| Next changeset 1:c2bed8cc8fc1 (2019-08-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea |
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added:
hyphy_slac.xml macros.xml test-data/absrel-in1.fa test-data/absrel-in1.nhx test-data/absrel-out1.json test-data/busted-out1.json test-data/fel-out1.json test-data/fubar-in1.fa test-data/fubar-in1.nhx test-data/fubar-out1.json test-data/meme-in1.fa test-data/meme-in1.nhx test-data/meme-out1.json test-data/params.json test-data/slac-out1.json |
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| diff -r 000000000000 -r 9da003917dcb hyphy_slac.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hyphy_slac.xml Thu Jan 17 04:24:25 2019 -0500 |
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| @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0"> + <description>Single Likelihood Ancestor Counting</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"> + <![CDATA[ + ln -s '$input_file' slac_input.fa && + ln -s '$input_nhx' slac_input.nhx && + echo $gencodeid > tool_params && + echo `pwd`/slac_input.fa >> tool_params && + echo `pwd`/slac_input.nhx >> tool_params && + echo '$branches' >> tool_params && + echo '$number_of_samples' >> tool_params && + echo '$p_value' >> tool_params && + @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/SLAC.bf > '$slac_log' + ]]> + </command> + <inputs> + <expand macro="inputs" /> + <expand macro="gencode" /> + <expand macro="branches" /> + <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" /> + <param name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty" /> + </inputs> + <outputs> + <data name="slac_log" format="txt" /> + <data name="slac_output" format="json" from_work_dir="slac_input.fa.SLAC.json" /> + </outputs> + <tests> + <test> + <param name="input_file" ftype="fasta" value="absrel-in1.fa" /> + <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" /> + <output name="slac_output" file="slac-out1.json" compare="sim_size" /> + </test> + </tests> + <help> + <![CDATA[ +SLAC (Single-Likelihood Ancestor Counting) uses a combination of maximum-likelihood and counting approaches to infer nonsynonymous and synonymous substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. SLAC assumes that the selection pressure for each site is constant along the entire phylogeny. + ]]> + </help> + <expand macro="citations"> + <citation type="doi">10.1093/molbev/msi105</citation> + </expand> +</tool> |
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| diff -r 000000000000 -r 9da003917dcb macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jan 17 04:24:25 2019 -0500 |
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| @@ -0,0 +1,57 @@ +<?xml version="1.0"?> +<macros> + <xml name="inputs"> + <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> + <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> + </xml> + <xml name="gencode"> + <param name="gencodeid" type="select" label="Genetic code"> + <option value="1">Universal code</option> + <option value="2">Vertebrate mitochondrial DNA code</option> + <option value="3">Yeast mitochondrial DNA code</option> + <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> + <option value="5">Invertebrate mitochondrial DNA code</option> + <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> + <option value="7">Echinoderm mitochondrial DNA code</option> + <option value="8">Euplotid Nuclear code</option> + <option value="9">Alternative Yeast Nuclear code</option> + <option value="10">Ascidian mitochondrial DNA code</option> + <option value="11">Flatworm mitochondrial DNA code</option> + <option value="12">Blepharisma Nuclear code</option> + </param> + </xml> + <xml name="branches"> + <param name="branches" type="select" label="Set of branches to test"> + <option value="1">All branches</option> + <option value="2">Internal branches</option> + <option value="3">Leaf branches</option> + <option value="4">Unlabeled branches</option> + </param> + </xml> + <xml name="version_command"> + <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/bti079</citation> + <yield /> + </citations> + </xml> + <token name="@VERSION@">2.3.14</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">hyphy</requirement> + <yield /> + </requirements> + </xml> + <token name="@HYPHY_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` && +export HYPHY_PATH=`dirname \$HYPHY` && +export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` && +cat tool_params | HYPHYMP LIBPATH=\$HYPHY_LIB ]]> + </token> + <token name="@HYPHYMPI_INVOCATION@"><![CDATA[export HYPHY=`which HYPHYMP` && +export HYPHY_PATH=`dirname \$HYPHY` && +export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../lib/hyphy` && +cat tool_params | mpirun -np \${GALAXY_SLOTS:-1} HYPHYMPI LIBPATH=\$HYPHY_LIB ]]> + </token> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 9da003917dcb test-data/absrel-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.fa Thu Jan 17 04:24:25 2019 -0500 |
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| @@ -0,0 +1,20 @@ +>Human +AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Chimp +GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Baboon +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>RhMonkey +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Cow +------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT +>Pig +---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT +>Horse +------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGAAACATTTCATTTGAGCCTTCTAGAGATGGTCTCAAAACCTAATATCTCCTGGAGCTGCACCAACACCACCCTGACCTGCGAGGTGACAAAAGGAACTGACTTTGAGTTAAAACTCTATCTAAATGGGAGAATGATCCAAAAAAGTCCTCGCAAAGTCATCGTATACAAGCGGGCCAGCAACCAAATTGCGTCCTTCAAGTGCACAGCCAATAACACAGTCAGCGAGGAAAGCAGCTCTGTGGTCATCAGGTGTACAGAGAAAGGTCTGGAT +>Cat +---------GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC +>Mouse +---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC +>Rat +---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC |
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| diff -r 000000000000 -r 9da003917dcb test-data/absrel-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.nhx Thu Jan 17 04:24:25 2019 -0500 |
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| @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.097950); \ No newline at end of file |
