| Previous changeset 16:79df97a1bc0f (2018-02-23) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults commit 4406735e44aba20859c252be39f4e99df28c7a92 |
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modified:
evaluation.py glob_report.xml test-data/1.cluster.top5.result.aln_1.R2R.sto.pdf test-data/RESULTS.zip |
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added:
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/2.cluster.all test-data/2.cluster.top5.alirna.ps test-data/2.cluster.top5.aln.ps test-data/combined_cm_out test-data/evaluation1.txt |
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| diff -r 79df97a1bc0f -r f93c868203cc evaluation.py --- a/evaluation.py Fri Feb 23 10:46:41 2018 -0500 +++ b/evaluation.py Sat Oct 27 13:23:06 2018 -0400 |
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| @@ -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: |
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| diff -r 79df97a1bc0f -r f93c868203cc glob_report.xml --- 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> |
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| diff -r 79df97a1bc0f -r f93c868203cc glob_report.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glob_report.xml.orig Sat Oct 27 13:23:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,268 @@\n+<<<<<<< HEAD\n+<tool id="glob_report" name="cluster_collection_report" version="0.4" >\n+=======\n+<tool id="glob_report" name="cluster_collection_report" version="0.3" >\n+>>>>>>> edc317491e1fdf1233bd9b45376dc05abf6eabd5\n+ <requirements>\n+ <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>\n+ <requirement type="package" version=\'0.5\'>perl-array-utils</requirement>\n+ <requirement type="package" version=\'0.18.1\'>scikit-learn</requirement>\n+ <requirement type="package" version=\'1.8.10\'>locarna</requirement>\n+ <requirement type="package" version=\'2.1\'>rnaz</requirement>\n+ <requirement type="package" version="1.1.2">infernal</requirement>\n+ <requirement type="package" version=\'2.2.10\'>viennarna</requirement>\n+ <requirement type="package" version=\'1.3.26\'>graphicsmagick</requirement>\n+ <requirement type="package" version=\'0.6.1\'>rscape</requirement>\n+ <requirement type="package" version=\'6.0\'>unzip</requirement>\n+ \n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+ <![CDATA[\n+ unzip $FASTA &> /dev/null &&\n+\n+ mkdir ./CMSEARCH &&\n+ mkdir ./MODEL &&\n+\n+ #set $inputFiles = ""\n+\n+ #for $cms_res in $cmsearch_results:\n+ ###set $inputFiles += str($cms_res.element_identifier)+\',\'\n+ ln -f -s \'$cms_res\' ./CMSEARCH/$cms_res.element_identifier &&\n+ #end for\n+ #set $inputFiles = $inputFiles[:-1]\n+\n+ #set $inputFilesTrees = ""\n+\n+ #for $mods in $model_tree_files:\n+ ###set $inputFilesTrees += str($mods.element_identifier)+\',\'\n+ ln -f -s \'$mods\' ./MODEL/$mods.element_identifier &&\n+ #end for\n+ #set $inputFilesTrees = $inputFilesTrees[:-1]\n+\n+ \n+ \'glob_res.pl\'\n+ ##\'$inputFiles\'\n+ $merge_cluster_ol\n+ $merge_overlap\n+ $min_cluster_size\n+ $cm_min_bitscore\n+ $cm_max_eval\n+ $cm_bitscore_sig\n+ $partition_type \'\'\n+ $cut_type\n+ ##\'$inputFilesTrees\'\n+ $results_top_num\n+ #if $iteration_num.iteration_num_selector:\n+ $iteration_num.CI\n+ $final_partition_soft\n+ $final_partition_used_cmsearch\n+ \'$combined_cm\'\n+\n+ #end if\n+\n+ #if str($advanced_opts.advanced_opts_selector) == "show":\n+ #if str($advanced_opts.param_type.param_type_selector) == "gclust":\n+ $advanced_opts.param_type.p\n+ $advanced_opts.param_type.max_diff_am\n+ $advanced_opts.param_type.max_diff\n+ $advanced_opts.param_type.tau\n+ $advanced_opts.param_type.struct_weight\n+ $advanced_opts.param_type.indel_opening\n+ $advanced_opts.param_type.indel\n+ $advanced_opts.param_type.alifold_consensus_dp\n+ #end if\n+ #end if\n+\n+ &&\n+<<<<<<< HEAD\n+ python \'$__tool_directory__/evaluation.py\' FASTA/ RESULTS/\n+=======\n+ python \'$__tool_directory__/evaluation.py\'\n+>>>>>>> edc317491e1fdf1233bd9b45376dc05abf6eabd5\n+ \n+ #if $cdhit:\n+ &&\n+ python \'$__tool_directory__/addCdhitseqs.py\' \'$cdhit\'\n+ #end if\n+]]>\n+ </command>\n+ <inputs>\n+ <param type="data" name="FASTA" format="zip" />\n+ <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>\n+ <param type="data" name="model_tree_files" format="txt" multiple="True"/>\n+ <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>\n+ <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>\n+ <param type="data" name="cdhit" format="txt" optional="true"/>\n+ <conditional name="iteration_num">\n+ <param name="iteration_num_se'..b'ame="partition_type" value="0"/>\n+ <param name="cut_type" value="0"/>\n+ <conditional name="iteration_num">\n+ <param name="iteration_num_selector" value="false"/>\n+ </conditional>\n+ <param name="merge_cluster_ol" value="0.66"/>\n+ <param name="merge_overlap" value="0.51"/>\n+ <param name="min_cluster_size" value="3"/>\n+ <param name="cm_min_bitscore" value="20"/>\n+ <param name="cm_max_eval" value="0.001"/>\n+ <param name="cm_bitscore_sig" value="0"/>\n+ <output name="final_stats" file="RESULTS/cluster.final.stats" />\n+ <output_collection name="clusters" type="list">\n+ <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>\n+ <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>\n+ \n+ </output_collection>\n+ <output_collection name="partitions">\n+ <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">\n+ <assert_contents>\n+ <has_text text="1.1 1.1 " />\n+ <has_text text="1.2 1.2" />\n+ </assert_contents>\n+ </element>\n+ <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">\n+ <assert_contents>\n+ <has_text text="MODEL CLASS 0 0" />\n+ <!--has_text text="1.2" />\n+ <has_text text="1.1" /-->\n+ </assert_contents>\n+ </element>\n+ <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />\n+ <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />\n+ <element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />\n+ <element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>\n+ </output_collection>\n+ <param name="results_top_num" value="5"/>\n+ <output_collection name="topSecondaryStruct" type="list">\n+ <element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />\n+ <element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />\n+ </output_collection>\n+ <output_collection name="topDot" type="list">\n+ <element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png" ftype="png" compare="sim_size" />\n+ <element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png" ftype="png" compare="sim_size" />\n+ </output_collection>\n+\n+ <output_collection name="rscapePlot" type="list">\n+ <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" />\n+ <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" />\n+ </output_collection>\n+\n+ <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/>\n+\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+**What it does**\n+\n+Post-processing. Redundant clusters are merged and instances that belong to multiple clusters\n+are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of\n+instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.\n+Cluster members are finally ranked by their CM bitscore.\n+\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="bibtex">@inproceedings{costa2010fast,\n+ title={Fast neighborhood subgraph pairwise distance kernel},\n+ author={Costa, Fabrizio and De Grave, Kurt},\n+ booktitle={Proceedings of the 26th International Conference on Machine Learning},\n+ pages={255--262},\n+ year={2010},\n+ organization={Omnipress}\n+ }\n+ </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 79df97a1bc0f -r f93c868203cc test-data/1.cluster.all --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.cluster.all Sat Oct 27 13:23:06 2018 -0400 |
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| @@ -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 |
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| diff -r 79df97a1bc0f -r f93c868203cc test-data/1.cluster.all.fa --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/1.cluster.top5.alirna.ps --- /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 |
| [ |
| b"@@ -0,0 +1,417 @@\n+%!PS-Adobe-3.0 EPSF-3.0\n+%%Creator: ViennaRNA-2.3.1\n+%%CreationDate: Tue May 30 20:24:19 2017\n+%%Title: RNA Secondary Structure Plot\n+%%BoundingBox: 0 0 700 700\n+%%DocumentFonts: Helvetica\n+%%Pages: 1\n+%%EndComments\n+\n+%Options: --noLP \n+% to switch off outline pairs of sequence comment or\n+% delete the appropriate line near the end of the file\n+\n+%%BeginProlog\n+/RNAplot 100 dict def\n+RNAplot begin\n+/fsize 14 def\n+/outlinecolor {0.2 setgray} bind def\n+/paircolor {0.2 setgray} bind def\n+/seqcolor {0 setgray} bind def\n+/cshow { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def\n+/min { 2 copy gt { exch } if pop } bind def\n+/max { 2 copy lt { exch } if pop } bind def\n+/arccoords { % i j arccoords\n+ % puts optimal x1 y1 x2 y2 coordinates used in bezier curves from i to j\n+ % onto the stack\n+ dup 3 -1 roll dup 4 -1 roll lt dup dup 5 2 roll {exch} if\n+ dup 3 -1 roll dup 3 -1 roll exch sub 1 sub dup\n+ 4 -2 roll 5 -1 roll {exch} if 4 2 roll\n+ sequence length dup 2 div exch 3 1 roll lt \n+ {exch 5 -1 roll pop 4 -2 roll exch 4 2 roll}\n+ { 4 2 roll 5 -1 roll dup 6 1 roll {exch} if\n+ 4 -2 roll exch pop dup 3 -1 roll dup 4 1 roll\n+ exch add 4 -1 roll dup 5 1 roll sub 1 sub\n+ 5 -1 roll not {4 -2 roll exch 4 2 roll} if\n+ }ifelse\n+ % compute the scalingfactor and prepare (1-sf) and sf*r\n+ 2 mul exch cpr 3 1 roll div dup\n+ 3 -1 roll mul exch 1 exch sub exch\n+ % compute the coordinates\n+ 3 -1 roll 1 sub coor exch get aload pop % get coord for i\n+ 4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate y1\n+ 4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate x1\n+ 5 -1 roll 1 sub coor exch get aload pop % get