <param name="alifold_consensus_dp" + type="boolean" checked="True" + truevalue="--alifold-consensus-dp" falsevalue=" " + label="Compute consensus dot plot by alifold" /> + + </when> + <when value="locarna"> + </when> + </conditional> + + </when> + </conditional> + + </inputs> + <outputs> + <data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats" /> + <data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval" /> + <data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part" /> + <data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch" /> + <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters" /> + <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output" /> + <collection name="clusters" type="list" label="CLUSTERS"> + <discover_datasets pattern="(?P<name>^.*\.all$)" directory="RESULTS" /> + </collection> + <collection name="partitions" type="list" label="Partitions"> + <discover_datasets pattern="(?P<name>^.*$)" directory="RESULTS/partitions" /> + </collection> + <collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps"> + <discover_datasets format="png" pattern="(?P<name>^.*\.alirna.png$)" /> + </collection> + <collection name="topDot" type="list" label="Top $results_top_num aln.ps"> + <discover_datasets format="png" pattern="(?P<name>^.*\.aln.png$)" /> + </collection> + <collection name="rscapePlot" type="list" label="R-scape Plot"> + <discover_datasets format="pdf" pattern="(?P<name>^.*\.pdf$)" /> + </collection> + <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip" /> + </outputs> + <tests> + <test> + <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> + <param name="cmsearch_results" value="1.1.tree,1.2.tree"/> + <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> + <param name="combined_cm_out" value="combined_cm_out"/> + <param name="partition_type" value="0"/> + <param name="cut_type" value="0"/> + <conditional name="iteration_num"> + <param name="iteration_num_selector" value="false"/> + </conditional> + <param name="merge_cluster_ol" value="0.66"/> + <param name="merge_overlap" value="0.51"/> + <param name="min_cluster_size" value="3"/> + <param name="cm_min_bitscore" value="20"/> + <param name="cm_max_eval" value="0.001"/> + <param name="cm_bitscore_sig" value="0"/> + <output name="final_stats" file="RESULTS/cluster.final.stats" /> + <output_collection name="clusters" type="list"> + <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/> + <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/> + + </output_collection> + <output_collection name="partitions"> + <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains"> + <assert_contents> + <has_text text="1.1 1.1 " /> + <has_text text="1.2 1.2" /> + </assert_contents> + </element> + <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains"> + <assert_contents> + <has_text text="MODEL CLASS 0 0" /> + <!--has_text text="1.2" /> + <has_text text="1.1" /--> + </assert_contents> + </element> + <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" /> + <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" /> + <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" /> + <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/> + </output_collection> + <param name="results_top_num" value="5"/> + <output_collection name="topSecondaryStruct" type="list"> + <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> + <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" /> + </output_collection> + <output_collection name="topDot" type="list"> + <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" /> + <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" /> + </output_collection> + + <output_collection name="rscapePlot" type="list"> + <element name="1.cluster.top5.result.aln_1.R2R.sto.pdf" file="1.