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| diff -r 000000000000 -r 9da003917dcb test-data/absrel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-out1.json Thu Jan 17 04:24:25 2019 -0500 |
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| b'@@ -0,0 +1,456 @@\n+{\n+ "analysis":{\n+ "info":"aBSREL (Adaptive branch-site random effects likelihood)\\n uses an adaptive random effects branch-site model framework\\n to test whether each branch has evolved under positive selection,\\n using a procedure which infers an optimal number of rate categories per branch.",\n+ "version":"2.0",\n+ "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353",\n+ "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree"\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n+ }\n+ },\n+ "fits":{\n+ "Nucleotide GTR":{\n+ "Log Likelihood":-3531.96369518556,\n+ "estimated parameters":24,\n+ "AIC-c":7112.577796875186,\n+ "Equilibrium frequencies":[\n+ [0.3563279857397504],\n+ [0.1837789661319073],\n+ [0.2402852049910873],\n+ [0.2196078431372549]\n+ ],\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435,\n+ "Substitution rate from nucleotide C to nucleotide T":1.018295973581558,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544\n+ },\n+ "display order":0\n+ },\n+ "Baseline MG94xREV":{\n+ "Log Likelihood":-3450.669934819203,\n+ "estimated parameters":46,\n+ "AIC-c":6995.711784065174,\n+ "Equilibrium frequencies":[\n+ [0.04787662253946073],\n+ [0.03913388100305117],\n+ [0.04844580322128512],\n+ [0.0407178971288476],\n+ [0.01817959331488358],\n+ [0.01485982100934833],\n+ [0.01839572120297191],\n+ [0.01546129971531724],\n+ [0.0190238172858878],\n+ [0.01554988139098808],\n+ [0.01924998172104109],\n+ [0.01617929156565557],\n+ [0.02798385246472159],\n+ [0.02287372613761008],\n+ [0.02831653817605838],\n+ [0.02379958245776909],\n+ [0.01680670574479072],\n+ [0.01373763619452979],\n+ [0.01700651207463693],\n+ [0.01429369239710176],\n+ [0.006381800954137531],\n+ [0.005216421415661322],\n+ [0.006457670922102578],\n+ [0.00542756570877943],\n+ [0.006678159032689796],\n+ [0.005458661598138652],\n+ [0.00675755225029668],\n+ [0.00567961101013393],\n+ [0.009823507779659469],\n+ [0.008029638769211124],\n+ [0.009940294440024354],\n+ [0.008354653231583485],\n+ [0.0329096029621651],\n+ [0.02689998621179963],\n+ [0.03330084840219455],\n+ [0.02798881284619018],\n+ [0.01249635346589736],\n+ [0.01021439657952951],\n+ [0.01264491622176376],\n+ [0.01062784315018763],\n+ [0.01307665913959002],\n+ [0.01068873273724336],\n+ [0.0132321208528494],\n+ [0.01112137894012831],\n+ [0.01923563996618058],\n+ [0.01572302316926395],\n+ [0.01946432265285621],\n+ [0.01635944157725275],\n+ [0.01977100255021048],\n+ [0.02057127040149398],\n+ [0.009184593415672956],\n+ [0.007507396443725858],\n+ [0.009293784349897772],\n+ [0.007811272183233558],\n+ [0.007856024926654371],\n+ [0.009725369116048951],\n+ ['..b'1\n+ },\n+ "Node1":{\n+ "Nucleotide GTR":0.2772613398768408,\n+ "Baseline MG94xREV":0.2903229694372956,\n+ "Baseline MG94xREV omega ratio":0.4389914526526448,\n+ "Rate classes":2,\n+ "Full adaptive model":0.3664538683295676,\n+ "Rate Distributions":[\n+ [0.1934444279004118, 0.7920338324503209],\n+ [2.595458156723663, 0.2079661675496791]\n+ ],\n+ "LRT":1.095302853601424,\n+ "Uncorrected P-value":0.232551772988317,\n+ "Corrected P-value":1\n+ },\n+ "Node12":{\n+ "Nucleotide GTR":0.01783922546179193,\n+ "Baseline MG94xREV":0.01797212760838867,\n+ "Baseline MG94xREV omega ratio":0.3712490894908597,\n+ "Rate classes":1,\n+ "Full adaptive model":0.01648897148329989,\n+ "Rate Distributions":[\n+ [0.3341484726344874, 1]\n+ ],\n+ "LRT":0,\n+ "Uncorrected P-value":1,\n+ "Corrected P-value":1\n+ },\n+ "Node2":{\n+ "Nucleotide GTR":0.06619058539001231,\n+ "Baseline MG94xREV":0.06580724801157116,\n+ "Baseline MG94xREV omega ratio":0.6811307469311604,\n+ "Rate classes":2,\n+ "Full adaptive model":0.1259563484776556,\n+ "Rate Distributions":[\n+ [0, 0.902872882268449],\n+ [33.80023214939837, 0.09712711773155103]\n+ ],\n+ "LRT":7.670975764417562,\n+ "Uncorrected P-value":0.007599562698001494,\n+ "Corrected P-value":0.09119475237601793\n+ },\n+ "Node3":{\n+ "Nucleotide GTR":0.09883236156840018,\n+ "Baseline MG94xREV":0.102749851157051,\n+ "Baseline MG94xREV omega ratio":1.47449378631578,\n+ "Rate classes":2,\n+ "Full adaptive model":0.1389308407753113,\n+ "Rate Distributions":[\n+ [0, 0.7024206790833775],\n+ [8.065310624699681, 0.2975793209166225]\n+ ],\n+ "LRT":6.598417720076213,\n+ "Uncorrected P-value":0.0131150962965953,\n+ "Corrected P-value":0.1442660592625483\n+ },\n+ "Node8":{\n+ "Nucleotide GTR":0.1061134663636472,\n+ "Baseline MG94xREV":0.110140333084973,\n+ "Baseline MG94xREV omega ratio":1.896243438714738,\n+ "Rate classes":2,\n+ "Full adaptive model":0.2165540926910564,\n+ "Rate Distributions":[\n+ [1, 0.9077840705139004],\n+ [33.32075865076668, 0.09221592948609958]\n+ ],\n+ "LRT":7.97288393366216,\n+ "Uncorrected P-value":0.006519360772582139,\n+ "Corrected P-value":0.08475169004356781\n+ },\n+ "Node9":{\n+ "Nucleotide GTR":0.02566719422260768,\n+ "Baseline MG94xREV":0.02590165433349057,\n+ "Baseline MG94xREV omega ratio":0.4071738826525522,\n+ "Rate classes":1,\n+ "Full adaptive model":0.02766629863085238,\n+ "Rate Distributions":[\n+ [0.4488424899910019, 1]\n+ ],\n+ "LRT":0,\n+ "Uncorrected P-value":1,\n+ "Corrected P-value":1\n+ }\n+ },\n+ "attributes":{\n+ "original name":{\n+ "attribute type":"node label",\n+ "display order":-1\n+ },\n+ "Nucleotide GTR":{\n+ "attribute type":"branch length",\n+ "display order":0\n+ },\n+ "Baseline MG94xREV":{\n+ "attribute type":"branch length",\n+ "display order":1\n+ },\n+ "Baseline MG94xREV omega ratio":{\n+ "attribute type":"branch label",\n+ "display order":1\n+ },\n+ "Rate classes":{\n+ "attribute type":"branch label",\n+ "display order":2\n+ },\n+ "Full adaptive model":{\n+ "attribute type":"branch length",\n+ "display order":2\n+ },\n+ "Rate Distributions":{\n+ "attribute type":"branch label",\n+ "display order":3\n+ },\n+ "LRT":{\n+ "attribute type":"branch label",\n+ "display order":4\n+ },\n+ "Uncorrected P-value":{\n+ "attribute type":"branch label",\n+ "display order":5\n+ },\n+ "Corrected P-value":{\n+ "attribute type":"branch label",\n+ "display order":6\n+ }\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 9da003917dcb test-data/busted-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out1.json Thu Jan 17 04:24:25 2019 -0500 |