coord for j\n+ % duplicate j coord\n+ dup 3 -1 roll dup 4 1 roll exch 8 2 roll\n+ 6 -1 roll dup 7 1 roll mul 5 -1 roll dup 6 1 roll add exch % calculate y2\n+ 6 -1 roll mul 5 -1 roll add exch % calculate x2\n+ 6 -2 roll % reorder\n+} bind def\n+/drawoutline {\n+ gsave outlinecolor newpath\n+ coor 0 get aload pop 0.8 0 360 arc % draw 5' circle of 1st sequence\n+ currentdict /cutpoint known % check if cutpoint is defined\n+ {coor 0 cutpoint getinterval\n+ {aload pop lineto} forall % draw outline of 1st sequence\n+ coor cutpoint 1 add get aload pop\n+ 2 copy moveto 0.8 0 360 arc % draw 5' circle of 2nd sequence\n+ coor cutpoint 1 add coor length cutpoint 1 add sub getinterval\n+ {aload pop lineto} forall} % draw outline of 2nd sequence\n+ {coor {aload pop lineto} forall} % draw outline as a whole\n+ ifelse\n+ stroke grestore\n+} bind def\n+/drawpairs {\n+ paircolor\n+ 0.7 setlinewidth\n+ [9 3.01] 9 setdash\n+ newpath\n+ pairs {aload pop\n+ currentdict (cpr) known\n+ { exch dup\n+ coor exch 1 sub get aload pop moveto\n+ exch arccoords curveto\n+ }\n+ { coor exch 1 sub get aload pop moveto\n+ coor exch 1 sub get aload pop lineto\n+ }ifelse\n+ } forall\n+ stroke\n+} bind def\n+% draw bases\n+/drawbases {\n+ [] 0 setdash\n+ seqcolor\n+ 0\n+ coor {\n+ aload pop moveto\n+ dup sequence exch 1 getinterval cshow\n+ 1 add\n+ } forall\n+ pop\n+} bind def\n+\n+/init {\n+ /Helvetica findfont fsize scalefont setfont\n+ 1 setlinejoin\n+ 1 setlinecap\n+ 0.8 setlinewidth\n+ % find the coordinate range\n+ /xmax -1000 def /xmin 10000 def\n+ /ymax -1000 def /ymin 10000 def\n+ coor {\n+ aload pop\n+ dup ymin lt {dup /ymin exch def} if\n+ dup ymax gt {/ymax exch def} {pop} ifelse\n+ dup xmin lt {dup /xmin exch def} if\n+ dup xmax gt {/xmax exch def} {pop} ifelse\n+ } forall\n+ /size {xmax xmin sub ymax ymin sub max} bind def\n+ /width {xmax xmin sub} bind def\n+ /height {ymax ymin sub} bind def\n+ 10 10 translate\n+ 680 size 10 add div dup scale\n+ size width sub width xmin sub xmax sub add 2 div 5 add\n+ size height sub height ymin sub ymax sub add 2 div 5 add\n+ translate\n+} bind def\n+end\n+RNAplot begin\n+% extra definitions for standard anotations\n+/min { 2 copy gt { exch }"..b'orpair\n+ % draw basepair i,j in color\n+ % 1 index 0.00 ne {\n+ gsave\n+ newpath\n+ hsb\n+ fsize setlinewidth\n+ currentdict (cpr) known\n+ {\n+ exch dup\n+ coor exch 1 sub get aload pop moveto\n+ exch arccoords curveto\n+ }\n+ { 1 sub coor exch get aload pop moveto\n+ 1 sub coor exch get aload pop lineto\n+ } ifelse\n+ stroke\n+ grestore\n+ % } if\n+} bind def\n+end\n+\n+%%EndProlog\n+RNAplot begin\n+% data start here\n+/sequence (\\\n+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGU_________CCCCGGUUCGAAACCGGGCGGAAACA\\\n+) def\n+/coor [\n+[126.01442719 205.80749512]\n+[125.44680786 190.81823730]\n+[124.87918091 175.82897949]\n+[124.31156158 160.83972168]\n+[123.74394226 145.85047913]\n+[123.17631531 130.86122131]\n+[122.60869598 115.87195587]\n+[107.91925812 124.77088928]\n+[91.87033844 122.99333954]\n+[80.97422791 112.51052094]\n+[66.42591858 116.16383362]\n+[51.87760544 119.81713867]\n+[47.74618530 134.60993958]\n+[36.76065063 145.34370422]\n+[21.87605476 149.13108826]\n+[7.09627628 144.95332336]\n+[-3.60299659 133.93420410]\n+[-7.34371328 