| Next changeset 1:ed8c7191b322 (2016-12-22) |
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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053 |
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added:
evaluation.py glob_report.xml test-data/1.1.model.tree.fa test-data/1.2.model.tree.fa test-data/1.tabular test-data/2.tabular test-data/FASTA.zip test-data/RESULTS/1.cluster.all test-data/RESULTS/1.cluster.all.fa test-data/RESULTS/1.cluster.part test-data/RESULTS/1.cluster.stats test-data/RESULTS/2.cluster.all test-data/RESULTS/2.cluster.all.fa test-data/RESULTS/2.cluster.part test-data/RESULTS/2.cluster.stats test-data/RESULTS/cluster.final.stats test-data/RESULTS/fullTab.tabular test-data/RESULTS/partitions/final_overlap.map test-data/RESULTS/partitions/final_overlap.matrix test-data/RESULTS/partitions/final_partition.hard.best test-data/RESULTS/partitions/final_partition.hard.merged test-data/RESULTS/partitions/final_partition.soft test-data/RESULTS/partitions/final_partition.used_cmsearch |
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| diff -r 000000000000 -r b797e13169a0 evaluation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/evaluation.py Fri Dec 16 07:34:49 2016 -0500 |
| [ |
| @@ -0,0 +1,51 @@ +import glob +from os import system +import re + + +def sh(script): + system("bash -c '%s'" % script) + + +dataNames = "FASTA/data.names" +listOfClusters = [] +listOfClasses = [] +cluster_seqs_stats_path = "RESULTS/*.cluster.all" +cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path) + +blackList = [] +numberOfClusters = 0 +for singleFile in sorted(cluster_seqs_stats_files): + numberOfClusters += 1 + with open(singleFile, "r") as f: + for line in f.readlines(): + uniqueId = line.split()[6] + clustNum = line.split()[1] + rnaClass, sep, tail = uniqueId.partition("_") + listOfClasses.append(rnaClass) + listOfClusters.append(clustNum) + with open(dataNames, "r") as names: + for line in names.readlines(): + fullUniqeId = line.split()[3] + rnaClass, sep, tail = fullUniqeId.partition("_") + short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0] + if short_unique == uniqueId: + blackList.append(uniqueId) + +numberOfClusters += 1 # 1 cluster for all unassigned seqs +with open(dataNames, "r") as names: + for line in names.readlines(): + fullUniqeId = line.split()[3] + rnaClass, sep, tail = fullUniqeId.partition("_") + short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0] + rnaClass, sep, tail = fullUniqeId.partition("_") + if short_unique not in blackList: + listOfClasses.append(rnaClass) + listOfClusters.append(str(numberOfClusters)) + numberOfClusters += 1 # separate cluster for all unassigned seqs + +toWrite = "" +for i in range(len(listOfClusters)): + toWrite += listOfClasses[i] + "\t" + listOfClusters[i] + '\n' +with open("RESULTS/fullTab.tabular", "w") as full: + full.write(toWrite) |
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| diff -r 000000000000 -r b797e13169a0 glob_report.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glob_report.xml Fri Dec 16 07:34:49 2016 -0500 |
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| @@ -0,0 +1,139 @@ +<tool id="glob_report" name="Report_Results" version="0.1"> + <requirements> + <requirement type="package" version="0.1">graphclust-wrappers</requirement> + <requirement type="package" version='0.5'>perl-array-utils</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + + unzip $FASTA &> /dev/null && + + #set $inputFiles = "" + + #for $cms_res in $cmsearch_results: + #set $inputFiles += str($cms_res)+',' + #end for + #set $inputFiles = $inputFiles[:-1] + + #set $inputFilesTrees = "" + + #for $mods in $model_tree_files: + #set $inputFilesTrees += str($mods)+',' + #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' + #if $iteration_num.iteration_num_selector: + $iteration_num.CI + + $final_partition_soft + $final_partition_used_cmsearch + #end if + + && + python '$__tool_directory__/evaluation.py' +]]> + </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"/> + <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" /> + </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=""/> + </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" /> + <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> + </outputs> + <tests> + <test> + <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/> + <param name="cmsearch_results" value="1.tabular,2.tabular"/> + <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/> + <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="1"/> + <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> + </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> |
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| diff -r 000000000000 -r b797e13169a0 test-data/1.1.model.tree.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.1.model.tree.fa Fri Dec 16 07:34:49 2016 -0500 |