| [ |
| b'@@ -0,0 +1,361 @@\n+{\n+ "analysis":{\n+ "info":"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.",\n+ "version":"1.2",\n+ "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",\n+ "authors":"Sergei L Kosakovsky Pond",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"\n+ },\n+ "input":{\n+ "file name":"/Users/stephenshank/Documents/Galaxy/tools-iuc/tools/hyphy/test-data/absrel-in1.fa",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n+ }\n+ },\n+ "background":0,\n+ "fits":{\n+ "Nucleotide GTR":{\n+ "Log Likelihood":-3531.963798530155,\n+ "estimated parameters":24,\n+ "AIC-c":7112.142458295762,\n+ "Equilibrium frequencies":[\n+ [0.3563279857397504],\n+ [0.1837789661319073],\n+ [0.2402852049910873],\n+ [0.2196078431372549]\n+ ],\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,\n+ "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378\n+ },\n+ "display order":0\n+ },\n+ "MG94xREV with separate rates for branch sets":{\n+ "Log Likelihood":-3466.725508616141,\n+ "estimated parameters":31,\n+ "AIC-c":6996.530451399855,\n+ "Equilibrium frequencies":[\n+ [0.04785168648208005],\n+ 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[0.01061792547971484],\n+ [0.01306446616325414],\n+ [0.01067875601941112],\n+ [0.01321977470017749],\n+ [0.01111100011404158],\n+ [0.01921770557551369],\n+ [0.01570834862514353],\n+ [0.01944616295744266],\n+ [0.01634417558076203],\n+ [0.01975257768318274],\n+ [0.02055210293142003],\n+ [0.009176034326710849],\n+ [0.007500393094996483],\n+ [0.00928511773266342],\n+ [0.007803986567571961],\n+ [0.007848'..b'1561323465,\n+ "constrained":0.001757260248005238\n+ },\n+ "RhMonkey":{\n+ "original name":"RhMonkey",\n+ "Nucleotide GTR":0.003773669075849421,\n+ "MG94xREV with separate rates for branch sets":0.003717699096857038,\n+ "unconstrained":0.003672835047422234,\n+ "constrained":0.00373144096412681\n+ },\n+ "Cow":{\n+ "original name":"Cow",\n+ "Nucleotide GTR":0.2483322373763571,\n+ "MG94xREV with separate rates for branch sets":0.2480141631033857,\n+ "unconstrained":0.2960120156157274,\n+ "constrained":0.2592686681333873\n+ },\n+ "Pig":{\n+ "original name":"Pig",\n+ "Nucleotide GTR":0.187244836750842,\n+ "MG94xREV with separate rates for branch sets":0.1926081878751187,\n+ "unconstrained":0.2187526946336905,\n+ "constrained":0.1943776301130502\n+ },\n+ "Horse":{\n+ "original name":"Horse",\n+ "Nucleotide GTR":0.2091766851769093,\n+ "MG94xREV with separate rates for branch sets":0.2111575880588217,\n+ "unconstrained":0.2572135566477119,\n+ "constrained":0.218486450878766\n+ },\n+ "Cat":{\n+ "original name":"Cat",\n+ "Nucleotide GTR":0.266381043956941,\n+ "MG94xREV with separate rates for branch sets":0.273601177885004,\n+ "unconstrained":0.3292215104251173,\n+ "constrained":0.28483085314287\n+ },\n+ "Mouse":{\n+ "original name":"Mouse",\n+ "Nucleotide GTR":0.1181831744338598,\n+ "MG94xREV with separate rates for branch sets":0.1201847378516324,\n+ "unconstrained":0.1489713993010398,\n+ "constrained":0.1233480139851019\n+ },\n+ "Rat":{\n+ "original name":"Rat",\n+ "Nucleotide GTR":0.06669700444436912,\n+ "MG94xREV with separate rates for branch sets":0.0670850471739789,\n+ "unconstrained":0.07366345007817726,\n+ "constrained":0.06713082546371778\n+ },\n+ "Node1":{\n+ "Nucleotide GTR":0.276880831396131,\n+ "MG94xREV with separate rates for branch sets":0.2843521449765504,\n+ "unconstrained":0.459085769955035,\n+ "constrained":0.3115534692518958\n+ },\n+ "Node12":{\n+ "Nucleotide GTR":0.01783434870161725,\n+ "MG94xREV with separate rates for branch sets":0.01788794906051452,\n+ "unconstrained":0.01828498503175797,\n+ "constrained":0.01770410398930177\n+ },\n+ "Node2":{\n+ "Nucleotide GTR":0.06617535490721377,\n+ "MG94xREV with separate rates for branch sets":0.06447679597474805,\n+ "unconstrained":0.0623969317369398,\n+ "constrained":0.06097949807503514\n+ },\n+ "Node3":{\n+ "Nucleotide GTR":0.09884524766349881,\n+ "MG94xREV with separate rates for branch sets":0.1017497956116402,\n+ "unconstrained":0.1285021744856729,\n+ "constrained":0.1065011238088613\n+ },\n+ "Node8":{\n+ "Nucleotide GTR":0.1061610073141143,\n+ "MG94xREV with separate rates for branch sets":0.1093806684969149,\n+ "unconstrained":0.1348034716617685,\n+ "constrained":0.1118205234697939\n+ },\n+ "Node9":{\n+ "Nucleotide GTR":0.02568007351415409,\n+ "MG94xREV with separate rates for branch sets":0.02593963430985144,\n+ "unconstrained":0.02761127562964508,\n+ "constrained":0.02639493109700932\n+ }\n+ },\n+ "attributes":{\n+ "original name":{\n+ "attribute type":"node label",\n+ "display order":0\n+ },\n+ "Nucleotide GTR":{\n+ "attribute type":"branch length",\n+ "display order":0\n+ },\n+ "MG94xREV with separate rates for branch sets":{\n+ "attribute type":"branch length",\n+ "display order":1\n+ },\n+ "unconstrained":{\n+ "attribute type":"branch length",\n+ "display order":0\n+ },\n+ "constrained":{\n+ "attribute type":"branch length",\n+ "display order":1\n+ }\n+ }\n+ },\n+ "test results":{\n+ "LRT":44.77492170961614,\n+ "p-value":1.893429857346973e-10\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/fel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fel-out1.json Thu Jan 17 04:24:25 2019 -0500 |
| [ |