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" /> + <element name="2.cluster.top5.result.aln_1.R2R.sto.pdf" file="2.cluster.top5.result.aln_1.R2R.sto.pdf" ftype="pdf" compare="sim_size" /> + </output_collection> + + <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/> + + </test> + </tests> + <help> + <![CDATA[ + +**What it does** + +Post-processing. Redundant clusters are merged and instances that belong to multiple clusters +are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of +instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. +Cluster members are finally ranked by their CM bitscore. + + ]]> + </help> + <citations> + <citation type="bibtex">@inproceedings{costa2010fast, + title={Fast neighborhood subgraph pairwise distance kernel}, + author={Costa, Fabrizio and De Grave, Kurt}, + booktitle={Proceedings of the 26th International Conference on Machine Learning}, + pages={255--262}, + year={2010}, + organization={Omnipress} + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.cluster.all Sat Oct 27 13:23:06 2018 -0400 @@ -0,0 +1,34 @@ +SEQ31#1#73#+ RESULT 1 CM_SCORE 88.9 MODEL 1.1 ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005 +SEQ9#1#73#+ RESULT 1 CM_SCORE 87.8 MODEL 1.1 ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005 +SEQ32#1#73#+ RESULT 1 CM_SCORE 87.3 MODEL 1.1 ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005 +SEQ13#1#82#+ RESULT 1 CM_SCORE 86.3 MODEL 1.1 ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005 +SEQ28#1#71#+ RESULT 1 CM_SCORE 80.7 MODEL 1.1 ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005 +SEQ46#1#72#+ RESULT 1 CM_SCORE 78.4 MODEL 1.1 ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005 +SEQ17#1#71#+ RESULT 1 CM_SCORE 77.7 MODEL 1.1 ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005 +SEQ37#1#82#+ RESULT 1 CM_SCORE 76.3 MODEL 1.1 ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005 +SEQ10#1#73#+ RESULT 1 CM_SCORE 76.3 MODEL 1.1 ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005 +SEQ23#1#74#+ RESULT 1 CM_SCORE 75.9 MODEL 1.1 ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005 +SEQ30#1#72#+ RESULT 1 CM_SCORE 74.9 MODEL 1.1 ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005 +SEQ16#1#72#+ RESULT 1 CM_SCORE 74.9 MODEL 1.1 ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005 +SEQ18#1#72#+ RESULT 1 CM_SCORE 72.9 MODEL 1.1 ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005 +SEQ35#1#72#+ RESULT 1 CM_SCORE 71.9 MODEL 1.1 ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005 +SEQ7#1#83#+ RESULT 1 CM_SCORE 71.2 MODEL 1.1 ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005 +SEQ33#1#72#+ RESULT 1 CM_SCORE 69.2 MODEL 1.1 ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005 +SEQ29#1#66#+ RESULT 1 CM_SCORE 31.0 MODEL 1.1 ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005 +SEQ11#1#82#+ RESULT 1 CM_SCORE 88.3 CMSEARCH 1.1 ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005 +SEQ36#1#73#+ RESULT 1 CM_SCORE 83.0 CMSEARCH 1.1 ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005 +SEQ12#1#82#+ RESULT 1 CM_SCORE 82.7 CMSEARCH 1.1 ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005 +SEQ26#1#72#+ RESULT 1 CM_SCORE 82.0 CMSEARCH 1.1 ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005 +SEQ5#1#72#+ RESULT 1 CM_SCORE 81.7 CMSEARCH 1.1 ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005 +SEQ50#1#73#+ RESULT 1 CM_SCORE 80.8 CMSEARCH 1.1 ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005 +SEQ15#1#73#+ RESULT 1 CM_SCORE 80.6 CMSEARCH 1.1 ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005 +SEQ24#1#73#+ RESULT 1 CM_SCORE 80.3 CMSEARCH 1.1 ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005 +SEQ4#1#73#+ RESULT 1 CM_SCORE 79.2 CMSEARCH 1.1 ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005 +SEQ20#1#72#+ RESULT 1 CM_SCORE 75.8 CMSEARCH 1.1 ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005 +SEQ21#1#74#+ RESULT 1 CM_SCORE 74.8 CMSEARCH 1.1 ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005 +SEQ45#1#72#+ RESULT 1 CM_SCORE 71.6 CMSEARCH 1.1 ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005 +SEQ19#1#82#+ RESULT 1 CM_SCORE 69.0 CMSEARCH 1.1 ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005 +SEQ22#1#72#+ RESULT 1 CM_SCORE 48.1 CMSEARCH 1.1 ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005 +SEQ40#1#66#+ RESULT 1 CM_SCORE 44.2 CMSEARCH 1.1 ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005 +SEQ14#1#73#+ RESULT 1 CM_SCORE 29.5 CMSEARCH 1.1 ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005 +SEQ39#1#69#+ RESULT 1 CM_SCORE 21.6 CMSEARCH 1.1 ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.cluster.all.fa Sat Oct 27 13:23:06 2018 -0400 @@ -0,0 +1,66 @@ +>SEQ36_26_73_+ RESULT 1 SCORE 46.5 EVALUE 2.1e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39 +GUUCGCCUAACACGCGAAAGGUCCCUGGAUCAAAACCAGGCGGAAACA +>SEQ11_26_82_+ RESULT 1 SCORE 50.0 EVALUE 4.6e-09 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16 +GUUGGACUUGAAAUCCAAUGGGGUCUCCCCGCGCAGGUUCGAACCCUGCUCGCUGCG +>SEQ35_26_65_+ RESULT 1 SCORE 42.0 EVALUE 4.1e-08 CLUSTER 1.1 LOC MISS ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38 +UCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGC +>SEQ23_27_74_+ RESULT 1 SCORE 47.1 EVALUE 1.6e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27 +GUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA +>SEQ45_25_72_+ RESULT 1 SCORE 41.4 EVALUE 1.8e-07 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4 +GCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAACCAUCCUCUGCUA +>SEQ17_25_71_+ RESULT 1 SCORE 48.2 EVALUE 9.8e-09 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21 +UCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA +>SEQ31_26_73_+ RESULT 1 SCORE 53.2 EVALUE 1.2e-09 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34 +GUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA +>SEQ5_26_65_+ RESULT 1 SCORE 43.3 EVALUE 2.2e-08 CLUSTER 1.1 LOC MISS ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10 +UCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGU +>SEQ33_26_72_+ RESULT 1 SCORE 42.6 EVALUE 1.1e-07 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36 +CCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG +>SEQ7_27_76_+ RESULT 1 SCORE 39.0 EVALUE 1.8e-07 CLUSTER 1.1 LOC MISS ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12 +GCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACU +>SEQ26_26_65_+ RESULT 1 SCORE 42.9 EVALUE 2.6e-08 CLUSTER 1.1 LOC MISS ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2 +UCUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGU +>SEQ22_26_65_+ RESULT 1 SCORE 31.6 EVALUE 5.9e-06 CLUSTER 1.1 LOC MISS ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26 +GGAGAAUUUUGGAUUCUCAGGGAUGGGUUCGAUUCUCAUA +>SEQ28_25_71_+ RESULT 1 SCORE 51.1 EVALUE 2.8e-09 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31 +UCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA +>SEQ30_25_72_+ RESULT 1 SCORE 41.2 EVALUE 2e-07 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33 +UCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC +>SEQ9_26_73_+ RESULT 1 SCORE 52.7 EVALUE 1.4e-09 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14 +GUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA +>SEQ37_27_75_+ RESULT 1 SCORE 43.0 EVALUE 2.6e-08 CLUSTER 1.1 LOC MISS ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3 +GCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACC +>SEQ15_26_73_+ RESULT 1 SCORE 49.2 EVALUE 6.6e-09 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1 +GUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA +>SEQ32_26_73_+ RESULT 1 SCORE 54.0 EVALUE 8.3e-10 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35 +AUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA +>SEQ12_26_82_+ RESULT 1 SCORE 47.0 EVALUE 1.7e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17 +GAUGGACUUGAAAUCCAUUGGGGUUUCCCCGCGCAGGUUCGAAUCCUGUCGGCUACG +>SEQ46_26_72_+ RESULT 1 SCORE 45.5 EVALUE 3.2e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5 +UCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA +>SEQ24_26_73_+ RESULT 1 SCORE 45.0 EVALUE 4e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28 +GGAGGACUGUAGAUCCUUAGGUCGCUGGUUCGAUUCCGGCUCGAAGGA +>SEQ18_26_72_+ RESULT 1 SCORE 45.5 EVALUE 3.1e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22 +AGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA +>SEQ10_26_73_+ RESULT 1 SCORE 45.6 EVALUE 3e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15 +AUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG +>SEQ21_27_74_+ RESULT 1 SCORE 45.0 EVALUE 3.9e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25 +GUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACG +>SEQ19_27_82_+ RESULT 1 SCORE 49.1 EVALUE 6.9e-09 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23 +AGCAGACUCUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCA +>SEQ14_26_66_+ RESULT 1 SCORE 33.9 EVALUE 2e-06 CLUSTER 1.1 LOC MISS ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19 +GCUUAGCUGUUAACUAAGUGUUUGUGGGUUUAAGUCCCAUU +>SEQ13_26_82_+ RESULT 1 SCORE 46.5 EVALUE 2e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18 +GAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG +>SEQ20_25_72_+ RESULT 1 SCORE 40.8 EVALUE 2.4e-07 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24 +AUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCAGGUGCCCCCU +>SEQ40_21_66_+ RESULT 1 SCORE 30.4 EVALUE 2.1e-05 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005_rep.42 +AUUGAAUUGCAAAUUCGAAGAAGCAGCUUCAAACCUGCCGGGGCUU +>SEQ4_26_73_+ RESULT 1 SCORE 44.8 EVALUE 4.4e-08 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0 +ACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAUUCUCGCUGGGGCUU +>SEQ50_26_73_+ RESULT 1 SCORE 48.8 EVALUE 7.8e-09 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9 +AUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCG +>SEQ16_25_72_+ RESULT 1 SCORE 40.4 EVALUE 2.8e-07 CLUSTER 1.2 LOC MISS ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20 +GCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA +>SEQ29_21_59_+ RESULT 1 SCORE 24.3 EVALUE 0.0002 CLUSTER 1.1 LOC MISS ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32 +CAUUGGACUGUAAAUCUAAAGACAGGGGUUAGGCCUCUU
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.cluster.top5.alirna.ps Sat Oct 27 13:23:06 2018 -0400 @@ -0,0 +1,417 @@ +%!PS-Adobe-3.0 EPSF-3.0 +%%Creator: ViennaRNA-2.3.1 +%%CreationDate: Tue May 30 20:24:19 2017 +%%Title: RNA Secondary Structure Plot +%%BoundingBox: 0 0 700 700 +%%DocumentFonts: Helvetica +%%Pages: 1 +%%EndComments + +%Options: --noLP +% to switch off outline pairs of sequence comment or +% delete the appropriate line near the end of the file + +%%BeginProlog +/RNAplot 100 dict def +RNAplot begin +/fsize 14 def +/outlinecolor {0.2 setgray} bind def +/paircolor {0.2 setgray} bind def +/seqcolor {0 setgray} bind def +/cshow { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def +/min { 2 copy gt { exch } if pop } bind def +/max { 2 copy lt { exch } if pop } bind def +/arccoords { % i j arccoords + % puts optimal x1 y1 x2 y2 coordinates used in bezier curves from i to j + % onto the stack + dup 3 -1 roll dup 4 -1 roll lt dup dup 5 2 roll {exch} if + dup 3 -1 roll dup 3 -1 roll exch sub 1 sub dup + 4 -2 roll 5 -1 roll {exch} if 4 2 roll + sequence