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| @@ -0,0 +1,40 @@ +>7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12 +GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA +>9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14 +GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA +>10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15 +GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG +>15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1 +GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA +>16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20 +GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA +>17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21 +GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA +>18 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22 +GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA +>23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27 +GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA +>28 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31 +GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA +>30 SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33 +GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC +>31 SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34 +GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA +>32 SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35 +GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA +>33 SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36 +UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG +>35 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38 +UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU +>37 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3 +GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA +>46 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5 +UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA +>51 SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006_rep.0 +GGCUGGCUUUAGCUCAGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGCCCUCUU +>52 SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1 +GGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU +>53 SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2 +GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU +>54 SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3 +GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU |
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| diff -r 000000000000 -r b797e13169a0 test-data/1.2.model.tree.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.2.model.tree.fa Fri Dec 16 07:34:49 2016 -0500 |
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| @@ -0,0 +1,40 @@ +>1 SEQ1#1#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001_rep.0 +GUCUAUGGCCAUACCACCCUGAAUGUGCUUGAUCUCAUCUGAUCUCGUGAAGCCAAGCAGGGUGGGGCCUAGUUAGUACUUGGAUGGGAGACUUCCUGGGAAUAUAAGCUGCUGUUGGCU +>3 SEQ3#1#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001_rep.2 +GUCUACAGCCAUACCAUCCUGAACAUGCCAGAUCUUGUCUGACCUCUGAAGCUAAGCAGGGUCAAGCCUGGUUAGUACUUGGGAGAAGCUGGUGUGGCUAGACC +>39 SEQ39#1#69#+ ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41 +GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGUUGUAGUCCGUGCGAGAAUA +>55 SEQ55#1#113#+ ORIGID RF00019_rep.0_V00584.1/39-151_55 ORIGHEAD RF00019_rep.0 +GGCUGGUCCGAAGGUAGUGAGUUAUCUCAAUUGAUUGUUCACAGUCAGUUACAGAUCGAACUCCUUGUUCUACUCUUUCCCCCCUUCUCACUACUGCACUUGACUAGUCUUUU +>56 SEQ56#1#95#+ ORIGID RF00019_rep.1_L32608.1/283-377_56 ORIGHEAD RF00019_rep.1 +GGCUGGUCCGAUGGUAGUGGGUUAUCAGAACUUAUUAACAUUAGUGUCACUAAAGUUGGUAUACAACCCCCCACUGCUAAAUUUGACUGGCUUUU +>57 SEQ57#1#102#+ ORIGID RF00019_rep.2_ABBA01033605.1/1707-1808_57 ORIGHEAD RF00019_rep.2 +GGCUGGUCCGAGUGCAGUGGUGUUUACAACUAAUUGAUCACAACCAGUUACAGAUUUCUUUGUUCCUUCUCCACUCCCACUGCUUCACUUGACUAGCCUUUU +>59 SEQ59#1#79#+ ORIGID RF00027_rep.0_AF480570.1/1-79_59 ORIGHEAD RF00027_rep.0 +GUGAGGUAGUAAGUUGUAUUGUUGUGGGGUAGGGAUAUUAGGCCCCAAUUAGAAGAUAACUAUACAACUUACUACUUUC +>72 SEQ72#1#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618_rep.0 +ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGCUUUGCCUUGGUGCAGUUUUUGGAGAA +>75 SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3 +ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA +>78 SEQ78#1#80#+ ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11 +GGUAUUUGAAGAUGCGGUUGACCAUGGUGUGUACGCUUUAUUUGUGACGUAGGACACAUGGUCUACUUCUUCUCAAUAUC +>79 SEQ79#1#79#+ ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12 +GGUACUUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUUAUUGACUUCGAAUAAUACAUGGUUGAUCUUUUCUCAGUAUC +>80 SEQ80#1#79#+ ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13 +GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC +>81 SEQ81#1#77#+ ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1 +GGUACUGGAGGAGAGGUUAUCUGUGUUUUUUCCCUUUAUUUAUGAUGAAAAAUAUGGUGCACUUCUAUUUGAGAAUC +>82 SEQ82#1#81#+ ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2 +GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC +>84 SEQ84#1#79#+ ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4 +GGUACUCGAAUGGAGGUUGUCCAUGGUGUGUUCAUUUUAUUUAUGAUGAGUAUUACAUGGCCAAUCUCCUUUCGGUACU +>85 SEQ85#1#79#+ ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5 +GGUGCUUAAAGAAUGGCUGUCCGUAGUAUGGUCUCUAUAUUUAUGAUGAUUAAUAUCGGACAACCAUUGUUUUAGUAUC +>86 SEQ86#1#79#+ ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6 +GGUACUUAAGGGGGAGGUGGGCUUUGAAUAAUAAGUUUAUUGACGUGGAAUAUACAAGGGCAAGCUCUCUGUGAGUAUC +>87 SEQ87#1#78#+ ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7 +GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC +>88 SEQ88#1#81#+ ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8 +GGUACUGGUGGAGAGGUCUUCCAUGAUGCAUUCGAUUUAUUUUUUGACCAAUCCUACAUAGUGGACUCUUUUGAAAGCAUU +>89 SEQ89#1#80#+ ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9 +GGUACUUGGAGAGAUAGUAGACCGUAUAGCGUACGCUUUAUCUGUGACGUAUGUAACACGGUCCACUAACCCUCAGUAUC |