| b'@@ -0,0 +1,450 @@\n+{\n+ "analysis":{\n+ "info":"FEL (Fixed Effects Likelihood)\\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\\n The estimates aggregate information over all branches,\\n so the signal is derived from\\n pervasive diversification or conservation. A subset of branches can be selected\\n for testing as well, in which case an additional (nuisance) parameter will be\\n inferred -- the non-synonymous rate on branches NOT selected for testing.\\n Multiple partitions within a NEXUS file are also supported\\n for recombination - aware analysis.\\n ",\n+ "version":"2.00",\n+ "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",\n+ "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree"\n+ },\n+ "input":{\n+ "file name":"/Users/stephenshank/Documents/Data/Datamonkey/CD2.fasta",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n+ }\n+ },\n+ "fits":{\n+ "Nucleotide GTR":{\n+ "Log Likelihood":-3531.963798530155,\n+ "estimated parameters":24,\n+ "AIC-c":7112.142458295762,\n+ "Equilibrium frequencies":[\n+ [0.3563279857397504],\n+ [0.1837789661319073],\n+ [0.2402852049910873],\n+ [0.2196078431372549]\n+ ],\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,\n+ "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378\n+ },\n+ "display order":0\n+ },\n+ "Global MG94xREV":{\n+ "Log Likelihood":-3466.725508616141,\n+ "estimated parameters":31,\n+ "AIC-c":6996.530451399855,\n+ "Equilibrium frequencies":[\n+ [0.04785168648208005],\n+ [0.03911346079312019],\n+ [0.04842054060317301],\n+ [0.04069665666515385],\n+ [0.01817010744778396],\n+ [0.01485205303123071],\n+ [0.01838611113045968],\n+ [0.01545321970309948],\n+ [0.0190138898893362],\n+ [0.01554175184587827],\n+ [0.01923992433904378],\n+ [0.01617083546230154],\n+ [0.02796925133965702],\n+ [0.02286176927319543],\n+ [0.02830174586718859],\n+ [0.02378714529482007],\n+ [0.01687870337957799],\n+ [0.01379647304851128],\n+ [0.01707935503225849],\n+ [0.01435491300079667],\n+ [0.006409133648843443],\n+ [0.005238757839512795],\n+ [0.006485324528555602],\n+ [0.005450807083377185],\n+ [0.006706760641638982],\n+ [0.005482034985409045],\n+ [0.006786489669196017],\n+ [0.005703931360295163],\n+ [0.009865581170012171],\n+ [0.008064021368173151],\n+ 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0.318977273245592, 2.942901296371888],\n+ [3.88753619664278e-15, 1.779262169776622, 1.549159808629328, 1.288480285336618, 0.2563282037478503, 2.280724121673174],\n+ [137.6200023666397, 1.712312972734741, 2.612335663828599, 4.571254357285468, 0.03251275075427451, 63.52993609974021],\n+ [0.9069803858948896, 1.008331374883533, 0.9795641413367016, 0.006632998551161506, 0.9350894763840309, 1.696743112350582],\n+ [1.250218074119796, 2.685270528336648, 2.279331033581541, 0.4656302199387952, 0.4950043706394306, 3.99928134132692],\n+ [0.5981237480607854, 1.191515517605649, 0.9684057167421628, 0.3651500230254783, 0.5456598635374844, 1.793902873797072],\n+ [5.567356236371868, 1.655977785625157, 2.134648959148231, 0.8514639837247273, 0.3561385136046764, 4.60397510129604],\n+ [0, 0, 0, 0, 1, 0],\n+ [0.5915176036957202, 0.7772525687759813, 0.7215979531128016, 0.05398776775817282, 0.8162640993312603, 1.259941036310695],\n+ [0, 0.543676760549953, 0.4362855008937696, 0.8539326132569869, 0.3554421959431151, 0.6969049998601837],\n+ [1.00226665989553, 0.6268338660673796, 0.7169253651929272, 0.1172739583266811, 0.7320101172431673, 1.250193047146509],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [2.797676857161142, 0.824684447244541, 1.167394064072366, 1.285234262338761, 0.2569280765461694, 2.303990803636788]\n+ ]\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/fubar-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-in1.fa Thu Jan 17 04:24:25 2019 -0500 |
| b |
| b'@@ -0,0 +1,326 @@\n+>KF789585\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCCCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGACACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAATTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGGCTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGGGATCTAATAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n+>CY025485\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCATCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAGTGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGGAATCTGCAACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAATTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTGCTTGCAAAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAGAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCAGCCTATATGCTCAAGCACCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCCGAGTAAGGGATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGACAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGCTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGACCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGACCTAACTGACTCAGAAATGAACAAATTGTTTGAAAGAACAAAAAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n+>KC535396\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGA'..b'GAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n+>CY012232\n+ATGAAGACTATCATTGCTTTGAGCTACATTTTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACAGCAACGCTGTGCCTGGGACACCATGCAGTGCCAAACGGAACGCTAGTGAAAACAATCACGAATGATCAAATTGAAGTGACTAATGCTACTGAGCTGGTTCAGAGTTCCCCAACAGGTAGAATATGCGACAGTCCTCACCGAATCCTTGATGGAAAGAACTGCACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGGCTTCCAAAATAAGGAATGGGACCTTTTTGTTGAACGCAGCAAAGCTTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCAGGCACCCTGGAGTTTACCAACGAAAACTTCAATTGGACTGGAGTCGCTCAGGATGGGAAAAGCTATGCTTGCAAAAGGGGATCTGTTAACAGTTTCTTTAGTAGATTGAATTGGTTGCACAAATTAGAATACAAATATCCAGCGCTGAACGTGACTATGCCAAACAATGGCAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGAGCACGGACAGTGACCAAACCAGCCTATATGTCCGAGCATCAGGGAAAGTCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGGATATCGGGTATAGACCATGGGTAAGGGGTCTTTCCAGTAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAATAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAATGGGAAAAGCTCAATAATGAGGTCAGATGCACCCATTGGCAACTGCAGTTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAGGATCACATATGGGGCCTGCCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGTTTCATAGAGAATGGTTGGGAGGGAATGGTAGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAGGGCACAGGACAAGCTGCAGATCTTAAAAGCACTCAAGCAGCAATCGACCAAATCAACGGGAAACTGAATAGGTTAGTCGAGAAAACGAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAAGACACTAAAATAGATCTCTGGTCTTACAATGCGGAGCTTCTTGTTGCTCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTATTTGAAAGAACAAGGAAGCAACTGAGGGAAAATGCTGAGGACATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGTTGTTTTGCTTGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n+>EU199367\n+ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAGTCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n' |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/fubar-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-in1.nhx Thu Jan 17 04:24:25 