length dup 2 div exch 3 1 roll lt + {exch 5 -1 roll pop 4 -2 roll exch 4 2 roll} + { 4 2 roll 5 -1 roll dup 6 1 roll {exch} if + 4 -2 roll exch pop dup 3 -1 roll dup 4 1 roll + exch add 4 -1 roll dup 5 1 roll sub 1 sub + 5 -1 roll not {4 -2 roll exch 4 2 roll} if + }ifelse + % compute the scalingfactor and prepare (1-sf) and sf*r + 2 mul exch cpr 3 1 roll div dup + 3 -1 roll mul exch 1 exch sub exch + % compute the coordinates + 3 -1 roll 1 sub coor exch get aload pop % get coord for i + 4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate y1 + 4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate x1 + 5 -1 roll 1 sub coor exch get aload pop % get coord for j + % duplicate j coord + dup 3 -1 roll dup 4 1 roll exch 8 2 roll + 6 -1 roll dup 7 1 roll mul 5 -1 roll dup 6 1 roll add exch % calculate y2 + 6 -1 roll mul 5 -1 roll add exch % calculate x2 + 6 -2 roll % reorder +} bind def +/drawoutline { + gsave outlinecolor newpath + coor 0 get aload pop 0.8 0 360 arc % draw 5' circle of 1st sequence + currentdict /cutpoint known % check if cutpoint is defined + {coor 0 cutpoint getinterval + {aload pop lineto} forall % draw outline of 1st sequence + coor cutpoint 1 add get aload pop + 2 copy moveto 0.8 0 360 arc % draw 5' circle of 2nd sequence + coor cutpoint 1 add coor length cutpoint 1 add sub getinterval + {aload pop lineto} forall} % draw outline of 2nd sequence + {coor {aload pop lineto} forall} % draw outline as a whole + ifelse + stroke grestore +} bind def +/drawpairs { + paircolor + 0.7 setlinewidth + [9 3.01] 9 setdash + newpath + pairs {aload pop + currentdict (cpr) known + { exch dup + coor exch 1 sub get aload pop moveto + exch arccoords curveto + } + { coor exch 1 sub get aload pop moveto + coor exch 1 sub get aload pop lineto + }ifelse + } forall + stroke +} bind def +% draw bases +/drawbases { + [] 0 setdash + seqcolor + 0 + coor { + aload pop moveto + dup sequence exch 1 getinterval cshow + 1 add + } forall + pop +} bind def + +/init { + /Helvetica findfont fsize scalefont setfont + 1 setlinejoin + 1 setlinecap + 0.8 setlinewidth + % find the coordinate range + /xmax -1000 def /xmin 10000 def + /ymax -1000 def /ymin 10000 def + coor { + aload pop + dup ymin lt {dup /ymin exch def} if + dup ymax gt {/ymax exch def} {pop} ifelse + dup xmin lt {dup /xmin exch def} if + dup xmax gt {/xmax exch def} {pop} ifelse + } forall + /size {xmax xmin sub ymax ymin sub max} bind def + /width {xmax xmin sub} bind def + /height {ymax ymin sub} bind def + 10 10 translate + 680 size 10 add div dup scale + size width sub width xmin sub xmax sub add 2 div 5 add + size height sub height ymin sub ymax sub add 2 div 5 add + translate +} bind def +end +RNAplot begin +% extra definitions for standard anotations +/min { 2 copy gt { exch } if pop } bind def +/BLACK { 0 0 0 } def +/RED { 1 0 0 } def +/GREEN { 0 1 0 } def +/BLUE { 0 0 1 } def +/WHITE { 1 1 1 } def +/LabelFont { % font size LabelFont + exch findfont exch fsize mul scalefont setfont +} bind def +/Label { % i dx dy (text) Label + % write text at base i plus offset dx, dy + 4 3 roll 1 sub coor exch get aload pop moveto + 3 1 roll fsize mul exch fsize mul exch rmoveto + show +} bind def +/cmark { % i cmark draw circle around base i + newpath 1 sub coor exch get aload pop + fsize 2 div 0 360 arc stroke +} bind def +/gmark { % i j c gmark + % draw basepair i,j with c counter examples in gray + gsave + 3 min [0 0.33 0.66 0.9] exch get setgray + 1 sub dup coor exch get aload pop moveto + sequence exch 1 getinterval cshow + 1 sub dup coor exch get aload pop moveto + sequence exch 1 getinterval cshow + grestore +} bind def +/segmark { % f i j lw r g b segmark + % mark segment [i,j] with outline width lw and color rgb + % use omark and Fomark instead + gsave + setrgbcolor