119.03780365]\n+[-3.11964059 104.27119446]\n+[7.93296814 93.60651398]\n+[22.84101677 89.91250610]\n+[37.59431458 94.18284607]\n+[48.22429657 105.26882935]\n+[62.77260971 101.61552429]\n+[77.32091522 97.96221161]\n+[93.74244690 75.59227753]\n+[122.92980194 84.59557343]\n+[115.84320831 71.37512970]\n+[108.75661469 58.15468216]\n+[101.67002106 44.93423462]\n+[94.58342743 31.71378899]\n+[79.24071503 28.69135094]\n+[69.47061157 16.48155785]\n+[69.88626099 0.84949923]\n+[80.29140472 -10.82384396]\n+[95.77305603 -13.02667522]\n+[109.02124786 -4.71888638]\n+[113.78059387 10.17683983]\n+[107.80387115 24.62719536]\n+[114.89046478 37.84764099]\n+[121.97705841 51.06808853]\n+[129.06365967 64.28853607]\n+[136.15025330 77.50897980]\n+[130.14912415 63.76174545]\n+[129.68310547 48.76898575]\n+[134.81886292 34.67558289]\n+[144.82167053 23.49776077]\n+[158.26051331 16.83462524]\n+[173.21282959 15.63941574]\n+[187.53950500 20.08312035]\n+[199.19094849 29.53001785]\n+[206.50028992 42.62862396]\n+[208.42185974 57.50503159]\n+[204.68074036 72.03101349]\n+[195.81214905 84.12845612]\n+[183.08483887 92.06668854]\n+[168.31959534 94.71005249]\n+[153.62709045 91.67971802]\n+[168.02673340 95.88093567]\n+[182.42637634 100.08216095]\n+[196.82603455 104.28337860]\n+[211.22567749 108.48459625]\n+[224.12878418 99.65035248]\n+[239.68653870 101.22833252]\n+[250.55305481 112.47345734]\n+[251.59750366 128.07612610]\n+[242.32670593 140.66921997]\n+[227.11805725 144.30670166]\n+[213.15261841 137.27102661]\n+[207.02444458 122.88423920]\n+[192.62480164 118.68302155]\n+[178.22515869 114.48180389]\n+[163.82551575 110.28057861]\n+[149.42587280 106.07936096]\n+[137.59794617 115.30433655]\n+[138.16557312 130.29359436]\n+[138.73320007 145.28285217]\n+[139.30081177 160.27210999]\n+[139.86843872 175.26136780]\n+[140.43606567 190.25062561]\n+[141.00367737 205.23986816]\n+[143.92169189 224.40065002]\n+] def\n+/pairs [\n+[1 81]\n+[2 80]\n+[3 79]\n+[4 78]\n+[5 77]\n+[6 76]\n+[7 75]\n+[10 25]\n+[11 24]\n+[12 23]\n+[27 43]\n+[28 42]\n+[29 41]\n+[30 40]\n+[31 39]\n+[58 74]\n+[59 73]\n+[60 72]\n+[61 71]\n+[62 70]\n+] def\n+\n+init\n+\n+% Start Annotations\n+1 81 0.0 1 colorpair\n+2 80 0.16 1 colorpair\n+3 79 0.16 1 colorpair\n+4 78 0.16 1 colorpair\n+5 77 0.16 1 colorpair\n+6 76 0.32 1 colorpair\n+7 75 0.16 1 colorpair\n+10 25 0.0 1 colorpair\n+11 24 0.16 1 colorpair\n+12 23 0.16 1 colorpair\n+27 43 0.16 1 colorpair\n+28 42 0.0 1 colorpair\n+29 41 0.16 1 colorpair\n+30 40 0.0 1 colorpair\n+31 39 0.16 1 colorpair\n+58 74 0.16 1 colorpair\n+59 73 0.0 1 colorpair\n+60 72 0.16 1 colorpair\n+61 71 0.0 1 colorpair\n+62 70 0.0 1 colorpair\n+\n+% End Annotations\n+% switch off outline pairs or bases by removing these lines\n+drawoutline\n+drawpairs\n+drawbases\n+% Start Annotations\n+2 cmark\n+80 cmark\n+3 cmark\n+79 cmark\n+4 cmark\n+78 cmark\n+5 cmark\n+77 cmark\n+6 cmark\n+76 cmark\n+7 cmark\n+75 cmark\n+11 cmark\n+24 cmark\n+12 cmark\n+23 cmark\n+27 cmark\n+43 cmark\n+29 cmark\n+41 cmark\n+31 cmark\n+39 cmark\n+58 cmark\n+74 cmark\n+60 cmark\n+72 cmark\n+\n+% End Annotations\n+% show it\n+showpage\n+end\n+%%EOF\n' |
| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/1.cluster.top5.aln.ps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.cluster.top5.aln.ps Sat Oct 27 13:23:06 2018 -0400 |