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| diff -r 000000000000 -r b797e13169a0 test-data/1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.tabular Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,46 @@ +SEQ11 - dataset_2087 - cm 1 72 1 82 + no 1 0.62 0.0 88.8 1.1e-38 ! ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16 +SEQ13 - dataset_2087 - cm 1 72 1 82 + no 1 0.56 0.0 87.5 3.5e-38 ! ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18 +SEQ31 - dataset_2087 - cm 1 72 1 73 + no 1 0.56 0.0 84.9 3.1e-37 ! ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34 +SEQ37 - dataset_2087 - cm 1 72 1 82 + no 1 0.63 0.0 84.9 3.4e-37 ! ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3 +SEQ12 - dataset_2087 - cm 1 72 1 82 + no 1 0.57 0.0 84.8 3.7e-37 ! ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17 +SEQ9 - dataset_2087 - cm 1 72 1 73 + no 1 0.56 0.0 83.8 8.7e-37 ! ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14 +SEQ32 - dataset_2087 - cm 1 72 1 73 + no 1 0.58 0.0 82.5 2.6e-36 ! ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35 +SEQ28 - dataset_2087 - cm 1 72 1 71 + no 1 0.62 0.0 82.4 3e-36 ! ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31 +SEQ7 - dataset_2087 - cm 1 72 1 83 + no 1 0.63 0.0 81.0 9.6e-36 ! ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12 +SEQ46 - dataset_2087 - cm 1 72 1 72 + no 1 0.65 0.0 80.9 1.1e-35 ! ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5 +SEQ26 - dataset_2087 - cm 1 72 1 72 + no 1 0.50 0.0 80.0 2.4e-35 ! ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2 +SEQ5 - dataset_2087 - cm 1 72 1 72 + no 1 0.51 0.0 79.6 3.2e-35 ! ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10 +SEQ24 - dataset_2087 - cm 1 72 1 73 + no 1 0.56 0.0 79.0 5.6e-35 ! ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28 +SEQ17 - dataset_2087 - cm 1 72 1 71 + no 1 0.59 0.0 78.9 6.2e-35 ! ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21 +SEQ36 - dataset_2087 - cm 1 72 1 73 + no 1 0.51 0.0 78.5 8.3e-35 ! ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39 +SEQ50 - dataset_2087 - cm 1 72 1 73 + no 1 0.56 0.0 78.4 9.1e-35 ! ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9 +SEQ15 - dataset_2087 - cm 1 72 1 73 + no 1 0.53 0.0 76.6 4.5e-34 ! ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1 +SEQ21 - dataset_2087 - cm 1 72 1 74 + no 1 0.61 0.0 76.3 5.7e-34 ! ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25 +SEQ23 - dataset_2087 - cm 1 72 1 74 + no 1 0.61 0.0 76.3 5.7e-34 ! ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27 +SEQ4 - dataset_2087 - cm 1 72 1 73 + no 1 0.56 0.0 75.1 1.7e-33 ! ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0 +SEQ16 - dataset_2087 - cm 1 72 1 72 + no 1 0.61 0.0 74.7 2.3e-33 ! ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20 +SEQ18 - dataset_2087 - cm 1 72 1 72 + no 1 0.58 0.0 73.6 6.2e-33 ! ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22 +SEQ10 - dataset_2087 - cm 1 72 1 73 + no 1 0.62 0.0 73.3 8.3e-33 ! ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15 +SEQ20 - dataset_2087 - cm 1 72 1 72 + no 1 0.56 0.0 73.3 8.3e-33 ! ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24 +SEQ30 - dataset_2087 - cm 1 72 1 72 + no 1 0.61 0.0 72.3 1.9e-32 ! ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33 +SEQ35 - dataset_2087 - cm 1 72 1 72 + no 1 0.65 0.0 71.7 3.2e-32 ! ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38 +SEQ19 - dataset_2087 - cm 1 72 1 82 + no 1 0.59 0.0 69.4 2.5e-31 ! ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23 +SEQ33 - dataset_2087 - cm 1 72 1 72 + no 1 0.62 0.0 69.3 2.5e-31 ! ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36 +SEQ45 - dataset_2087 - cm 1 72 1 72 + no 1 0.60 0.0 69.3 2.7e-31 ! ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4 +SEQ22 - dataset_2087 - cm 1 72 1 72 + no 1 0.49 0.0 47.8 3.6e-23 ! ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26 +SEQ14 - dataset_2087 - cm 1 72 2 72 + no 1 0.41 0.0 45.6 2.5e-22 ! ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19 +SEQ29 - dataset_2087 - cm 1 72 1 66 + no 1 0.42 0.0 34.4 4.1e-18 ! ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32 +SEQ39 - dataset_2087 - cm 1 72 1 69 + no 1 0.39 0.0 21.4 3.5e-13 ! ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41 +SEQ40 - dataset_2087 - cm 1 72 1 66 + no 1 0.45 0.0 17.8 8e-12 ! ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005_rep.42 +SEQ34 - dataset_2087 - cm 1 72 1 68 + no 1 0.34 0.0 13.6 3.4e-10 ! ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005_rep.37 +SEQ42 - dataset_2087 - cm 1 72 1 69 + no 1 0.38 0.0 13.1 5e-10 ! ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44 +SEQ6 - dataset_2087 - cm 1 72 1 66 + no 1 0.38 0.0 10.1 6.6e-09 ! ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11 +SEQ27 - dataset_2087 - cm 1 72 1 69 + no 1 0.43 0.0 8.0 4.3e-08 ! ORIGID RF00005_rep.30_AL132988.4/95773-95841_27 ORIGHEAD RF00005_rep.30 +SEQ48 - dataset_2087 - cm 1 72 1 71 + no 1 0.35 0.0 6.7 1.3e-07 ! ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005_rep.7 +SEQ41 - dataset_2087 - cm 1 72 1 68 + no 1 0.26 0.1 6.3 1.9e-07 ! ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005_rep.43 +SEQ25 - dataset_2087 - cm 1 72 1 69 + no 1 0.29 0.0 5.3 4.5e-07 ! ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005_rep.29 +SEQ43 - dataset_2087 - cm 1 72 1 71 + no 1 0.41 0.0 4.7 7.6e-07 ! ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45 +SEQ8 - dataset_2087 - cm 1 72 1 70 + no 1 0.33 0.0 3.1 3.1e-06 ! ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13 +SEQ44 - dataset_2087 - cm 1 72 1 69 + no 1 0.42 0.0 0.7 2.5e-05 ! ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005_rep.46 +SEQ38 - dataset_2087 - cm 1 72 1 65 + no 1 0.23 0.5 -0.9 0.0001 ! ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40 +SEQ47 - dataset_2087 - cm 1 72 1 68 + no 1 0.24 0.5 -5.2 0.0044 ! ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6 |
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| diff -r 000000000000 -r b797e13169a0 test-data/2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.tabular Fri Dec 16 07:34:49 2016 -0500 |
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| @@ -0,0 +1,14 @@ +SEQ82 - dataset_2088 - cm 1 80 1 81 + no 1 0.38 0.0 86.6 1.9e-28 ! ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2 +SEQ76 - dataset_2088 - cm 1 80 1 79 + no 1 0.53 0.0 81.8 7.1e-27 ! ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0 +SEQ84 - dataset_2088 - cm 1 80 1 79 + no 1 0.41 0.0 79.8 3.2e-26 ! ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4 +SEQ79 - dataset_2088 - cm 1 80 1 79 + no 1 0.38 0.0 76.7 3.4e-25 ! ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12 +SEQ89 - dataset_2088 - cm 1 80 1 80 + no 1 0.46 0.0 75.4 9e-25 ! ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9 +SEQ78 - dataset_2088 - cm 1 80 1 80 + no 1 0.43 0.0 74.4 2e-24 ! ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11 +SEQ85 - dataset_2088 - cm 1 80 1 79 + no 1 0.35 0.0 73.2 5.1e-24 ! ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5 +SEQ87 - dataset_2088 - cm 1 80 1 78 + no 1 0.38 0.0 72.1 1.2e-23 ! ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7 +SEQ81 - dataset_2088 - cm 1 80 1 77 + no 1 0.35 0.0 70.3 4.6e-23 ! ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1 +SEQ86 - dataset_2088 - cm 1 80 1 79 + no 1 0.43 0.0 69.6 7.6e-23 ! ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6 +SEQ88 - dataset_2088 - cm 1 80 1 81 + no 1 0.40 0.0 62.3 2e-20 ! ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8 +SEQ80 - dataset_2088 - cm 1 80 1 79 + no 1 0.53 0.0 57.6 6.6e-19 ! ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13 +SEQ77 - dataset_2088 - cm 1 80 1 77 + no 1 0.55 0.0 56.6 1.5e-18 ! ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10 +SEQ83 - dataset_2088 - cm 1 80 1 79 + no 1 0.44 0.0 18.8 4.2e-06 ! ORIGID RF00641_rep.3_AADD01141098.1/2614-2692_83 ORIGHEAD RF00641_rep.3 |
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| diff -r 000000000000 -r b797e13169a0 test-data/FASTA.zip |
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| Binary file test-data/FASTA.zip has changed |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/1.cluster.all --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/1.cluster.all Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,33 @@ +CLUSTER 1 CM_SCORE 84.9 MODEL 1.1 RF00005_rep.34 +CLUSTER 1 CM_SCORE 84.9 MODEL 1.1 RF00005_rep.3 +CLUSTER 1 CM_SCORE 83.8 MODEL 1.1 RF00005_rep.14 +CLUSTER 1 CM_SCORE 82.5 MODEL 1.1 RF00005_rep.35 +CLUSTER 1 CM_SCORE 82.4 MODEL 1.1 RF00005_rep.31 +CLUSTER 1 CM_SCORE 81.0 MODEL 1.1 RF00005_rep.12 +CLUSTER 1 CM_SCORE 80.9 MODEL 1.1 RF00005_rep.5 +CLUSTER 1 CM_SCORE 78.9 MODEL 1.1 RF00005_rep.21 +CLUSTER 1 CM_SCORE 76.6 MODEL 1.1 RF00005_rep.1 +CLUSTER 1 CM_SCORE 76.3 MODEL 1.1 RF00005_rep.27 +CLUSTER 1 CM_SCORE 74.7 MODEL 1.1 RF00005_rep.20 +CLUSTER 1 CM_SCORE 73.6 MODEL 1.1 RF00005_rep.22 +CLUSTER 1 CM_SCORE 73.3 MODEL 1.1 RF00005_rep.15 +CLUSTER 1 CM_SCORE 72.3 MODEL 1.1 RF00005_rep.33 +CLUSTER 1 CM_SCORE 71.7 MODEL 1.1 RF00005_rep.38 +CLUSTER 1 CM_SCORE 69.3 MODEL 1.1 RF00005_rep.36 +CLUSTER 1 CM_SCORE 21.4 MODEL 1.1 RF00005_rep.41 +CLUSTER 1 CM_SCORE 88.8 CMSEARCH 1.1 RF00005_rep.16 +CLUSTER 1 CM_SCORE 87.5 CMSEARCH 1.1 RF00005_rep.18 +CLUSTER 1 CM_SCORE 84.8 CMSEARCH 1.1 RF00005_rep.17 +CLUSTER 1 CM_SCORE 80.0 CMSEARCH 1.1 RF00005_rep.2 +CLUSTER 1 CM_SCORE 79.6 CMSEARCH 1.1 RF00005_rep.10 +CLUSTER 1 CM_SCORE 79.0 CMSEARCH 1.1 RF00005_rep.28 +CLUSTER 1 CM_SCORE 78.5 CMSEARCH 1.1 RF00005_rep.39 +CLUSTER 1 CM_SCORE 78.4 CMSEARCH 1.1 RF00005_rep.9 +CLUSTER 1 CM_SCORE 76.3 CMSEARCH 1.1 RF00005_rep.25 +CLUSTER 1 CM_SCORE 75.1 CMSEARCH 1.1 RF00005_rep.0 +CLUSTER 1 CM_SCORE 73.3 CMSEARCH 1.1 RF00005_rep.24 +CLUSTER 1 CM_SCORE 69.4 CMSEARCH 1.1 RF00005_rep.23 +CLUSTER 1 CM_SCORE 69.3 CMSEARCH 1.1 RF00005_rep.4 +CLUSTER 1 CM_SCORE 47.8 CMSEARCH 1.1 RF00005_rep.26 +CLUSTER 1 CM_SCORE 45.6 CMSEARCH 1.1 RF00005_rep.19 +CLUSTER 1 CM_SCORE 34.4 CMSEARCH 1.1 RF00005_rep.32 |