setlinewidth + newpath + 1 sub exch 1 sub dup + coor exch get aload pop moveto + currentdict (cpr) known + { + 3 -1 roll dup 4 1 roll dup + { + 3 1 roll dup 3 -1 roll dup + 4 1 roll exch 5 2 roll exch + } + { + 3 1 roll exch + } ifelse + 1 exch { coor exch get aload pop lineto } for + { + dup 3 1 roll 1 add exch 1 add arccoords pop pop + 4 2 roll 5 -1 roll coor exch get aload pop curveto + } if + } + { + exch 1 exch { + coor exch get aload pop lineto + } for + } ifelse + { closepath fill } if stroke + grestore +} bind def +/omark { % i j lw r g b omark + % stroke segment [i..j] with linewidth lw, color rgb + false 7 1 roll segmark +} bind def +/Fomark { % i j r g b Fomark + % fill segment [i..j] with color rgb + % should precede drawbases + 1 4 1 roll true 7 1 roll segmark +} bind def +/BFmark{ % i j k l r g b BFmark + % fill block between pairs (i,j) and (k,l) with color rgb + % should precede drawbases + gsave + setrgbcolor + newpath + currentdict (cpr) known + { + dup 1 sub coor exch get aload pop moveto % move to l + dup 1 sub 4 -1 roll dup 5 1 roll 1 sub 1 exch + { coor exch get aload pop lineto } for % lines from l to j + 3 -1 roll 4 -1 roll dup 5 1 roll arccoords curveto % curve from j to i + exch dup 4 -1 roll 1 sub exch 1 sub 1 exch + { coor exch get aload pop lineto } for % lines from i to k + exch arccoords curveto% curve from k to l + } + { exch 4 3 roll exch 1 sub exch 1 sub dup + coor exch get aload pop moveto + exch 1 exch { coor exch get aload pop lineto } for + exch 1 sub exch 1 sub dup + coor exch get aload pop lineto + exch 1 exch { coor exch get aload pop lineto } for + } ifelse + closepath fill stroke + grestore +} bind def +/hsb { + dup 0.3 mul 1 exch sub sethsbcolor +} bind def +/colorpair { % i j hue sat colorpair + % draw basepair i,j in color + % 1 index 0.00 ne { + gsave + newpath + hsb + fsize setlinewidth + currentdict (cpr) known + { + exch dup + coor exch 1 sub get aload pop moveto + exch arccoords curveto + } + { 1 sub coor exch get aload pop moveto + 1 sub coor exch get aload pop lineto + } ifelse + stroke + grestore + % } if +} bind def +end + +%%EndProlog +RNAplot begin +% data start here +/sequence (\ +GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGU_________CCCCGGUUCGAAACCGGGCGGAAACA\ +) def +/coor [ +[126.01442719 205.80749512] +[125.44680786 190.81823730] +[124.87918091 175.82897949] +[124.31156158 160.83972168] +[123.74394226 145.85047913] +[123.17631531 130.86122131] +[122.60869598 115.87195587] +[107.91925812 124.77088928] +[91.87033844 122.99333954] +[80.97422791 112.51052094] +[66.42591858 116.16383362] +[51.87760544 119.81713867] +[47.74618530 134.60993958] +[36.76065063 145.34370422] +[21.87605476 149.13108826] +[7.09627628 144.95332336] +[-3.60299659 133.93420410] +[-7.34371328 119.03780365] +[-3.11964059 104.27119446] +[7.93296814 93.60651398] +[22.84101677 89.91250610] +[37.59431458 94.18284607] +[48.22429657 105.26882935] +[62.77260971 101.61552429] +[77.32091522 97.96221161] +[93.74244690 75.59227753] +[122.92980194 84.59557343] +[115.84320831 71.37512970] +[108.75661469 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--- a/test-data/1.cluster.top5.result.aln_1.R2R.sto.pdf Fri Feb 23 10:46:41 2018 -0500 +++ b/test-data/1.cluster.top5.result.aln_1.R2R.sto.pdf Sat Oct 27 13:23:06 2018 -0400 @@ -71,12 +71,6 @@ 92.815958 30.658227 l S 72 w -81.834458 40.910727 m -99.909458 40.910727 l -99.909458 35.525727 l -81.834458 35.525727 l -h -f 1.44 w 88.927958 38.218227 m 92.815958 38.218227 l @@ -864,7 +858,7 @@ << /Font <</FH 5 0 R>> /ProcSet[/PDF/Text/ImageC]/XObject << >>/ExtGState<</GS0 10 0 R>>/Properties<</MC0<</Color[20224.0 -32768.0 -1.0]/Title(Layer 1)/Visible true/Preview true/Editable true/Printed true/Dimmed true>>>>>> endobj 8 0 obj -14624 +14532 endobj 1 0 