| Previous changeset 5:2442e8b5e363 (2020-02-17) Next changeset 7:f40d481b7c8b (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_fel.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 2442e8b5e363 -r 4eba0baf0278 hyphy_fel.xml --- a/hyphy_fel.xml Mon Feb 17 14:54:30 2020 -0500 +++ b/hyphy_fel.xml Thu Feb 20 18:15:14 2020 -0500 |
| [ |
| @@ -23,7 +23,7 @@ <expand macro="gencode"/> <expand macro="branches"/> <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> - <param name="include_srv" type="select" label="Include synonymous rate variation"> + <param name="include_srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site"> <option value="Yes">Yes (recommended)</option> <option value="No">No</option> </param> @@ -40,12 +40,89 @@ </test> </tests> <help><![CDATA[ -FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method assumes that the selection pressure for each site is constant along the entire phylogeny. +FEL : Fixed effects likelihood +============================== + +What question does this method answer? +-------------------------------------- + +Which site(s) in a gene are subject to pervasive, i.e. consistently across the entire phylogeny, 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. As such, FEL is ideally suited to identify sites under positive selection which +represent candidate sites subject to strong selective pressures across the entire phylogeny. + +FEL is our recommended method for analyzing small-to-medium size datasets when one wishes only to study pervasive selection at individual sites. + +Brief description +----------------- + +FEL (Fixed Effects Likelihood) estimates site-wise synonymous (alpha) +and non-synonymous rates (beta), and uses a likelihood ratio test to +determine if beta != alpha at a site. The estimates aggregate +information over all branches, so the signal is derived from pervasive +diversification or conservation. 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 +----- + +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 +------ -See the online documentation_ for more information. +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/FEL for an example) + +Further reading +--------------- + +http://hyphy.org/methods/selection-methods/#FEL + + +Tool options +------------ + +:: + + --code Which genetic code to use -.. _documentation: http://hyphy.org/methods/selection-methods/#fel - ]]></help> + --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 + + --srv Include site-to-site synonymous rate variation? + Yes [default] or No + + + + +]]> + + </help> + <expand macro="citations"> <citation type="doi">10.1093/molbev/msi105</citation> </expand> |
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| diff -r 2442e8b5e363 -r 4eba0baf0278 macros.xml --- a/macros.xml Mon Feb 17 14:54:30 2020 -0500 +++ b/macros.xml Thu Feb 20 18:15:14 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 2442e8b5e363 -r 4eba0baf0278 test-data/gard-in1.fa --- a/test-data/gard-in1.fa Mon Feb 17 14:54:30 2020 -0500 +++ b/test-data/gard-in1.fa Thu Feb 20 18:15:14 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 2442e8b5e363 -r 4eba0baf0278 test-data/gard-out1.nex --- a/test-data/gard-out1.nex Mon Feb 17 14:54:30 2020 -0500 +++ b/test-data/gard-out1.nex Thu Feb 20 18:15:14 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 2442e8b5e363 -r 4eba0baf0278 test-data/meme-in1.fa --- a/test-data/meme-in1.fa Mon Feb 17 14:54:30 2020 -0500 +++ b/test-data/meme-in1.fa Thu Feb 20 18:15:14 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 2442e8b5e363 -r 4eba0baf0278 test-data/meme-in1.nhx --- a/test-data/meme-in1.nhx Mon Feb 17 14:54:30 2020 -0500 +++ b/test-data/meme-in1.nhx Thu Feb 20 18:15:14 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 2442e8b5e363 -r 4eba0baf0278 test-data/meme-out1.json --- a/test-data/meme-out1.json Mon Feb 17 14:54:30 2020 -0500 +++ b/test-data/meme-out1.json Thu Feb 20 18:15:14 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' |