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| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/1.cluster.all.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/1.cluster.all.fa Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,66 @@ +>SEQ22_1_72_+ RESULT 1 SCORE 47.8 EVALUE 3.6e-23 CLUSTER 1.1 LOC ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26 +UAGGAUGGGGUGUGAUAGGUGGCACGGAGAAUUUUGGAUUCUCAGGGAUGGGUUCGAUUCUCAUAGUCCUAG +>SEQ37_1_82_+ RESULT 1 SCORE 84.9 EVALUE 3.4e-37 CLUSTER 1.1 LOC ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3 +GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA +>SEQ23_1_74_+ RESULT 1 SCORE 76.3 EVALUE 5.7e-34 CLUSTER 1.1 LOC ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27 +GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA +>SEQ50_1_73_+ RESULT 1 SCORE 78.4 EVALUE 9.1e-35 CLUSTER 1.1 LOC ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9 +GCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCG +>SEQ39_1_69_+ RESULT 1 SCORE 21.4 EVALUE 3.5e-13 CLUSTER 1.1 LOC ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41 +GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGUUGUAGUCCGUGCGAGAAUA +>SEQ46_1_72_+ RESULT 1 SCORE 80.9 EVALUE 1.1e-35 CLUSTER 1.1 LOC ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5 +UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA +>SEQ17_1_71_+ RESULT 1 SCORE 78.9 EVALUE 6.2e-35 CLUSTER 1.1 LOC ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21 +GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA +>SEQ24_1_73_+ RESULT 1 SCORE 79.0 EVALUE 5.6e-35 CLUSTER 1.1 LOC ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28 +CCUUCGAUAGCUCAGCUGGUAGAGCGGAGGACUGUAGAUCCUUAGGUCGCUGGUUCGAUUCCGGCUCGAAGGA +>SEQ7_1_83_+ RESULT 1 SCORE 81.0 EVALUE 9.6e-36 CLUSTER 1.1 LOC ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12 +GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA +>SEQ32_1_73_+ RESULT 1 SCORE 82.5 EVALUE 2.6e-36 CLUSTER 1.1 LOC ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35 +GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA +>SEQ20_1_72_+ RESULT 1 SCORE 73.3 EVALUE 8.3e-33 CLUSTER 1.1 LOC ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24 +GGGGGUAUAGCUCAGGGGUAGAGCAUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCAGGUGCCCCCU +>SEQ36_1_73_+ RESULT 1 SCORE 78.5 EVALUE 8.3e-35 CLUSTER 1.1 LOC ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39 +GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCCUGGAUCAAAACCAGGCGGAAACA +>SEQ10_1_73_+ RESULT 1 SCORE 73.3 EVALUE 8.3e-33 CLUSTER 1.1 LOC ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15 +GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG +>SEQ28_1_71_+ RESULT 1 SCORE 82.4 EVALUE 3e-36 CLUSTER 1.1 LOC ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31 +GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA +>SEQ35_1_72_+ RESULT 1 SCORE 71.7 EVALUE 3.2e-32 CLUSTER 1.1 LOC ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38 +UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU +>SEQ21_1_74_+ RESULT 1 SCORE 76.3 EVALUE 5.7e-34 CLUSTER 1.1 LOC ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25 +GUCUCUGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACG +>SEQ16_1_72_+ RESULT 1 SCORE 74.7 EVALUE 2.3e-33 CLUSTER 1.1 LOC ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20 +GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA +>SEQ30_1_72_+ RESULT 1 SCORE 72.3 EVALUE 1.9e-32 CLUSTER 1.1 LOC ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33 +GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC +>SEQ12_1_82_+ RESULT 1 SCORE 84.8 EVALUE 3.7e-37 CLUSTER 1.1 LOC ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17 +GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUUGAAAUCCAUUGGGGUUUCCCCGCGCAGGUUCGAAUCCUGUCGGCUACG +>SEQ33_1_72_+ RESULT 1 SCORE 69.3 EVALUE 2.5e-31 CLUSTER 1.1 LOC ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36 +UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG +>SEQ19_1_82_+ RESULT 1 SCORE 69.4 EVALUE 2.5e-31 CLUSTER 1.1 LOC ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23 +GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUCUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCA +>SEQ15_1_73_+ RESULT 1 SCORE 76.6 EVALUE 4.5e-34 CLUSTER 1.1 LOC ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1 +GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA +>SEQ45_1_72_+ RESULT 1 SCORE 69.3 EVALUE 2.7e-31 CLUSTER 1.1 LOC ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4 +AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAACCAUCCUCUGCUA +>SEQ14_2_72_+ RESULT 1 SCORE 45.6 EVALUE 2.5e-22 CLUSTER 1.1 LOC ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19 +AGAUUGAAGCCAGUUGAUUAGGGUGCUUAGCUGUUAACUAAGUGUUUGUGGGUUUAAGUCCCAUUGGUCUA +>SEQ18_1_72_+ RESULT 1 