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +((KF790010:0.001247,CY147300:0.000623):0.0,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623):0.000624):0.0,((CY141224:0.001247,(CY147305:0.0,KF790037:0.000623):0.000623):0.0,(((KF790403:0.000623,KF761507:0.001876):0.0,KC526205:0.000623):0.0,((CY169303:0.0,(KF789585:0.000623,CY141202:0.000623):0.000623):0.000623,(((KJ667974:0.002501,KJ938675:0.001873):0.000623,CY134876:0.0):0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125):0.0):0.0,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873):0.000623):0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624):0.000626):0.001249,((CY168407:0.004394,CY183065:0.003128):0.0,(KF598733:0.002501,((KC892174:0.0,(KF685747:0.000624,CY168471:0.000625):0.00375):0.000624,(((KC892685:0.000624,KC892641:0.0):0.001874,KC893110:0.001249):0.0,(KC892480:0.0,(JX913043:0.001249,(KF551075:0.00125,((CY114509:0.0,(KC892889:0.0,KC893018:0.002498):0.005006):0.001877,(((KC892519:0.0,KC892498:0.000624):0.002497,KC892266:0.000623):0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883):0.001875):0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247):0.001872):0.0,(KC535363:0.000623,((KC535396:0.000623,(KC882883:0.0,KC882867:0.000623):0.003124):0.0,((KC535378:0.001872,KC535375:0.002498):0.0,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:0.0,FJ179354:0.003124):0.0):0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117):0.0):0.000622,(CY173095:0.001245,(((CY173191:0.0,CY037703:0.001247):0.000622,CY035062:0.00249):0.0,((CY173255:0.001871,(CY044748:0.0,GQ385846:0.001247):0.000623):0.0,((CY027075:0.000623,(EU199367:0.0,CY172823:0.000623):0.0):0.000623,(((CY172847:0.000623,CY025643:0.0):0.000623,CY172839:0.000623):0.001247,(((CY026251:0.002497,CY092241:0.00125):0.000624,CY026019:0.000623):0.0,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623):0.001248):0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628):0.000621):0.0,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059):0.008843):0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491):0.001243):0.003763,(AB434109:0.006307,(((CY088198:0.001245,CY088475:0.000621):0.0,CY000257:0.000621):0.002494,((CY112957:0.003135,CY006859:0.001253):0.000616,((CY000721:0.001243,(CY114493:0.0,CY090885:0.002483):0.002488):0.0,((CY001792:0.000621,(CY001600:0.00062,CY002368:0.001865):0.0):0.0,((CY002304:0.002489,(CY006163:0.001242,CY003632:0.00062):0.0):0.00062,(CY001920:0.003739,(CY001912:0.002498,((CY001504:0.0,CY006060:0.001241):0.00062,((CY001744:0.0,CY002136:0.00124):0.00062,((CY114309:0.003746,(CY006899:0.001874,CY112901:0.001863):0.002496):0.000618,(((CY006579:0.001245,CY006283:0.000621):0.001244,CY007979:0.001864):0.0,((CY006499:0.001241,(CY006491:0.001863,CY006635:0.00124):0.0):0.00062,(((CY036847:0.002495,CY010004:0.001867):0.000621,CY012200:0.000621):0.0,(((CY010028:0.001242,CY009732:0.001242):0.0,CY010012:0.002484):0.001875,(((CY010020:0.002497,CY011416:0.001237):0.001252,CY009484:0.00062):0.005658,((CY010036:0.0,(CY039879:0.002489,CY039880:0.000621):0.002487):0.003109,((CY010628:0.000619,(CY010716:0.002485,CY010516:0.001239):0.0):0.000619,((CY012728:0.0,CY013701:0.000621):0.001243,(((CY012760:0.001239,CY013200:0.001239):0.0,CY011888:0.005614):0.0,((CY013693:0.000619,(CY012184:0.002484,CY013669:0.00124):0.00124):0.0,((CY112669:0.004353,(CY112556:0.001861,CY011896:0.000619):0.00186):0.0,(CY112605:0.001243,(CY012224:0.006953,((CY012512:0.000619,(CY012896:0.00062,CY012232:0.00062):0.000621):0.0,(CY011848:0.0,(((CY011328:0.0,CY114221:0.000619):0.001241,CY011560:0.00124):0.0,((CY012456:0.000619,CY011824:0.00124):0.0,CY017283:0.000619):0.0):0.0):0.0):0.002439):0.008263):0.000618):0.0):0.0):0.000617):0.012609):0.000619):0.001215):0.003782):0.000613):0.006878):0.0):0.001862):0.0):0.0):0.001863):0.001862):0.001245):0.0):0.001241):0.021084):0.000623):0.00065):0.003713):0.002495):0.0):0.005637):0.00313):0.002515):0.001876):0.0):0.000623):0.0):0.003749):0.0):0.0):0.000623):0.000623):0.001872):0.002503):0.0):0.0):0.000623):0.001468):0.00189):0.002721):0.002524):0.0):0.000624):0.0):0.0):0.0):0.000623):0.001248):0.001255):0.000619):0.0):0.0):0.0):0.000623):0.0):0.0):0.0):0.0; |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/fubar-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-out1.json Thu Jan 17 04:24:25 2019 -0500 |
| b |
| b'@@ -0,0 +1,3909 @@\n+{\n+ "analysis":{\n+ "info":"Perform a Fast Unbiased AppRoximate Bayesian (FUBAR)\\n analysis of a coding sequence alignment to determine whether some\\n sites have been subject to pervasive purifying or diversifying\\n selection.\\n\\n Please note that a FUBAR analysis generates a cache and a results JSON file in the same directory as\\n directory as the original alignment. HyPhy needs to have write\\n privileges to this directory. For example if the original file is in\\n /home/sergei/FUBAR/data/pol.nex then at the end of a FUBAR run, there\\n will also exist FUBAR-generated files /home/sergei/FUBAR/data/pol.nex.FUBAR.json,\\n /home/sergei/FUBAR/data/pol.nex.fubrar.cache. They also\\n provide checkpointing so that a partially completed analysis can be\\n restarted.",\n+ "version":"2.0",\n+ "citation":"FUBAR: a fast, unconstrained bayesian approximation for inferring selection (2013), Mol Biol Evol. 30(5):1196-205",\n+ "authors":"Sergei L Kosakovsky Pond",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment (possibly partitioned) and a phylogenetic tree (one per partition)"\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpZU5xzE/job_working_directory/002/2526/working/fubar_input.fa",\n+ "number of sequences":163,\n+ "number of sites":566,\n+ "partition count":1,\n+ "trees":{\n+ "0":"(KF790010:0.001247,CY147300:0.000623,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623)Node7:0.000624)Node5:1e-10,((CY141224:0.001247,(CY147305:1e-10,KF790037:0.000623)Node13:0.000623)Node11:1e-10,(((KF790403:0.000623,KF761507:0.001876)Node18:1e-10,KC526205:0.000623)Node17:1e-10,((CY169303:1e-10,(KF789585:0.000623,CY141202:0.000623)Node25:0.000623)Node23:0.000623,(((KJ667974:0.002501,KJ938675:0.001873)Node30:0.000623,CY134876:1e-10)Node29:0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125)Node37:1e-10)Node35:1e-10,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873)Node43:0.000623)Node41:0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624)Node51:0.000626)Node49:0.001249,((CY168407:0.004394,CY183065:0.003128)Node55:1e-10,(KF598733:0.002501,((KC892174:1e-10,(KF685747:0.000624,CY168471:0.000625)Node63:0.00375)Node61:0.000624,(((KC892685:0.000624,KC892641:1e-10)Node68:0.001874,KC893110:0.001249)Node67:1e-10,(KC892480:1e-10,(JX913043:0.001249,(KF551075:0.00125,((CY114509:1e-10,(KC892889:1e-10,KC893018:0.002498)Node81:0.005006)Node79:0.001877,(((KC892519:1e-10,KC892498:0.000624)Node86:0.002497,KC892266:0.000623)Node85:0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883)Node93:0.001875)Node91:0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247)Node99:0.001872)Node97:1e-10,(KC535363:0.000623,((KC535396:0.000623,(KC882883:1e-10,KC882867:0.000623)Node107:0.003124)Node105:1e-10,((KC535378:0.001872,KC535375:0.002498)Node111:1e-10,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:1e-10,FJ179354:0.003124)Node119:1e-10)Node117:0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117)Node125:1e-10)Node123:0.000622,(CY173095:0.001245,(((CY173191:1e-10,CY037703:0.001247)Node132:0.000622,CY035062:0.00249)Node131:1e-10,((CY173255:0.001871,(CY044748:1e-10,GQ385846:0.001247)Node139:0.000623)Node137:1e-10,((CY027075:0.000623,(EU199367:1e-10,CY172823:0.000623)Node145:1e-10)Node143:0.000623,(((CY172847:0.000623,CY025643:1e-10)Node150:0.000623,CY172839:0.000623)Node149:0.001247,(((CY026251:0.002497,CY092241:0.00125)Node156:0.000624,CY026019:0.000623)Node155:1e-10,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623)Node163:0.001248)Node161:0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628)Node173:0.000621)Node171:1e-10,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059)Node179:0.008843)Node177:0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491)Node187:0.001243)Node185:0.003763,(AB434109:0.006307,(((CY088198:0.0012'..b'},\n+ "Node286":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node29":{\n+ "Nucleotide GTR":0.0005897474508257188\n+ },\n+ "Node290":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node291":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node293":{\n+ "Nucleotide GTR":0.00117430959838688\n+ },\n+ "Node296":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node297":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node299":{\n+ "Nucleotide GTR":0.00176761199218168\n+ },\n+ "Node30":{\n+ "Nucleotide GTR":0.0005898078881093438\n+ },\n+ "Node302":{\n+ "Nucleotide GTR":0.0005848345127768663\n+ },\n+ "Node304":{\n+ "Nucleotide GTR":0.007745275417429301\n+ },\n+ "Node306":{\n+ "Nucleotide GTR":0.002330629204008603\n+ },\n+ "Node307":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node309":{\n+ "Nucleotide GTR":0.0005885956619248423\n+ },\n+ "Node312":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node314":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node315":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node316":{\n+ "Nucleotide GTR":0.001176407357032325\n+ },\n+ "Node320":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node321":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node34":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node35":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node37":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node4":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node40":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node41":{\n+ "Nucleotide GTR":0.001772862258434722\n+ },\n+ "Node43":{\n+ "Nucleotide GTR":0.0005878632625248081\n+ },\n+ "Node46":{\n+ "Nucleotide GTR":0.0005879445935582034\n+ },\n+ "Node48":{\n+ "Nucleotide GTR":0.001184645468765879\n+ },\n+ "Node49":{\n+ "Nucleotide GTR":0.001181793995876719\n+ },\n+ "Node5":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node51":{\n+ "Nucleotide GTR":0.0005898360185680268\n+ },\n+ "Node54":{\n+ "Nucleotide GTR":0.001180511953516042\n+ },\n+ "Node55":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node58":{\n+ "Nucleotide GTR":0.00058961101366409\n+ },\n+ "Node60":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node61":{\n+ "Nucleotide GTR":0.0005896414839818972\n+ },\n+ "Node63":{\n+ "Nucleotide GTR":0.00295495604791381\n+ },\n+ "Node66":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node67":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node68":{\n+ "Nucleotide GTR":0.001772143799097988\n+ },\n+ "Node7":{\n+ "Nucleotide GTR":0.0005903801268444384\n+ },\n+ "Node72":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node74":{\n+ "Nucleotide GTR":0.0005900700305158231\n+ },\n+ "Node76":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node78":{\n+ "Nucleotide GTR":0.002369096606403036\n+ },\n+ "Node79":{\n+ "Nucleotide GTR":0.001772323973649173\n+ },\n+ "Node81":{\n+ "Nucleotide GTR":0.004730848174672563\n+ },\n+ "Node84":{\n+ "Nucleotide GTR":0.002072779597743145\n+ },\n+ "Node85":{\n+ "Nucleotide GTR":0.00147286203050845\n+ },\n+ "Node86":{\n+ "Nucleotide GTR":0.002362326634870749\n+ },\n+ "Node90":{\n+ "Nucleotide GTR":0.001781845478584892\n+ },\n+ "Node91":{\n+ "Nucleotide GTR":0.003853035355238686\n+ },\n+ "Node93":{\n+ "Nucleotide GTR":0.001777432790890143\n+ },\n+ "Node96":{\n+ "Nucleotide GTR":0.0008853901614979664\n+ },\n+ "Node97":{\n+ "Nucleotide GTR":0\n+ },\n+ "Node99":{\n+ "Nucleotide GTR":0.00177368320099115\n+ }\n+ },\n+ "attributes":{\n+ "original name":{\n+ "attribute type":"node label",\n+ "display order":-1\n+ },\n+ "Nucleotide GTR":{\n+ "attribute type":"branch length",\n+ "display order":0\n+ }\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/meme-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.fa Thu Jan 17 04:24:25 2019 -0500 |
| b |
