| Previous changeset 4:8366d5b28b49 (2020-02-17) Next changeset 6:2c0308ac90e1 (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_meme.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 8366d5b28b49 -r 4d5768ad6316 hyphy_meme.xml --- a/hyphy_meme.xml Mon Feb 17 14:53:45 2020 -0500 +++ b/hyphy_meme.xml Thu Feb 20 18:11:41 2020 -0500 |
| [ |
| @@ -37,11 +37,86 @@ </test> </tests> <help><![CDATA[ -MEME employs a mixed-effects maximum likelihood approach to test the hypothesis that individual sites have been subject to episodic positive or diversifying selection. In other words, MEME aims to detect sites evolving under positive selection under a proportion of branches. +MEME: Mixed Effects Model of Evolution +====================================== + +What question does this method answer? +-------------------------------------- + +Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a +single lineage or subset of lineages, diversifying selection? + +Recommended Applications +------------------------ + +The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics +(or balancing selection), including adaptive immune escape by viruses. +MEME is ideally suited to identify sites under positive selection which +represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny. + +MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection. +MEME is therefore our recommended method if maximum power is desired. + + +Brief description +----------------- + +MEME (Mixed Effects Model of Evolution) estimates a site-wise synonymous +(alpha) and a two-category mixture of non-synonymous (beta-, with +proportion p-, and beta+ with proportion [1-p-]) rates, and uses a +likelihood ratio test to determine if beta+ > α at a site. The +estimates aggregate information over a proportion of branches at a site, +so the signal is derived from episodic diversification, which is a +combination of strength of selection [effect size] and the proportion of +the tree affected. A subset of branches can be selected for testing as +well, in which case an additional (nuisance) parameter will be inferred +-- the non-synonymous rate on branches NOT selected for testing. + +Input +----- -See the online documentation_ for more information. +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. + + +Output +------ + +A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). + +A custom visualization module for viewing these results is available (see http://vision.hyphy.org/MEME for an example) + +Further reading +--------------- + +http://hyphy.org/methods/selection-methods/#MEME + -.. _documentation: http://hyphy.org/methods/selection-methods/#meme +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/) + + --pvalue The significance level used to determine significance + + ]]></help> <expand macro="citations"> <citation type="doi">10.1371/journal.pgen.1002764</citation> |
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| diff -r 8366d5b28b49 -r 4d5768ad6316 macros.xml --- a/macros.xml Mon Feb 17 14:53:45 2020 -0500 +++ b/macros.xml Thu Feb 20 18:11:41 2020 -0500 |
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| @@ -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 8366d5b28b49 -r 4d5768ad6316 test-data/gard-in1.fa --- a/test-data/gard-in1.fa Mon Feb 17 14:53:45 2020 -0500 +++ b/test-data/gard-in1.fa Thu Feb 20 18:11:41 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 8366d5b28b49 -r 4d5768ad6316 test-data/gard-out1.nex --- a/test-data/gard-out1.nex Mon Feb 17 14:53:45 2020 -0500 +++ b/test-data/gard-out1.nex Thu Feb 20 18:11:41 2020 -0500 |
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| 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 8366d5b28b49 -r 4d5768ad6316 test-data/meme-in1.fa --- a/test-data/meme-in1.fa Mon Feb 17 14:53:45 2020 -0500 +++ b/test-data/meme-in1.fa Thu Feb 20 18:11:41 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 8366d5b28b49 -r 4d5768ad6316 test-data/meme-in1.nhx --- a/test-data/meme-in1.nhx Mon Feb 17 14:53:45 2020 -0500 +++ b/test-data/meme-in1.nhx Thu Feb 20 18:11:41 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 8366d5b28b49 -r 4d5768ad6316 test-data/meme-out1.json --- a/test-data/meme-out1.json Mon Feb 17 14:53:45 2020 -0500 +++ b/test-data/meme-out1.json Thu Feb 20 18:11:41 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' |