SCORE 73.6 EVALUE 6.2e-33 CLUSTER 1.1 LOC ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22 +GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA +>SEQ9_1_73_+ RESULT 1 SCORE 83.8 EVALUE 8.7e-37 CLUSTER 1.1 LOC ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14 +GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA +>SEQ5_1_72_+ RESULT 1 SCORE 79.6 EVALUE 3.2e-35 CLUSTER 1.1 LOC ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10 +GGUCCCAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGGACCU +>SEQ11_1_82_+ RESULT 1 SCORE 88.8 EVALUE 1.1e-38 CLUSTER 1.1 LOC ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16 +GCAGCGAUGGCCGAGUGGUUAAGGCGUUGGACUUGAAAUCCAAUGGGGUCUCCCCGCGCAGGUUCGAACCCUGCUCGCUGCG +>SEQ29_1_66_+ RESULT 1 SCORE 34.4 EVALUE 4.1e-18 CLUSTER 1.1 LOC ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32 +GGUAAAAUGGCUGAGUGAAGCAUUGGACUGUAAAUCUAAAGACAGGGGUUAGGCCUCUUUUUACCA +>SEQ26_1_72_+ RESULT 1 SCORE 80.0 EVALUE 2.4e-35 CLUSTER 1.1 LOC ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2 +GGUUCCAUGGUGUAAUGGUUAGCACUCUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGAACCU +>SEQ4_1_73_+ RESULT 1 SCORE 75.1 EVALUE 1.7e-33 CLUSTER 1.1 LOC ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0 +GGCUCCAUAGCUCAGGGGUUAGAGCACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAUUCUCGCUGGGGCUU +>SEQ13_1_82_+ RESULT 1 SCORE 87.5 EVALUE 3.5e-38 CLUSTER 1.1 LOC ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18 +GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG +>SEQ31_1_73_+ RESULT 1 SCORE 84.9 EVALUE 3.1e-37 CLUSTER 1.1 LOC ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34 +GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/1.cluster.part --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/1.cluster.part Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,33 @@ +SEQ22#1#72#+ 47.8 3.6e-23 1.1 1.1 1 +SEQ37#1#82#+ 84.9 3.4e-37 1.1 1.1 1 +SEQ23#1#74#+ 76.3 5.7e-34 1.1 1.1 1 +SEQ50#1#73#+ 78.4 9.1e-35 1.1 1.1 1 +SEQ39#1#69#+ 21.4 3.5e-13 1.1 1.1 1 +SEQ46#1#72#+ 80.9 1.1e-35 1.1 1.1 1 +SEQ17#1#71#+ 78.9 6.2e-35 1.1 1.1 1 +SEQ24#1#73#+ 79.0 5.6e-35 1.1 1.1 1 +SEQ7#1#83#+ 81.0 9.6e-36 1.1 1.1 1 +SEQ32#1#73#+ 82.5 2.6e-36 1.1 1.1 1 +SEQ20#1#72#+ 73.3 8.3e-33 1.1 1.1 1 +SEQ36#1#73#+ 78.5 8.3e-35 1.1 1.1 1 +SEQ10#1#73#+ 73.3 8.3e-33 1.1 1.1 1 +SEQ28#1#71#+ 82.4 3e-36 1.1 1.1 1 +SEQ35#1#72#+ 71.7 3.2e-32 1.1 1.1 1 +SEQ21#1#74#+ 76.3 5.7e-34 1.1 1.1 1 +SEQ16#1#72#+ 74.7 2.3e-33 1.1 1.1 1 +SEQ30#1#72#+ 72.3 1.9e-32 1.1 1.1 1 +SEQ12#1#82#+ 84.8 3.7e-37 1.1 1.1 1 +SEQ33#1#72#+ 69.3 2.5e-31 1.1 1.1 1 +SEQ19#1#82#+ 69.4 2.5e-31 1.1 1.1 1 +SEQ15#1#73#+ 76.6 4.5e-34 1.1 1.1 1 +SEQ45#1#72#+ 69.3 2.7e-31 1.1 1.1 1 +SEQ14#2#72#+ 45.6 2.5e-22 1.1 1.1 1 +SEQ18#1#72#+ 73.6 6.2e-33 1.1 1.1 1 +SEQ9#1#73#+ 83.8 8.7e-37 1.1 1.1 1 +SEQ5#1#72#+ 79.6 3.2e-35 1.1 1.1 1 +SEQ11#1#82#+ 88.8 1.1e-38 1.1 1.1 1 +SEQ29#1#66#+ 34.4 4.1e-18 1.1 1.1 1 +SEQ26#1#72#+ 80.0 2.4e-35 1.1 1.1 1 +SEQ4#1#73#+ 75.1 1.7e-33 1.1 1.1 1 +SEQ13#1#82#+ 87.5 3.5e-38 1.1 1.1 1 +SEQ31#1#73#+ 84.9 3.1e-37 1.1 1.1 1 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/1.cluster.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/1.cluster.stats Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +CLUSTER 1 SEQS 33 IDS_UNIQUE 33 MODELS 1 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/2.cluster.all --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/2.cluster.all Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,13 @@ +CLUSTER 2 CM_SCORE 86.6 MODEL 1.2 RF00641_rep.2 +CLUSTER 2 CM_SCORE 79.8 MODEL 1.2 RF00641_rep.4 +CLUSTER 2 CM_SCORE 76.7 MODEL 1.2 RF00641_rep.12 +CLUSTER 2 CM_SCORE 75.4 MODEL 1.2 RF00641_rep.9 +CLUSTER 2 CM_SCORE 74.4 MODEL 1.2 RF00641_rep.11 +CLUSTER 2 CM_SCORE 73.2 MODEL 1.2 RF00641_rep.5 +CLUSTER 2 CM_SCORE 72.1 MODEL 1.2 RF00641_rep.7 +CLUSTER 2 CM_SCORE 70.3 MODEL 1.2 RF00641_rep.1 +CLUSTER 2 CM_SCORE 69.6 MODEL 1.2 RF00641_rep.6 +CLUSTER 2 CM_SCORE 62.3 MODEL 1.2 RF00641_rep.8 +CLUSTER 2 CM_SCORE 57.6 MODEL 1.2 RF00641_rep.13 +CLUSTER 2 CM_SCORE 81.8 CMSEARCH 1.2 RF00641_rep.0 +CLUSTER 2 CM_SCORE 56.6 CMSEARCH 1.2 RF00641_rep.10 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/2.cluster.all.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/2.cluster.all.fa Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,26 @@ +>SEQ79_1_79_+ RESULT 2 SCORE 76.7 EVALUE 3.4e-25 CLUSTER 1.2 LOC ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12 +GGUACUUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUUAUUGACUUCGAAUAAUACAUGGUUGAUCUUUUCUCAGUAUC +>SEQ85_1_79_+ RESULT 2 SCORE 73.2 EVALUE 5.1e-24 CLUSTER 1.2 LOC ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5 +GGUGCUUAAAGAAUGGCUGUCCGUAGUAUGGUCUCUAUAUUUAUGAUGAUUAAUAUCGGACAACCAUUGUUUUAGUAUC +>SEQ87_1_78_+ RESULT 2 SCORE 72.1 EVALUE 1.2e-23 CLUSTER 1.2 LOC ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7 +GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC +>SEQ82_1_81_+ RESULT 2 SCORE 86.6 EVALUE 1.9e-28 CLUSTER 1.2 LOC ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2 +GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC +>SEQ77_1_77_+ RESULT 2 SCORE 