| b'@@ -0,0 +1,1 @@\n+>TREESPARROW_HENAN_1_2004\rATGGAGAAAATAGTGCTTCTTCGTGCAATGATCAATCTTGTTAAAAGTGA\rTCAGATTGGCGTTGGTTACCATGCAGACTACTCGACAGAGCAGGGTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAA\rAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\rTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCA\rACCCAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAATGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\rCCGAATGACGCTATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACCAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACAGGGCTCA\rGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\rGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r>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>TREESPARROW_HENAN_4_2004\rATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGCAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAACCTCTAAT\rTTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGAAGCCTCA'..b'AA\rTAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCGCTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCC------------------------\r>TREESPARROW_HENAN_2_2004\rATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATATTGGAA\rAAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT\rTTTGAAAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAGTGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAAAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCTGGGGAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGGGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG\rAACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA\rAAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAGAGTG\rAATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCG\rATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCA\rGAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA\rAAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA\rGGTCCGACTACAACTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC\rGGAACGTATGACTACCGGCTGGACTCAGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r>HONGKONG_1_538_97\r------------------------------------------------GA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA\rAGGACACACAACGGGAAGCTCTGCGATCTAAATGGAGTGAAACCTCTCAT\rTTTGAGGGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGT\rCCAGCCAATGACCTCTGTTATCCAGGGAATTTCAACGACTATGAAGAACT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCA\rTGTCCATACCTTGGGAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT\rCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGG\rAACATCAACACTGAACCAGAGATTGGTTCCAGAAATAGCTACTAGACCCA\rAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG\rCCGAATGATGCCATCAATTTCGAGAGTAATGGAAATTTCATTGCCCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCATTCCACAACATACACCCCCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTTCTTGCGACTGGACTCA\rGAAATACCCCTCAAAGGGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA\rGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACC\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTAACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rTAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAAATGGAAGACGGAT\rTCCTAGATGTCTGGACTTACAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTCGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAACTGGGTAATGGTTGTT\rTCGAATTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGT\rCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT\r\r\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/meme-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.nhx Thu Jan 17 04:24:25 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(((((((TREESPARROW_HENAN_1_2004{FG}:0.0111333782927653,TREESPARROW_HENAN_3_2004{FG}:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.00906278098731238):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,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,DUCK_VIETNAM_376_2005:0.007877615936285868):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,DUCK_VIETNAM_272_2005:0.009465302724994452) |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/meme-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-out1.json Thu Jan 17 04:24:25 2019 -0500 |
| [ |
| b'@@ -0,0 +1,9816 @@\n+{\n+ "analysis":{\n+ "info":"MEME (Mixed Effects Model of Evolution)\\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\\n uses a likelihood ratio test to determine if β+ > α at a site.\\n The estimates aggregate information over a proportion of branches at a site,\\n so the signal is derived from\\n episodic diversification, which is a combination of strength of selection [effect size] and\\n the proportion of the tree affected. A subset of branches can be selected\\n for testing as well, in which case an additional (nuisance) parameter will be\\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\\n for recombination - aware analysis.\\n ",\n+ "version":"2.0.1",\n+ "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",\n+ "authors":"Sergei L. Kosakovsky Pond, Steven Weaver",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree"\n+ },\n+ "fits":{\n+ "Nucleotide GTR":{\n+ "Log Likelihood":-4394.17778442101,\n+ "estimated parameters":47,\n+ "AIC-c":8882.482274823486,\n+ "Equilibrium frequencies":[\n+ [0.3460163217230355],\n+ [0.1876507375623983],\n+ [0.2296889898480005],\n+ [0.2366439508665657]\n+ ],\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.1602243049428088,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.1350661843114337,\n+ "Substitution rate from nucleotide C to nucleotide G":0.04669906431175039,\n+ "Substitution rate from nucleotide C to nucleotide T":1.290725939052547,\n+ "Substitution rate from nucleotide G to nucleotide T":0.1442807316736102\n+ },\n+ "display order":0\n+ },\n+ "Global MG94xREV":{\n+ "Log Likelihood":-4272.739394378317,\n+ "estimated 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0.982284632470087, 0, 0.6666666666666666, 0, 0.6869056237318886],\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+ [3.778232489478013, 2.03776205152443e-13, 0.02561078725613944, 0, 0.9743892127438606, 0, 0.6666666666666666, 0, 0.4381982550209036],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0]\n+ ]\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/params.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/params.json Thu Jan 17 04:24:25 2019 -0500 |
| [ |
| b'@@ -0,0 +1,280 @@\n+{\n+ "filepath": "/home/sweaver/datamonkey/datamonkey-js-dev/app/models/../../uploads/msa/5446bc0d355080301f18a8c6.fasta",\n+ "msa": [\n+ {\n+ "rawsites": 1698,\n+ "nj": 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"rawsites": 1698\n+ }\n+ ],\n+ "created": "2014-10-21T20:03:25.798Z"\n+ },\n+ "status_stack": [\n+ "In Queue",\n+ "Running",\n+ "Completed"\n+ ],\n+ "type": "relax"\n+}\n' |
| b |
