| Previous changeset 5:8c8640ca39d7 (2020-02-17) Next changeset 7:5e122852e898 (2020-02-29) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e" |
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modified:
hyphy_busted.xml macros.xml test-data/gard-in1.fa test-data/gard-out1.nex test-data/meme-in1.fa test-data/meme-in1.nhx test-data/meme-out1.json |
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| diff -r 8c8640ca39d7 -r f9a193154a55 hyphy_busted.xml --- a/hyphy_busted.xml Mon Feb 17 14:50:45 2020 -0500 +++ b/hyphy_busted.xml Thu Feb 20 18:16:58 2020 -0500 |
| [ |
| @@ -33,12 +33,83 @@ </test> </tests> <help><![CDATA[ -BUSTED will test for gene-wide selection at pre-specified lineages. This method is particularly useful for relatively small datasets (fewer than 10 taxa) where other methods may not have sufficient power to detect selection. This method is not suitable for identifying specific sites subject to positive selection. + +BUSTED : Bayesian UnresTricted Test of Episodic Diversification +=============================================================== + +What question does this method answer? +-------------------------------------- + +Is there evidence that some sites in the alignment have been subject to positive diversifying selection, +either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)? +In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time. +If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.), +then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power. + +Recommended Applications +------------------------ + +1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)? +2. Testing small or low-divergence alignments (i.e. ~30 sequences) for evidence of positive diversifying selection, where neither branch nor site level methods have sufficient power. + +Brief description +----------------- + +BUSTED (branch-site unrestricted statistical test of episodic +diversification) uses a random effects branch-site model fitted jointly +to all or a subset of tree branches in order to test for alignment-wide +evidence of episodic diversifying selection. Assuming there is evidence +of positive selection (i.e. there is an omega > 1), BUSTED will also +perform a quick evidence-ratio style analysis to explore which +individual sites may have been subject to selection. + + +Input +----- + +1. A *FASTA* sequence alignment. +2. A phylogenetic tree in the *Newick* format + +Note: the names of sequences in the alignment must match the names of the sequences in the tree. -See the online documentation_ for more information. + +Output +------ + +A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). + +For each tested branch the analysis will infer the appropriate number of selective regimes, +and whether or not there is statistical evidence of positive selection on that branch. + +A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example) + +Further reading +--------------- + +http://hyphy.org/methods/selection-methods/#busted + -.. _documentation: http://hyphy.org/methods/selection-methods/#busted - ]]></help> +Tool options +------------ +:: + + + --code Which genetic code to use + + --branches Which branches should be tested for selection? + All [default] : test all branches + + Internal : test only internal branches (suitable for + intra-host pathogen evolution for example, where terminal branches + may contain polymorphism data) + + Leaves: test only terminal (leaf) branches + + Unlabeled: if the Newick string is labeled using the {} notation, + test only branches without explicit labels + (see http://hyphy.org/tutorials/phylotree/) + ]]> + </help> <expand macro="citations"> <citation type="doi">10.1093/molbev/msv035</citation> </expand> |
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| diff -r 8c8640ca39d7 -r f9a193154a55 macros.xml --- a/macros.xml Mon Feb 17 14:50:45 2020 -0500 +++ b/macros.xml Thu Feb 20 18:16:58 2020 -0500 |
| [ |