| [ |
| b'@@ -0,0 +1,344 @@\n+%!PS-Adobe-3.0 EPSF-3.0\n+%%BoundingBox: 0 0 498 181\n+%%EndComments\n+% draws Vienna RNA like colored boxes\n+/box { % x1 y1 x2 y2 hue saturation\n+ gsave\n+ dup 0.3 mul 1 exch sub sethsbcolor\n+ exch 3 index sub exch 2 index sub rectfill\n+ grestore\n+} def\n+% draws a box in current color\n+/box2 { % x1 y1 x2 y2\n+ exch 3 index sub exch 2 index sub rectfill\n+} def\n+/string { % (Text) x y\n+ 6 add\n+ moveto\n+ show\n+} def\n+0 181 translate\n+1 -1 scale\n+/Courier findfont\n+[10 0 0 -10 0 0] makefont setfont\n+96.0 11.5 102.0 20.0 0.0 1 box\n+96.0 20.0 102.0 28.5 0.0 1 box\n+96.0 28.5 102.0 37.0 0.0 1 box\n+96.0 37.0 102.0 45.5 0.0 1 box\n+96.0 45.5 102.0 54.0 0.0 1 box\n+216.0 101.0 222.0 109.5 0.0 1 box\n+216.0 109.5 222.0 118.0 0.0 1 box\n+216.0 118.0 222.0 126.5 0.0 1 box\n+216.0 126.5 222.0 135.0 0.0 1 box\n+216.0 135.0 222.0 143.5 0.0 1 box\n+102.0 11.5 108.0 20.0 0.16 1 box\n+102.0 20.0 108.0 28.5 0.16 1 box\n+102.0 28.5 108.0 37.0 0.16 1 box\n+102.0 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| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/1.cluster.top5.result.aln_1.R2R.sto.pdf --- 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 |
| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/2.cluster.all --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.cluster.all Sat Oct 27 13:23:06 2018 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/2.cluster.top5.alirna.ps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.cluster.top5.alirna.ps Sat Oct 27 13:23:06 2018 -0400 |
| [ |
| b"@@ -0,0 +1,425 @@\n+%!PS-Adobe-3.0 EPSF-3.0\n+%%Creator: ViennaRNA-2.3.1\n+%%CreationDate: Tue May 30 20:24:21 2017\n+%%Title: RNA Secondary Structure Plot\n+%%BoundingBox: 0 0 700 700\n+%%DocumentFonts: Helvetica\n+%%Pages: 1\n+%%EndComments\n+\n+%Options: --noLP \n+% to switch off outline pairs of sequence comment or\n+% delete the appropriate line near the end of the file\n+\n+%%BeginProlog\n+/RNAplot 100 dict def\n+RNAplot begin\n+/fsize 14 def\n+/outlinecolor {0.2 setgray} bind def\n+/paircolor {0.2 setgray} bind def\n+/seqcolor {0 setgray} bind def\n+/cshow { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def\n+/min { 2 copy gt { exch } if pop } bind def\n+/max { 2 copy lt { exch } if pop } bind def\n+/arccoords { % i j arccoords\n+ % puts optimal x1 y1 x2 y2 coordinates used in bezier curves from i to j\n+ % onto the stack\n+ dup 3 -1 roll dup 4 -1 roll lt dup dup 5 2 roll {exch} if\n+ dup 3 -1 roll dup 3 -1 roll exch sub 1 sub dup\n+ 4 -2 roll 5 -1 roll {exch} if 4 2 roll\n+ sequence length dup 2 div exch 3 1 roll lt \n+ {exch 5 -1 roll pop 4 -2 roll exch 4 2 roll}\n+ { 4 2 roll 5 -1 roll dup 6 1 roll {exch} if\n+ 4 -2 roll exch pop dup 3 -1 roll dup 4 1 roll\n+ exch add 4 -1 roll dup 5 1 roll sub 1 sub\n+ 5 -1 roll not {4 -2 roll exch 4 2 roll} if\n+ }ifelse\n+ % compute the scalingfactor and prepare (1-sf) and sf*r\n+ 2 mul exch cpr 3 1 roll div dup\n+ 3 -1 roll mul exch 1 exch sub exch\n+ % compute the coordinates\n+ 3 -1 roll 1 sub coor exch get aload pop % get coord for i\n+ 4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate y1\n+ 4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate x1\n+ 5 -1 roll 1 sub coor exch get aload pop % get coord