obj << @@ -889,21 +883,21 @@ xref 0 11 0000000000 65535 f -0000015316 00000 n -0000015439 00000 n -0000015381 00000 n +0000015224 00000 n +0000015347 00000 n +0000015289 00000 n 0000000116 00000 n 0000000009 00000 n 0000000152 00000 n 0000000270 00000 n -0000015295 00000 n -0000015057 00000 n -0000014945 00000 n +0000015203 00000 n +0000014965 00000 n +0000014853 00000 n trailer << /Size 11 /Root 1 0 R >> startxref -15485 +15393 %%EOF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.cluster.all Sat Oct 27 13:23:06 2018 -0400 @@ -0,0 +1,4 @@ +SEQ74#1#100#+ RESULT 2 CM_SCORE 163.2 MODEL 1.2 ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618 +SEQ72#1#100#+ RESULT 2 CM_SCORE 163.1 MODEL 1.2 ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618 +SEQ73#1#100#+ RESULT 2 CM_SCORE 161.5 MODEL 1.2 ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618 +SEQ75#1#100#+ RESULT 2 CM_SCORE 160.5 MODEL 1.2 ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined_cm_out Sat Oct 27 13:23:06 2018 -0400 @@ -0,0 +1,53 @@ +##.1.1 +SEQ31 - dataset_60 - cm 1 73 1 73 + no 1 0.56 0.0 88.9 1.2e-150 ! ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005 +SEQ11 - dataset_60 - cm 1 73 1 82 + no 1 0.62 0.0 88.3 8e-150 ! ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005 +SEQ9 - dataset_60 - cm 1 73 1 73 + no 1 0.56 0.0 87.8 4.6e-149 ! ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005 +SEQ32 - dataset_60 - cm 1 73 1 73 + no 1 0.58 0.0 87.3 2.6e-148 ! ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005 +SEQ13 - dataset_60 - cm 1 73 1 82 + no 1 0.56 0.0 86.3 8.9e-147 ! ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005 +SEQ36 - dataset_60 - cm 1 73 1 73 + no 1 0.51 0.0 83.0 1.1e-141 ! ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005 +SEQ12 - dataset_60 - cm 1 73 1 82 + no 1 0.57 0.0 82.7 3.1e-141 ! ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005 +SEQ26 - dataset_60 - cm 1 73 1 72 + no 1 0.50 0.0 82.0 4.9e-140 ! ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005 +SEQ5 - dataset_60 - cm 1 73 1 72 + no 1 0.51 0.0 81.7 1.3e-139 ! ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005 +SEQ50 - dataset_60 - cm 1 73 1 73 + no 1 0.56 0.0 80.8 3.1e-138 ! ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005 +SEQ28 - dataset_60 - cm 1 73 1 71 + no 1 0.62 0.0 80.7 4.6e-138 ! ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005 +SEQ15 - dataset_60 - cm 1 73 1 73 + no 1 0.53 0.0 80.6 5.9e-138 ! ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005 +SEQ24 - dataset_60 - cm 1 73 1 73 + no 1 0.56 0.0 80.3 1.5e-137 ! ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005 +SEQ4 - dataset_60 - cm 1 73 1 73 + no 1 0.56 0.0 79.2 7.3e-136 ! ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005 +SEQ46 - dataset_60 - cm 1 73 1 72 + no 1 0.65 0.0 78.4 1.3e-134 ! ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005 +SEQ17 - dataset_60 - cm 1 73 1 71 + no 1 0.59 0.0 77.7 1.6e-133 ! ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005 +SEQ37 - dataset_60 - cm 1 73 1 82 + no 1 0.63 0.0 76.3 2.5e-131 ! ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005 +SEQ10 - dataset_60 - cm 1 73 1 73 + no 1 0.62 0.0 76.3 2.8e-131 ! ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005 +SEQ23 - dataset_60 - cm 1 73 1 74 + no 1 0.61 0.0 75.9 1.2e-130 ! ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005 +SEQ20 - dataset_60 - cm 1 73 1 72 + no 1 0.56 0.0 75.8 1.7e-130 ! ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005 +SEQ30 - dataset_60 - cm 1 73 1 72 + no 1 0.61 0.0 74.9 4e-129 ! ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005 +SEQ16 - dataset_60 - cm 1 73 1 72 + no 1 0.61 0.0 74.9 4e-129 ! ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005 +SEQ21 - dataset_60 - cm 1 73 1 74 + no 1 0.61 0.0 74.8 4.8e-129 ! ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005 +SEQ18 - dataset_60 - cm 1 73 1 72 + no 1 0.58 0.0 72.9 4.3e-126 ! ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005 +SEQ35 - dataset_60 - cm 1 73 1 72 + no 1 0.65 0.0 71.9 1.2e-124 ! ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005 +SEQ45 - dataset_60 - cm 1 73 1 72 + no 1 0.60 0.0 71.6 4.5e-124 ! ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005 +SEQ7 - dataset_60 - cm 1 73 1 83 + no 1 0.63 0.0 71.2 2e-123 ! ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005 +SEQ33 - dataset_60 - cm 1 73 1 72 + no 1 0.62 0.0 69.2 2e-120 ! ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005 +SEQ19 - dataset_60 - cm 1 73 1 82 + no 1 0.59 0.0 69.0 4e-120 ! ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005 +SEQ22 - dataset_60 - cm 1 73 1 72 + no 1 0.49 0.0 48.1 5.1e-88 ! ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005 +SEQ40 - dataset_60 - cm 1 73 1 66 + no 1 0.45 0.0 44.2 4.7e-82 ! ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005 +SEQ29 - dataset_60 - cm 1 73 1 66 + no 1 0.42 0.0 31.0 8.7e-62 ! ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005 +SEQ14 - dataset_60 - cm 1 73 1 73 + no 1 0.41 0.0 29.5 2.2e-59 ! ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005 +SEQ39 - dataset_60 - cm 1 73 1 69 + no 1 0.39 0.0 21.6 2.5e-47 ! ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005 +SEQ48 - dataset_60 - cm 1 73 1 71 + no 1 0.35 0.0 12.9 5.7e-34 ! ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005 +SEQ34 - dataset_60 - cm 1 73 1 68 + no 1 0.34 0.0 12.8 9.6e-34 ! ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005 +SEQ6 - dataset_60 - cm 1 73 1 66 + no 1 0.38 0.0 12.1 1.1e-32 ! ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005 +SEQ42 - dataset_60 - cm 1 73 1 69 + no 1 0.38 0.0 9.4 1.4e-28 ! ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005 +SEQ8 - dataset_60 - cm 1 73 1 70 + no 1 0.33 0.0 9.0 6.2e-28 ! ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005 +SEQ27 - dataset_60 - cm 1 73 1 69 + no 1 0.43 0.0 8.6 3.1e-27 ! ORIGID RF00005_rep.30_AL132988.4/95773-95841_27 ORIGHEAD RF00005 +SEQ41 - dataset_60 - cm 1 73 1 68 + no 1 0.26 0.1 7.7 6e-26 ! ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005 +SEQ43 - dataset_60 - cm 1 73 1 71 + no 1 0.41 0.0 4.3 1.1e-20 ! ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005 +SEQ25 - dataset_60 - cm 1 73 1 69 + no 1 0.29 0.0 4.2 1.8e-20 ! ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005 +SEQ44 - dataset_60 - cm 1 73 1 69 + no 1 0.42 0.0 1.2 6.2e-16 ! ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005 +SEQ38 - dataset_60 - cm 1 73 1 65 + no 1 0.23 0.5 -0.9 1.1e-12 ! ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005 +SEQ47 - dataset_60 - cm 1 73 1 68 + no 1 0.24 0.5 -1.5 9.1e-12 ! ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005 +SEQ49 - dataset_60 - cm 1 73 1 68 + no 1 0.35 0.0 -4.4 2.9e-07 ! ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005 +##.1.2 +SEQ74 - dataset_61 - cm 1 100 1 100 + no 1 0.51 0.0 163.2 7.9e-68 ! ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618 +SEQ72 - dataset_61 - cm 1 100 1 100 + no 1 0.49 0.0 163.1 8.9e-68 ! ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618 +SEQ73 - dataset_61 - cm 1 100 1 100 + no 1 0.49 0.0 161.5 3.4e-67 ! ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618 +SEQ75 - dataset_61 - cm 1 100 1 100 + no 1 0.44 0.0 160.5 8.2e-67 ! ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evaluation1.txt Sat Oct 27 13:23:06 2018 -0400 @@ -0,0 +1,5 @@ +completeness_score : 0.533962565156 +homogeneity_score : 1.0 +adjusted_rand_score : 0.551625093777 +adjusted_mutual_info_score : 0.291033044987 +v_measure_score : 0.696187217713