| @@ -6,6 +6,8 @@ </xml> <xml name="substitution"> <param name="model" type="select" label="Substitution model"> + <option value="GTR">GTR - General time reversible + model</option> <option value="LG">LG - Generalist empirical model from Le and Gascuel (2008)</option> <option value="HIVBm">HIVBm - Specialist empirical model @@ -26,10 +28,43 @@ for invertebrate mitochondrial genomes</option> <option value="gcpREV">gcpREV - Specialist empirical model for green plant chloroplast genomes</option> - <option value="GTR">GTR - General time reversible - model</option> </param> </xml> + + <xml name="conditional_posteriorEstimationMethod"> + <conditional name="posteriorEstimationMethod"> + <param argument="--method" type="select" label="Posterior estimation method"> + <option value="Variational-Bayes">0-th order Variational Bayes approximation</option> + <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option> + <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option> + </param> + <when value="Variational-Bayes"> + </when> + <when value="Metropolis-Hastings"> + <expand macro="mcmc_options" /> + </when> + <when value="Collapsed-Gibbs"> + <expand macro="mcmc_options" /> + </when> + </conditional> + </xml> + + <token name="@posteriorEstimationMethod_cmd@"> + #if $posteriorEstimationMethod.method != "Variational-Bayes" + --chains '$posteriorEstimationMethod.chains' + --chain-length '$posteriorEstimationMethod.chain_length' + --burn-in '$posteriorEstimationMethod.samples' + --samples '$posteriorEstimationMethod.samples_per_chain' + #end if + </token> + + <xml name="mcmc_options"> + <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" /> + <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" /> + <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" /> + <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" /> + </xml> + <xml name="gencode"> <param name="gencodeid" type="select" label="Genetic code"> <option value="Universal">Universal code</option> @@ -62,27 +97,28 @@ <option value="All">All branches</option> <option value="Internal">Internal branches</option> <option value="Leaves">Leaf branches</option> - <option value="'Unlabeled-branches'">Unlabeled - branches</option> + <option value="'Unlabeled-branches'">Unlabeled branches</option> </param> </xml> <xml name="citations"> <citations> - <citation type="doi">10.1093/bioinformatics/bti079</citation> + <citation type="doi">10.1093/molbev/msz197</citation> <yield/> </citations> </xml> - <token name="@VERSION@">2.5.3</token> + <token name="@VERSION@">2.5.4</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@"> - hyphy</requirement> + <requirement type="package" version="@VERSION@">hyphy</requirement> <yield/> </requirements> </xml> <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> - <token name="@HYPHY_ENVIRONMENT@"><![CDATA[export HYPHY=`which hyphy` && -export HYPHY_PATH=`dirname \$HYPHY` && -export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token> - <token name="@HYPHY_INVOCATION@"><![CDATA[@HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token> + <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ + export HYPHY=`which hyphy` && + export HYPHY_PATH=`dirname \$HYPHY` && + export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` &&]]></token> + <token name="@HYPHY_INVOCATION@"><![CDATA[ + @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB + ]]></token> </macros> |
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| diff -r 8c8640ca39d7 -r f9a193154a55 test-data/gard-in1.fa --- a/test-data/gard-in1.fa Mon Feb 17 14:50:45 2020 -0500 +++ b/test-data/gard-in1.fa Thu Feb 20 18:16:58 2020 -0500 |
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| b'@@ -1,735 +1,120 @@\n->TREESPARROW_HENAN_1_2004\n-ATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGA\n-TCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACA\n-CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAA\n-AAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\n-TTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\n-ACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGT\n-CCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\n-GAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCC\n-CCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\n-TGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\n-CAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCA\n-ACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\n-GCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\n-AACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\n-AAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\n-CCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\n-ATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTG\n-AATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\n-ATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\n-ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCA\n-GAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\n-GCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\n-GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\n-AAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\n-ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\n-TAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\n-TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\n-GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\n-GGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\n-TCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\n-GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\n-GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\n-CAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\n-GGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\n->HUMAN_VIETNAM_CL105_2005\n-ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGA\n-TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\n-CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\n-AAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAAT\n-TTTGAGAGATTGTAGTGTAGCTGGATGGCTACTCGGAAACCCAATGTGTG\n-ACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGTCAAT\n-CCAGTCAATGACCTCTGTTACCCAGGGGTTTTCAATGACTATGAAGAATT\n-GAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\n-CCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGTA\n-TGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\n-CAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA\n-ACCAAGAAGATCTTTTGGTAATATGGGGGATTCATCATCCTAATGATGCG\n-GCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\n-GACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCA\n-AAGTAAACGGGCAAAGTGGGAGGATGGAGTTCTTCTGGACAATTTTAAAA\n-CCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\n-ATATGCATACAAGATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\n-AATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\n-ATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGA\n-ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCA\n-GAAATAGCCCTCAAAAAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGA\n-GCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\n-GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACA\n-AAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\n-ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\n-CAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT\n-TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\n-GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\n-GGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\n-TCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\n-GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGATTAAAAAGAGA\n-GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT\n-CAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGATAGCT\n-GGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAA---------\n->TREESPARROW_HENAN_4_2004\n-ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\n-TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\n-CAATAATGCAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\n-AAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAACCTCTAAT\n-TTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\n-ACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\n-CCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\n-G'..b'TTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC\n+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC\n+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCATACAT\n+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n+>BRO5\n+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGAC\n+CACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCC\n+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT\n+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n+>BRO6\n+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC\n+CACCTGTAATACATAAAAACCC-AATTC--ACACCAAAA----CCCCCCC\n+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT\n+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n+>BRO7_1\n+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC\n+CACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCC\n+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT\n+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n+>BRO8\n+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC\n+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC\n+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT\n+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGAATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n+>BRO9\n+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC\n+CACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCCCCC\n+CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT\n+CAATTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n+>BRO10\n+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC\n+CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC\n+CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACAT\n+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGCACATAAAGCCATTTATCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n+>BRO11_1\n+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC\n+TACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCTGCC\n+CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTGTCACACAT\n+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGCACATAAAGTCATTTACCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n+>BRO12\n+ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGAC\n+TACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCTC\n+CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACAT\n+CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC\n+CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA\n+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T\n+CAGAT-AGGGGTCCCTTGACCACCATCC\n\\ No newline at end of file\n' |
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| diff -r 8c8640ca39d7 -r f9a193154a55 test-data/gard-out1.nex --- a/test-data/gard-out1.nex Mon Feb 17 14:50:45 2020 -0500 +++ b/test-data/gard-out1.nex Thu Feb 20 18:16:58 2020 -0500 |
| b |
| b"@@ -1,50 +0,0 @@\n-#NEXUS\n-\n-BEGIN TAXA;\n-\tDIMENSIONS NTAX = 21;\n-\tTAXLABELS\n-\t\t'TREESPARROW_HENAN_1_2004' 'TREESPARROW_HENAN_3_2004' 'TREESPARROW_HENAN_4_2004' 'CHICKEN_HEBEI_326_2005' 'SWINE_ANHUI_2004' 'TREESPARROW_HENAN_2_2004' 'CHICKEN_HONGKONG_915_97' 'GOOSE_HONGKONG_W355_97' 'DUCK_HONGKONG_Y283_97' 'HONGKONG_97_98' 'HONGKONG_538_97' 'DUCK_GUANGZHOU_20_2005' 'GOOSE_SHANTOU_2216_2005' 'PEREGRINEFALCON_HK_D0028_2004' 'CK_HK_WF157_2003' 'HUMAN_VIETNAM_CL105_2005' 'DUCK_VIETNAM_376_2005' 'VIETNAM_3062_2004' 'MALLARD_VIETNAM_16_2003' 'CHICKEN_THAILAND_KANCHANABURI_CK_160_2005' 'DUCK_VIETNAM_272_2005' ;\n-END;\n-\n-BEGIN CHARACTERS;\n-\tDIMENSIONS NCHAR = 1698;\n-\tFORMAT\n-\t\tDATATYPE = DNA\n-\t\tGAP=-\n-\t\tMISSING=?\n-\t;\n-\n-MATRIX\n-\t'TREESPARROW_HENAN_1_2004' ATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGATCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAAAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAATTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCTGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\n-\t'TREESPARROW_HENAN_3_2004' ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACTATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCGGATCATCCCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCAGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTACATACCCAACGATAAAGAGGAGCTACAATAATACCAACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAGCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAATTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCAGAAATAGCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACAAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAAGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATG"..b'7)Node6:0.006520820816328921,((DUCK_GUANGZHOU_20_2005:0.009483822383439561,(GOOSE_SHANTOU_2216_2005:0.007374093130581441,PEREGRINEFALCON_HK_D0028_2004:0.007242107381463219)Node14:0.0007056004954733679)Node12:0.00710363602212726,CK_HK_WF157_2003:0.00757594740908166)Node11:0.004227199989057285)Node5:0.001170889307235767,TREESPARROW_HENAN_3_2004:0.008919169512223372)Node4:0.0008380584919822353,(TREESPARROW_HENAN_4_2004:0.006708184198226799,((CHICKEN_HONGKONG_915_97:1e-10,(HONGKONG_97_98:0.006483231977175029,HONGKONG_538_97:1e-10)Node24:0.0003031375872603963)Node22:0.0001037022453470389,(GOOSE_HONGKONG_W355_97:1e-10,DUCK_HONGKONG_Y283_97:1e-10)Node27:0.002891685438446985)Node21:0.02744187404194088)Node19:0.002944759819938243)Node3:0.001672904530995233,SWINE_ANHUI_2004:0.01260983958335299)Node2:0.01303612329048956,DUCK_VIETNAM_272_2005:0.008088746451854261)Node1:0.0006545914783555439,((HUMAN_VIETNAM_CL105_2005:0.01105269263722943,DUCK_VIETNAM_376_2005:0.006417734235732284)Node33:0.002021990910251294,VIETNAM_3062_2004:0.002304874937323682)Node32:0.0006817702832121299,(MALLARD_VIETNAM_16_2003:0.005709114871229771,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.008864540916547606)Node37:9.336374870077841e-05);\n-\tTREE tree_2 = ((((((TREESPARROW_HENAN_1_2004:0.002586740118529802,TREESPARROW_HENAN_3_2004:0.003828953390398881)Node5:0.00187457851284572,TREESPARROW_HENAN_4_2004:0.0002656521581222459)Node4:0.008299727091877812,((CHICKEN_HEBEI_326_2005:0.01484958179784225,(SWINE_ANHUI_2004:1e-10,TREESPARROW_HENAN_2_2004:0.002239639293515125)Node12:0.01361271232984685)Node10:0.01278549184522065,((CHICKEN_HONGKONG_915_97:1e-10,GOOSE_HONGKONG_W355_97:1e-10)Node16:0.001326679361120118,((DUCK_HONGKONG_Y283_97:0.0006676977779578139,HONGKONG_538_97:1e-10)Node20:0.0006271503105586317,HONGKONG_97_98:0.004109899012531796)Node19:0.001653355437332724)Node15:0.01224714418221361)Node9:0.003429034672045344)Node3:0.005031763140085913,(((DUCK_GUANGZHOU_20_2005:0.004262245747717084,GOOSE_SHANTOU_2216_2005:0.004308213533754201)Node26:0.002157320455556664,CK_HK_WF157_2003:0.00647028357035998)Node25:4.000752717957338e-05,PEREGRINEFALCON_HK_D0028_2004:0.002090471815463569)Node24:0.003260422306103818)Node2:0.00707214212698231,DUCK_VIETNAM_272_2005:0.01454290899825338)Node1:0.0007147389821184919,(((HUMAN_VIETNAM_CL105_2005:0.004710041013757377,DUCK_VIETNAM_376_2005:0.01496207542884359)Node34:0.001166828623060772,MALLARD_VIETNAM_16_2003:0.003061545152147631)Node33:0.001134022328667363,VIETNAM_3062_2004:1e-10)Node32:0.0002767006572468676,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00405819047265216);\n-\tTREE tree_3 = (TREESPARROW_HENAN_1_2004:1.793736422068138e-05,((TREESPARROW_HENAN_3_2004:0.005512611253559831,TREESPARROW_HENAN_4_2004:0.000171467489882283)Node3:0.001655366533442949,(CHICKEN_HEBEI_326_2005:0.005483900345571787,(SWINE_ANHUI_2004:0.006320038544899231,(((CHICKEN_HONGKONG_915_97:1e-10,HONGKONG_97_98:1e-10)Node12:0.001309621960005619,(GOOSE_HONGKONG_W355_97:1e-10,HONGKONG_538_97:1e-10)Node15:0.0005799496924062597)Node11:0.01406566295495963,((DUCK_HONGKONG_Y283_97:999.9836725287659,(((HUMAN_VIETNAM_CL105_2005:0.002027831968935447,DUCK_VIETNAM_376_2005:0.003754856650868615)Node23:0.00177604858958343,(VIETNAM_3062_2004:0.002068037509299944,MALLARD_VIETNAM_16_2003:1e-10)Node26:0.0001623690336813484)Node22:0.0008290773242978894,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.004523465945045592,DUCK_VIETNAM_272_2005:0.005056282226890766)Node29:0.001128740164377167)Node21:0.01150309854222087)Node19:0.001994389759866116,(((DUCK_GUANGZHOU_20_2005:0.003847909099661096,GOOSE_SHANTOU_2216_2005:0.005686200296849465)Node34:0.006130725555048717,PEREGRINEFALCON_HK_D0028_2004:8.387427766777967e-05)Node33:0.0009906361822363255,CK_HK_WF157_2003:0.005714641337818262)Node32:0.004952071733007253)Node18:0.002028752021615747)Node10:0.004186888950236505)Node8:0.002350770416932014)Node6:0.002154523112988181)Node2:0.0002651492563879275,TREESPARROW_HENAN_2_2004:0.007562549920247083);\n-END;\n' |
| b |
| diff -r 8c8640ca39d7 -r f9a193154a55 test-data/meme-in1.fa --- a/test-data/meme-in1.fa Mon Feb 17 14:50:45 2020 -0500 +++ b/test-data/meme-in1.fa Thu Feb 20 18:16:58 2020 -0500 |
| b |
| b'@@ -1,1 +1,1 @@\n->HUMAN_VIETNAM_CL105_2005\rATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAAT\rTTTGAGAGATTGTAGTGTAGCTGGATGGCTACTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGTCAAT\rCCAGTCAATGACCTCTGTTACCCAGGGGTTTTCAATGACTATGAAGAATT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGTA\rTGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTAATATGGGGGATTCATCATCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCA\rAAGTAAACGGGCAAAGTGGGAGGATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAGATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCA\rGAAATAGCCCTCAAAAAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGA\rGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACA\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rCAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGATTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT\rCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGATAGCT\rGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAA---------\r>CHICKEN_HEBEI_326_2005\rATGGAGAGAATAGTGCTTCTTCTTGCAATAATCGGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAG\rAAGACACACAACGGGAAGCTCTGCAACCCAGATGGAGTGAAGCCTCTAAT\rTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTTATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGGCCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGGAGCCTCATCAGGGGTGAGCTCAGCA\rTGTTCCTATCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAATAATACATACCCACCAATAAAGGTGAGCTACAACAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCCAATGATGAG\rGCAGAGCAGATAAAGATCTATCAAAACCCAACCACCTATATTTCCGTTGG\rAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\rCCGAATGATGCTATCAATTTCGATAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCGATTATGAAAAGTG\rAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAATTCTAGTATGCCATTCCACAACATACACCCTCTCACCGTCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTCGCGACTGGACTCA\rGAAATGCCCCTCAAAGAGAGGGAGGAAGAAAAAAGAGAGGACTATTTGGA\rGCCATAGCAGGGTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\rTCCTAGATGTCTGGACTTATAACGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCATTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r>CHICKEN_HONGKONG_915_97\rATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA\rAGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCAT\rTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCA'..b'GGGAATTTAA\rCAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGGAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT\rCAATTTATTCTACAGTAGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCCTTATGGATGTGCTTCAATGGGTCGTTACAATGCAGAATT\r>CK_HK_WF157_2003\rATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACCCACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\rTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTG\rACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCATCCAATGACCTCTGTTACCCAGGGGATTTCAACAATTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGCTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCCTTCCACAACATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGACTAGTCCTTGCGACTGGGCTCA\rGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCGGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTAGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACTCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGT------\r>SWINE_ANHUI_1_2004\rATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGA\rTCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\rTTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCAGGGAAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCACCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rGACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAAAGTG\rAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCG\rATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCA\rGAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAGATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCGGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTGGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r\n\\ No newline at end of file\n' |
| b |
| diff -r 8c8640ca39d7 -r f9a193154a55 test-data/meme-in1.nhx --- a/test-data/meme-in1.nhx Mon Feb 17 14:50:45 2020 -0500 +++ b/test-data/meme-in1.nhx Thu Feb 20 18:16:58 2020 -0500 |
| b |
| @@ -1,1 +1,1 @@ -((((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97):0.02096173714686362):0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849) +((((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516):0.002095219592954275):0.003887237703073042)):0.003130608143291779,(CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849) |
| b |
| diff -r 8c8640ca39d7 -r f9a193154a55 test-data/meme-out1.json --- a/test-data/meme-out1.json Mon Feb 17 14:50:45 2020 -0500 +++ b/test-data/meme-out1.json Thu Feb 20 18:16:58 2020 -0500 |
| [ |
| b'@@ -4,568 +4,568 @@\n "0": [\n [0, 0, 1, 0, 0, 0, 1, 0, 0],\n [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 0, 1.817789942174416, 1, 0, 0.6666666666666666, 0, 0.1215618554703716],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 0, 1.900735833403759, 1, 0, 0.6666666666666666, 0, 0.1271087320415013],\n- [4.223295318660594, 0, 0.1812832787403597, 0, 0.8187167212596403, 0, 0.6666666666666666, 0, 0.1220041843130002],\n- [0, 0, 0, 1.454313013998262, 1, 0, 0.6666666666666666, 0, 0.0972549051541481],\n- [0, 0, 0, 3.87077558632765, 1, 0, 0.6666666666666666, 0, 0.2588520551613089],\n- [5.621376790757513, 1.370160457631764, 0.9999999999999731, 0.7647952134694137, 2.686739719592879e-14, 0, 0.6666666666666666, 0, 0.254019836850675],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 0, 1.424462463669818, 1, 0, 0.6666666666666666, 0, 0.09525869635105789],\n- [5.523939453749047, 0, 0.10495989356895, 0, 0.89504010643105, 0, 0.6666666666666666, 0, 0.1595776938144102],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 0, 1.857975844217296, 1, 0, 0.6666666666666666, 0, 0.1242492247327626],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [3.058609686328263, 0, 0.2099197871379, 0, 0.7900802128621, 0, 0.6666666666666666, 0, 