for j\n+ % duplicate j coord\n+ dup 3 -1 roll dup 4 1 roll exch 8 2 roll\n+ 6 -1 roll dup 7 1 roll mul 5 -1 roll dup 6 1 roll add exch % calculate y2\n+ 6 -1 roll mul 5 -1 roll add exch % calculate x2\n+ 6 -2 roll % reorder\n+} bind def\n+/drawoutline {\n+ gsave 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100.86514282]\n+[126.48009491 87.15043640]\n+[136.39979553 75.89878845]\n+[149.24496460 68.15272522]\n+[163.82543945 64.62996674]\n+[178.79025269 65.65692139]\n+[192.75280762 71.13842010]\n+[204.41941833 80.56658936]\n+[212.70909119 93.06784058]\n+[216.85374451 107.48386383]\n+[216.46936035 122.47894287]\n+[211.59153748 136.66368103]\n+[202.67224121 148.72378540]\n+[190.53790283 157.54182434]\n+[176.31283569 162.30076599]\n+[161.31506348 162.55963135]\n+[146.93423462 158.29446411]\n+[134.50280762 149.90045166]\n+[125.17218018 138.15458679]\n+[125.17218018 153.15458679]\n+[125.17218018 168.15458679]\n+[136.06672668 179.28770447]\n+[135.85304260 194.49984741]\n+[125.17218018 204.81752014]\n+[125.17218018 219.81752014]\n+[125.17218018 234.81752014]\n+[125.17218018 249.81752014]\n+[139.10159302 255.97311401]\n+[149.31823730 267.26647949]\n+[154.05200195 281.74096680]\n+[152.48275757 296.88882446]\n+[144.88235474 310.08557129]\n+[132.56762695 319.04476929]\n+] def\n+/pairs [\n+[7 94]\n+[8 93]\n+[9 92]\n+[10 91]\n+[13 88]\n+[14 87]\n+[15 86]\n+[16 67]\n+[17 66]\n+[18 64]\n+[19 63]\n+[20 62]\n+[21 60]\n+[22 59]\n+[23 58]\n+[25 56]\n+[26 55]\n+[27 54]\n+[28 53]\n+[29 52]\n+[30 51]\n+[31 50]\n+[32 49]\n+[38 46]\n+[39 45]\n+] def\n+\n+init\n+\n+% Start Annotations\n+7 94 0.0 0.6 colorpair\n+8 93 0.0 1 colorpair\n+9 92 0.0 1 colorpair\n+10 91 0.0 1 colorpair\n+13 88 0.0 1 colorpair\n+14 87 0.0 1 colorpair\n+15 86 0.0 1 colorpair\n+16 67 0.0 1 colorpair\n+17 66 0.16 1 colorpair\n+18 64 0.0 1 colorpair\n+19 63 0.0 1 colorpair\n+20 62 0.0 1 colorpair\n+21 60 0.0 1 colorpair\n+22 59 0.0 1 colorpair\n+23 58 0.16 1 colorpair\n+25 56 0.0 1 colorpair\n+26 55 0.0 1 colorpair\n+27 54 0.0 1 colorpair\n+28 53 0.0 1 colorpair\n+29 52 0.0 1 colorpair\n+30 51 0.0 1 colorpair\n+31 50 0.0 1 colorpair\n+32 49 0.16 1 colorpair\n+38 46 0.0 1 colorpair\n+39 45 0.32 1 colorpair\n+\n+% End Annotations\n+% switch off outline pairs or bases by removing these lines\n+drawoutline\n+drawpairs\n+drawbases\n+% Start Annotations\n+7 94 1 gmark\n+66 cmark\n+23 cmark\n+32 cmark\n+39 cmark\n+45 cmark\n+\n+% End Annotations\n+% show it\n+showpage\n+end\n+%%EOF\n' |
| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/2.cluster.top5.aln.ps --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.cluster.top5.aln.ps Sat Oct 27 13:23:06 2018 -0400 |
| [ |
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| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/RESULTS.zip |
| b |
| Binary file test-data/RESULTS.zip has changed |
| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/combined_cm_out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combined_cm_out Sat Oct 27 13:23:06 2018 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 79df97a1bc0f -r f93c868203cc test-data/evaluation1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evaluation1.txt Sat Oct 27 13:23:06 2018 -0400 |
| b |
| @@ -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 |