56.6 EVALUE 1.5e-18 CLUSTER 1.2 LOC ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10 +GGUACUCGGGGAGAGGUUACCCGAGCAACUUUGCAUCUGGACGACGAAUGUUGCUCGGUGAACCCCUUUUCGGUAUC +>SEQ80_1_79_+ RESULT 2 SCORE 57.6 EVALUE 6.6e-19 CLUSTER 1.2 LOC ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13 +GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC +>SEQ81_1_77_+ RESULT 2 SCORE 70.3 EVALUE 4.6e-23 CLUSTER 1.2 LOC ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1 +GGUACUGGAGGAGAGGUUAUCUGUGUUUUUUCCCUUUAUUUAUGAUGAAAAAUAUGGUGCACUUCUAUUUGAGAAUC +>SEQ78_1_80_+ RESULT 2 SCORE 74.4 EVALUE 2e-24 CLUSTER 1.2 LOC ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11 +GGUAUUUGAAGAUGCGGUUGACCAUGGUGUGUACGCUUUAUUUGUGACGUAGGACACAUGGUCUACUUCUUCUCAAUAUC +>SEQ76_1_79_+ RESULT 2 SCORE 81.8 EVALUE 7.1e-27 CLUSTER 1.2 LOC ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0 +GGUACUUGGAGAGAGGUGGUCCGUGGCGCGUUCGCUUUAUUUAUGGCGCACAUUACACGGUCGACCUCUUUGCAGUAUC +>SEQ86_1_79_+ RESULT 2 SCORE 69.6 EVALUE 7.6e-23 CLUSTER 1.2 LOC ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6 +GGUACUUAAGGGGGAGGUGGGCUUUGAAUAAUAAGUUUAUUGACGUGGAAUAUACAAGGGCAAGCUCUCUGUGAGUAUC +>SEQ89_1_80_+ RESULT 2 SCORE 75.4 EVALUE 9e-25 CLUSTER 1.2 LOC ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9 +GGUACUUGGAGAGAUAGUAGACCGUAUAGCGUACGCUUUAUCUGUGACGUAUGUAACACGGUCCACUAACCCUCAGUAUC +>SEQ88_1_81_+ RESULT 2 SCORE 62.3 EVALUE 2e-20 CLUSTER 1.2 LOC ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8 +GGUACUGGUGGAGAGGUCUUCCAUGAUGCAUUCGAUUUAUUUUUUGACCAAUCCUACAUAGUGGACUCUUUUGAAAGCAUU +>SEQ84_1_79_+ RESULT 2 SCORE 79.8 EVALUE 3.2e-26 CLUSTER 1.2 LOC ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4 +GGUACUCGAAUGGAGGUUGUCCAUGGUGUGUUCAUUUUAUUUAUGAUGAGUAUUACAUGGCCAAUCUCCUUUCGGUACU |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/2.cluster.part --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/2.cluster.part Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,13 @@ +SEQ79#1#79#+ 76.7 3.4e-25 1.2 1.2 2 +SEQ85#1#79#+ 73.2 5.1e-24 1.2 1.2 2 +SEQ87#1#78#+ 72.1 1.2e-23 1.2 1.2 2 +SEQ82#1#81#+ 86.6 1.9e-28 1.2 1.2 2 +SEQ77#1#77#+ 56.6 1.5e-18 1.2 1.2 2 +SEQ80#1#79#+ 57.6 6.6e-19 1.2 1.2 2 +SEQ81#1#77#+ 70.3 4.6e-23 1.2 1.2 2 +SEQ78#1#80#+ 74.4 2e-24 1.2 1.2 2 +SEQ76#1#79#+ 81.8 7.1e-27 1.2 1.2 2 +SEQ86#1#79#+ 69.6 7.6e-23 1.2 1.2 2 +SEQ89#1#80#+ 75.4 9e-25 1.2 1.2 2 +SEQ88#1#81#+ 62.3 2e-20 1.2 1.2 2 +SEQ84#1#79#+ 79.8 3.2e-26 1.2 1.2 2 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/2.cluster.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/2.cluster.stats Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +CLUSTER 2 SEQS 13 IDS_UNIQUE 13 MODELS 1 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/cluster.final.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/cluster.final.stats Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,2 @@ +CLUSTER 1 SEQS 33 IDS_UNIQUE 33 MODELS 1 +CLUSTER 2 SEQS 13 IDS_UNIQUE 13 MODELS 1 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/fullTab.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/fullTab.tabular Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,92 @@ +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00005 1 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00641 2 +RF00001 3 +RF00001 4 +RF00001 5 +RF00005 6 +RF00005 7 +RF00005 8 +RF00005 9 +RF00005 10 +RF00005 11 +RF00005 12 +RF00005 13 +RF00005 14 +RF00005 15 +RF00005 16 +RF00005 17 +RF00005 18 +RF00005 19 +RF00006 20 +RF00006 21 +RF00006 22 +RF00006 23 +RF00019 24 +RF00019 25 +RF00019 26 +RF00019 27 +RF00027 28 +RF00027 29 +RF00027 30 +RF00031 31 +RF00031 32 +RF00031 33 +RF00031 34 +RF00031 35 +RF00031 36 +RF00031 37 +RF00049 38 +RF00049 39 +RF00049 40 +RF00618 41 +RF00618 42 +RF00618 43 +RF00618 44 +RF00641 45 +RF00693 46 +RF00693 47 +RF00693 48 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_overlap.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/partitions/final_overlap.map Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,2 @@ +1.1 1.1 +1.2 1.2 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_overlap.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/partitions/final_overlap.matrix Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,4 @@ +# MODEL 1.1 1.2 +MODEL CLASS 0 0 +1.1 0 0 0 +1.2 0 0 0 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_partition.hard.best --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/partitions/final_partition.hard.best Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,46 @@ +SEQ11#1#82#+ 88.8 1.1e-38 1.1 1.1 1 +SEQ13#1#82#+ 87.5 3.5e-38 1.1 1.1 1 +SEQ31#1#73#+ 84.9 3.1e-37 1.1 1.1 1 +SEQ37#1#82#+ 84.9 3.4e-37 1.1 1.1 1 +SEQ12#1#82#+ 84.8 3.7e-37 1.1 1.1 1 +SEQ9#1#73#+ 83.8 8.7e-37 1.1 1.1 1 +SEQ32#1#73#+ 82.5 2.6e-36 1.1 1.1 1 +SEQ28#1#71#+ 82.4 3e-36 1.1 1.1 1 +SEQ7#1#83#+ 81.0 9.6e-36 1.1 1.1 1 +SEQ46#1#72#+ 80.9 1.1e-35 1.1 1.1 1 +SEQ26#1#72#+ 80.0 2.4e-35 1.1 1.1 1 +SEQ5#1#72#+ 79.6 3.2e-35 1.1 1.1 1 +SEQ24#1#73#+ 79.0 5.6e-35 1.1 1.1 1 +SEQ17#1#71#+ 78.9 6.2e-35 1.1 1.1 1 +SEQ36#1#73#+ 78.5 8.3e-35 1.1 1.1 1 +SEQ50#1#73#+ 78.4 9.1e-35 1.1 1.1 1 +SEQ15#1#73#+ 76.6 4.5e-34 1.1 1.1 1 +SEQ21#1#74#+ 76.3 5.7e-34 1.1 1.1 1 +SEQ23#1#74#+ 76.3 5.7e-34 1.1 1.1 1 +SEQ4#1#73#+ 75.1 1.7e-33 1.1 1.1 1 +SEQ16#1#72#+ 74.7 2.3e-33 1.1 1.1 1 +SEQ18#1#72#+ 73.6 6.2e-33 1.1 1.1 1 +SEQ10#1#73#+ 73.3 8.3e-33 1.1 1.1 1 +SEQ20#1#72#+ 73.3 8.3e-33 1.1 1.1 1 +SEQ30#1#72#+ 72.3 1.9e-32 1.1 1.1 1 +SEQ35#1#72#+ 71.7 3.2e-32 1.1 1.1 1 +SEQ19#1#82#+ 69.4 2.5e-31 1.1 1.1 1 +SEQ33#1#72#+ 69.3 2.5e-31 1.1 1.1 1 +SEQ45#1#72#+ 69.3 2.7e-31 1.1 1.1 1 +SEQ22#1#72#+ 47.8 3.6e-23 1.1 1.1 1 +SEQ14#2#72#+ 45.6 2.5e-22 1.1 1.1 1 +SEQ29#1#66#+ 34.4 4.1e-18 1.1 1.1 1 +SEQ39#1#69#+ 21.4 3.5e-13 1.1 1.1 1 +SEQ82#1#81#+ 86.6 1.9e-28 1.2 1.2 2 +SEQ76#1#79#+ 81.8 7.1e-27 1.2 1.2 2 +SEQ84#1#79#+ 79.8 3.2e-26 1.2 1.2 2 +SEQ79#1#79#+ 76.7 3.4e-25 1.2 1.2 2 +SEQ89#1#80#+ 75.4 9e-25 1.2 1.2 2 +SEQ78#1#80#+ 74.4 2e-24 1.2 1.2 2 +SEQ85#1#79#+ 73.2 5.1e-24 1.2 1.2 2 +SEQ87#1#78#+ 72.1 1.2e-23 1.2 1.2 2 +SEQ81#1#77#+ 70.3 4.6e-23 1.2 1.2 2 +SEQ86#1#79#+ 69.6 7.6e-23 1.2 1.2 2 +SEQ88#1#81#+ 62.3 2e-20 1.2 1.2 2 +SEQ80#1#79#+ 57.6 6.6e-19 1.2 1.2 2 +SEQ77#1#77#+ 56.6 1.5e-18 1.2 1.2 2 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_partition.hard.merged --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/partitions/final_partition.hard.merged Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,46 @@ +SEQ11#1#82#+ 88.8 1.1e-38 1.1 1.1 1 +SEQ13#1#82#+ 87.5 3.5e-38 1.1 1.1 1 +SEQ31#1#73#+ 84.9 3.1e-37 1.1 1.1 1 +SEQ37#1#82#+ 84.9 3.4e-37 1.1 1.1 1 +SEQ12#1#82#+ 84.8 3.7e-37 1.1 1.1 1 +SEQ9#1#73#+ 83.8 8.7e-37 1.1 1.1 1 +SEQ32#1#73#+ 82.5 2.6e-36 1.1 1.1 1 +SEQ28#1#71#+ 82.4 3e-36 1.1 1.1 1 +SEQ7#1#83#+ 81.0 9.6e-36 1.1 1.1 1 +SEQ46#1#72#+ 80.9 1.1e-35 1.1 1.1 1 +SEQ26#1#72#+ 80.0 2.4e-35 1.1 1.1 1 +SEQ5#1#72#+ 79.6 3.2e-35 1.1 1.1 1 +SEQ24#1#73#+ 79.0 5.6e-35 1.1 1.1 1 +SEQ17#1#71#+ 78.9 6.2e-35 1.1 1.1 1 +SEQ36#1#73#+ 78.5 8.3e-35 1.1 1.1 1 +SEQ50#1#73#+ 78.4 9.1e-35 1.1 1.1 1 +SEQ15#1#73#+ 76.6 4.5e-34 1.1 1.1 1 +SEQ21#1#74#+ 76.3 5.7e-34 1.1 1.1 1 +SEQ23#1#74#+ 76.3 5.7e-34 1.1 1.1 1 +SEQ4#1#73#+ 75.1 1.7e-33 1.1 1.1 1 +SEQ16#1#72#+ 74.7 2.3e-33 1.1 1.1 1 +SEQ18#1#72#+ 73.6 6.2e-33 1.1 1.1 1 +SEQ10#1#73#+ 73.3 8.3e-33 1.1 1.1 1 +SEQ20#1#72#+ 73.3 8.3e-33 1.1 1.1 1 +SEQ30#1#72#+ 72.3 1.9e-32 1.1 1.1 1 +SEQ35#1#72#+ 71.7 3.2e-32 1.1 1.1 1 +SEQ19#1#82#+ 69.4 2.5e-31 1.1 1.1 1 +SEQ33#1#72#+ 69.3 2.5e-31 1.1 1.1 1 +SEQ45#1#72#+ 69.3 2.7e-31 1.1 1.1 1 +SEQ22#1#72#+ 47.8 3.6e-23 1.1 1.1 1 +SEQ14#2#72#+ 45.6 2.5e-22 1.1 1.1 1 +SEQ29#1#66#+ 34.4 4.1e-18 1.1 1.1 1 +SEQ39#1#69#+ 21.4 3.5e-13 1.1 1.1 1 +SEQ82#1#81#+ 86.6 1.9e-28 1.2 1.2 2 +SEQ76#1#79#+ 81.8 7.1e-27 1.2 1.2 2 +SEQ84#1#79#+ 79.8 3.2e-26 1.2 1.2 2 +SEQ79#1#79#+ 76.7 3.4e-25 1.2 1.2 2 +SEQ89#1#80#+ 75.4 9e-25 1.2 1.2 2 +SEQ78#1#80#+ 74.4 2e-24 1.2 1.2 2 +SEQ85#1#79#+ 73.2 5.1e-24 1.2 1.2 2 +SEQ87#1#78#+ 72.1 1.2e-23 1.2 1.2 2 +SEQ81#1#77#+ 70.3 4.6e-23 1.2 1.2 2 +SEQ86#1#79#+ 69.6 7.6e-23 1.2 1.2 2 +SEQ88#1#81#+ 62.3 2e-20 1.2 1.2 2 +SEQ80#1#79#+ 57.6 6.6e-19 1.2 1.2 2 +SEQ77#1#77#+ 56.6 1.5e-18 1.2 1.2 2 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_partition.soft --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/partitions/final_partition.soft Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,46 @@ +SEQ11#1#82#+ 88.8 1.1e-38 1.1 1.1 1 +SEQ13#1#82#+ 87.5 3.5e-38 1.1 1.1 1 +SEQ31#1#73#+ 84.9 3.1e-37 1.1 1.1 1 +SEQ37#1#82#+ 84.9 3.4e-37 1.1 1.1 1 +SEQ12#1#82#+ 84.8 3.7e-37 1.1 1.1 1 +SEQ9#1#73#+ 83.8 8.7e-37 1.1 1.1 1 +SEQ32#1#73#+ 82.5 2.6e-36 1.1 1.1 1 +SEQ28#1#71#+ 82.4 3e-36 1.1 1.1 1 +SEQ7#1#83#+ 81.0 9.6e-36 1.1 1.1 1 +SEQ46#1#72#+ 80.9 1.1e-35 1.1 1.1 1 +SEQ26#1#72#+ 80.0 2.4e-35 1.1 1.1 1 +SEQ5#1#72#+ 79.6 3.2e-35 1.1 1.1 1 +SEQ24#1#73#+ 79.0 5.6e-35 1.1 1.1 1 +SEQ17#1#71#+ 78.9 6.2e-35 1.1 1.1 1 +SEQ36#1#73#+ 78.5 8.3e-35 1.1 1.1 1 +SEQ50#1#73#+ 78.4 9.1e-35 1.1 1.1 1 +SEQ15#1#73#+ 76.6 4.5e-34 1.1 1.1 1 +SEQ21#1#74#+ 76.3 5.7e-34 1.1 1.1 1 +SEQ23#1#74#+ 76.3 5.7e-34 1.1 1.1 1 +SEQ4#1#73#+ 75.1 1.7e-33 1.1 1.1 1 +SEQ16#1#72#+ 74.7 2.3e-33 1.1 1.1 1 +SEQ18#1#72#+ 73.6 6.2e-33 1.1 1.1 1 +SEQ10#1#73#+ 73.3 8.3e-33 1.1 1.1 1 +SEQ20#1#72#+ 73.3 8.3e-33 1.1 1.1 1 +SEQ30#1#72#+ 72.3 1.9e-32 1.1 1.1 1 +SEQ35#1#72#+ 71.7 3.2e-32 1.1 1.1 1 +SEQ19#1#82#+ 69.4 2.5e-31 1.1 1.1 1 +SEQ33#1#72#+ 69.3 2.5e-31 1.1 1.1 1 +SEQ45#1#72#+ 69.3 2.7e-31 1.1 1.1 1 +SEQ22#1#72#+ 47.8 3.6e-23 1.1 1.1 1 +SEQ14#2#72#+ 45.6 2.5e-22 1.1 1.1 1 +SEQ29#1#66#+ 34.4 4.1e-18 1.1 1.1 1 +SEQ39#1#69#+ 21.4 3.5e-13 1.1 1.1 1 +SEQ82#1#81#+ 86.6 1.9e-28 1.2 1.2 2 +SEQ76#1#79#+ 81.8 7.1e-27 1.2 1.2 2 +SEQ84#1#79#+ 79.8 3.2e-26 1.2 1.2 2 +SEQ79#1#79#+ 76.7 3.4e-25 1.2 1.2 2 +SEQ89#1#80#+ 75.4 9e-25 1.2 1.2 2 +SEQ78#1#80#+ 74.4 2e-24 1.2 1.2 2 +SEQ85#1#79#+ 73.2 5.1e-24 1.2 1.2 2 +SEQ87#1#78#+ 72.1 1.2e-23 1.2 1.2 2 +SEQ81#1#77#+ 70.3 4.6e-23 1.2 1.2 2 +SEQ86#1#79#+ 69.6 7.6e-23 1.2 1.2 2 +SEQ88#1#81#+ 62.3 2e-20 1.2 1.2 2 +SEQ80#1#79#+ 57.6 6.6e-19 1.2 1.2 2 +SEQ77#1#77#+ 56.6 1.5e-18 1.2 1.2 2 |
| b |
| diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_partition.used_cmsearch --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RESULTS/partitions/final_partition.used_cmsearch Fri Dec 16 07:34:49 2016 -0500 |
| b |
| @@ -0,0 +1,2 @@ +1.1 +1.2 |