0.08835829648556724],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [4.559377199598298, 0, 0.21, 0, 0.79, 0, 0.6666666666666666, 0, 0.1317130473340185],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [12.52835534598018, 0, 0.1028092111730828, 0, 0.8971907888269173, 0, 0.6666666666666666, 0, 0.3619239620814606],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [4.526013289893084, 0, 0.21, 0, 0.79, 0, 0.6666666666666666, 0, 0.1307492178402363],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [5.778235281128926, 0, 0.1048549336753811, 0, 0.895145066324619, 0, 0.6666666666666666, 0, 0.1669238897710598],\n- [0, 0, 0, 1.811443451630381, 1, 0, 0.6666666666666666, 0, 0.1211374438547285],\n- [4.16975333524863, 0, 0.1049198024571935, 0, 0.8950801975428065, 0, 0.6666666666666666, 0, 0.1204574428422312],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [6.067135083387604, 6.067135083387516, 0.313721188257573, 0, 0.686278811742427, 0, 0.6666666666666666, 0, 0.3025558868541813],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [12.64639196707219, 0, 0.1815339017197267, 0, 0.8184660982802733, 0, 0.6666666666666666, 0, 0.3653338495245107],\n- [11.47465033410186, 1.6250977062539, 0.6784748819617452, 1.547845247613481, 0.3215251180382548, 0, 0.6666666666666666, 0, 0.4384989474073118],\n- [2.150572226072722, 2.150572226072722, 0, 3.001300331424568, 1, 0, 0.6666666666666666, 0, 0.2628338207031371],\n- [0, 0, 0, 1.596774706161373, 1, 0, 0.6666666666666666, 0, 0.1067818077026798],\n- [4.743412316579805, 0, 0.0586026566410284, 0, 0.9413973433589716, 0, 0.6666666666666666, 0, 0.1370295247854218],\n- [0, 0, 1, 0, 0, 0, 1, 0, 0],\n- [3.682413523444095, 0, 0.10495989356895, 0, 0.89504010643105, 0, 0.6666666666666666, 0, 0.1063789823661781'..b'[0.2307510906732697],\n+ [0.2365287112368824] \n ],\n- "Log Likelihood":-3679.541894127126,\n+ "Log Likelihood":-3056.215005465311,\n "Rate Distributions":{\n- "Substitution rate from nucleotide A to nucleotide C":0.2089484190839437,\n+ "Substitution rate from nucleotide A to nucleotide C":0.1810796022573985,\n "Substitution rate from nucleotide A to nucleotide G":1,\n- "Substitution rate from nucleotide A to nucleotide T":0.1069376934774225,\n- "Substitution rate from nucleotide C to nucleotide G":0.01756475048192434,\n- "Substitution rate from nucleotide C to nucleotide T":1.483513244796427,\n- "Substitution rate from nucleotide G to nucleotide T":0.1186889750817524\n+ "Substitution rate from nucleotide A to nucleotide T":0.08708610799393901,\n+ "Substitution rate from nucleotide C to nucleotide G":0.02931879134098465,\n+ "Substitution rate from nucleotide C to nucleotide T":1.419136867291551,\n+ "Substitution rate from nucleotide G to nucleotide T":0.1065442350926398\n },\n "display order":0,\n- "estimated parameters":36\n+ "estimated parameters":20\n }\n },\n "input":{\n- "file name":"/tmp/tmpu23i1b/job_working_directory/000/3/working/meme_input.fa",\n- "number of sequences":13,\n+ "file name":"/tmp/tmpdqyv1aux/job_working_directory/000/3/working/./meme_input.fa",\n+ "number of sequences":5,\n "number of sites":566,\n "partition count":1,\n "trees":{\n- "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"\n+ "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:-1)Node3:0.003130608143291779,(CK_HK_WF157_2003:0.00663129750258774)Node9:0.004655295319725731)Node2:0.0116808817874948,(MALLARD_VIETNAM_16_2003:0.003244216605281072)Node11:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)"\n }\n },\n "tested":{\n "0":{\n "CHICKEN_CK_160_2005":"test",\n "CHICKEN_HEBEI_326_2005":"test",\n- "CHICKEN_HONGKONG_915_97":"test",\n "CK_HK_WF157_2003":"test",\n- "GOOSE_HONGKONG_W355_97":"test",\n- "GOOSE_SHANTOU_2216_2005":"test",\n- "HONGKONG_1_538_97":"test",\n- "HONGKONG_1_97_98":"test",\n- "HUMAN_VIETNAM_3062_2004":"test",\n- "HUMAN_VIETNAM_CL105_2005":"test",\n "MALLARD_VIETNAM_16_2003":"test",\n- "Node10":"test",\n "Node11":"test",\n- "Node13":"test",\n- "Node17":"test",\n- "Node18":"test",\n- "Node19":"test",\n "Node2":"test",\n- "Node23":"test",\n- "Node24":"test",\n- "Node25":"test",\n "Node3":"test",\n "Node4":"test",\n "Node5":"test",\n "Node7":"test",\n "Node9":"test",\n- "PEREGRINEFALCON_HK_D0028_2004":"test",\n "SWINE_ANHUI_1_2004":"test"\n }\n },\n "timers":{\n "MEME analysis":{\n "order":2,\n- "timer":249\n+ "timer":437\n },\n "Model fitting":{\n "order":1,\n- "timer":2\n+ "timer":4\n },\n "Total time":{\n "order":0,\n- "timer":252\n+ "timer":442\n }\n }\n }\n\\ No newline at end of file\n' |