| diff -r 000000000000 -r 9da003917dcb test-data/slac-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slac-out1.json Thu Jan 17 04:24:25 2019 -0500 |
| [ |
| b'@@ -0,0 +1,2076 @@\n+{\n+ "analysis":{\n+ "info":"SLAC (Single Likelihood Ancestor Counting)\\n uses a maximum likelihood ancestral state reconstruction\\n and minimum path substitution counting to estimate site - level\\n dS and dN,\\n and applies a simple binomial - based test to test\\n if dS differs drom dN.\\n The estimates aggregate information over all branches,\\n so the signal is derived from\\n pervasive diversification or conservation. A subset of branches can be selected\\n for testing as well.\\n Multiple partitions within a NEXUS file are also supported\\n for recombination - aware analysis.\\n ",\n+ "version":"2.00",\n+ "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222",\n+ "authors":"Sergei L Kosakovsky Pond and Simon DW Frost",\n+ "contact":"spond@temple.edu",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree"\n+ },\n+ "fits":{\n+ "Nucleotide GTR":{\n+ "Log Likelihood":-3531.963798530155,\n+ "estimated parameters":24,\n+ "AIC-c":7112.142458295762,\n+ "Equilibrium frequencies":[\n+ [0.3563279857397504],\n+ [0.1837789661319073],\n+ [0.2402852049910873],\n+ [0.2196078431372549]\n+ ],\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,\n+ "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378\n+ },\n+ "display order":0\n+ },\n+ "Global MG94xREV":{\n+ "Log Likelihood":-3466.724829119623,\n+ "estimated parameters":31,\n+ "AIC-c":6996.52909240682,\n+ "Equilibrium frequencies":[\n+ [0.04785168648208005],\n+ [0.03911346079312019],\n+ [0.04842054060317301],\n+ [0.04069665666515385],\n+ [0.01817010744778396],\n+ [0.01485205303123071],\n+ [0.01838611113045968],\n+ [0.01545321970309948],\n+ [0.0190138898893362],\n+ [0.01554175184587827],\n+ [0.01923992433904378],\n+ [0.01617083546230154],\n+ [0.02796925133965702],\n+ [0.02286176927319543],\n+ [0.02830174586718859],\n+ [0.02378714529482007],\n+ [0.01687870337957799],\n+ [0.01379647304851128],\n+ [0.01707935503225849],\n+ [0.01435491300079667],\n+ [0.006409133648843443],\n+ 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[0.01429258425298098],\n+ [0.01201267864744234]\n+ ],\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*":[\n+ [0.9952474740528205, 1]\n+ ]\n+ }'..b' 0.7667128671748024, 0.890841230650352, 0.8320854747642759, 1.723419162497329],\n+ [1, 2, 5, 0.4749999999999517, 0.3333333333333333, 5, 0.2374999999999758, -2.183160128350873, 1, 0.03782959914646881, 1.723419162497329],\n+ [0.843656832841698, 2.408185306598483, 2.938888888888878, 9.886111111111106, 0.2843369743316476, 4.574922684961112, 4.238621782785534, 1.594080406346652, 0.7883087325663475, 0.9345721380406598, 1.723419162497329],\n+ [0.4015666212427145, 2.598433378757286, 0, 0.4749999999999517, 0.1338555404142381, 0, 0.1828024546956531, 0.1060696426461699, 1, 1, 1.723419162497329],\n+ [0.7631315455164901, 2.303416321948652, 4, 8.579166666666659, 0.2598642419466547, 6.13519119941088, 3.924250265172389, 0.9761043336904643, 0.9485561128462242, 0.8823115672560321, 1.723419162497329],\n+ [1, 2, 0, 2, 0.3333333333333333, 0, 1, 0.5802418945783016, 0.6666666666666667, 1, 1.723419162497329],\n+ [0.5108071114874615, 2.57138242847146, 2, 3, 0.1702690371624872, 4.689333452586883, 1.205209935254436, -0.4366182159717286, 0.989584442823033, 0.5260318186931501, 1.723419162497329],\n+ [0.7355430390802056, 2.24582979842974, 0.5, 7.5, 0.2547488097891927, 0.6797698753634438, 3.49464769706217, 1.865065863585222, 0.2612708950448336, 1, 1.723419162497329],\n+ [0.6267060118898431, 2.238010426610814, 2, 2, 0.2199736580517843, 3.214404615308581, 0.9115992408219742, -0.4173100575643724, 0.9651119805840197, 0.5225975649035184, 1.723419162497329],\n+ [0.9101251033652521, 2.317095536064913, 2, 7.158333333333317, 0.303375034455084, 2.290533001213371, 3.425698572354657, 1.350172793073417, 0.6586555929582461, 0.9471075623091124, 1.723419162497329],\n+ [0.673672140559856, 2.489920391149622, 2.158333333333317, 8.13194444444443, 0.226629447539539, 4.126852101032075, 3.54552687644596, 1.976804163754458, 0.836071480785966, 1, 1.723419162497329],\n+ [0.6897615550532064, 2.790263254042777, 2.333333333333333, 8.526388888888887, 0.2304358158933025, 6.094648833588598, 3.276393298181066, 0.3613328345356598, 0.9231255898428308, 0.6686732177677085, 1.723419162497329],\n+ [0.7946586568361008, 2.167975169364766, 1, 6, 0.2715103527844899, 1.405104306225133, 2.818037808360176, 0.8363424597513123, 0.7430921944460164, 0.8718081545299928, 1.723419162497329],\n+ [0.925309922046851, 2.236871623721474, 2.579166666666659, 8.5, 0.3084366406822837, 2.925882077362623, 4.049552410687498, 1.364532301558911, 0.6461765519656628, 0.9254887173196068, 1.723419162497329],\n+ [0.9581686586422306, 2.13880638531327, 2, 5, 0.3193895528807435, 2.322358138625455, 2.415212293435113, 0.7773494920126088, 0.7795378572552829, 0.8920156958059355, 1.723419162497329],\n+ [0.7593283298052359, 2.460727196465021, 3, 8.526388888888887, 0.253391086431764, 4.622736289498208, 3.556429743974461, 1.477112310794914, 0.8989574146760382, 0.8927015041979159, 1.723419162497329],\n+ [0.5112602866741613, 2.217104081344285, 0, 0, 0.1873871000028779, 0, 0, 0, 1, 1, 1.723419162497329],\n+ [1, 1.952467466533022, 2, 4, 0.342663635137335, 2, 2.086372572382543, 0.63035887961715, 0.7821097289668139, 0.8770423554138478, 1.723419162497329],\n+ [0.75154665371034, 2.194207467544889, 0.7374999999999758, 2.895833333333293, 0.2591620486295864, 1.086891717767276, 1.342183608392251, 0.6579931372011264, 0.7050462382636092, 1, 1.723419162497329],\n+ [0.6018431830315369, 2.241218884393843, 1, 2, 0.2148519149742012, 1.661562393982619, 0.9093567672257744, -0.4364612179818503, 0.8845364432183682, 0.5159895622684771, 1.723419162497329],\n+ [1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 1.723419162497329],\n+ [1.401566621242714, 1.598433378757286, 0, 0, 0.4671888737475713, 0, 0, 0, 1, 1, 1.723419162497329],\n+ [0.5861816684921827, 2.463353001049777, 3, 4.158333333333317, 0.1963715666467496, 5.590266983451943, 1.70370382635879, -1.259842549492376, 0.9887093275905696, 0.2624813117321075, 1.723419162497329]\n+ ]\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |