| Next changeset 1:4e3212e05a8f (2021-04-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb" |
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added:
hyphy_strike_ambigs.xml macros.xml scripts/annotator.bf scripts/strike-ambigs.bf test-data/absrel-in1.fa test-data/absrel-in1.nhx test-data/absrel-out1.json test-data/annotate-in1.fa.gz test-data/annotate-in1.nhx test-data/annotate-out1-clade.nhx test-data/annotate-out1-full.nhx test-data/annotate-out1-int.nhx test-data/bgm-in1.fa test-data/bgm-in1.nhx test-data/bgm-out1.json test-data/busted-out1.json test-data/cfel-out1.json test-data/conv-in1.fa test-data/conv-out1.nhx test-data/fade-in1.fa test-data/fade-in1.nhx test-data/fade-out1.json test-data/fel-out1.json test-data/fubar-in1.fa.gz test-data/fubar-in1.nhx test-data/fubar-out1.json test-data/gard-in1.fa test-data/gard-out1.json test-data/gard-out1.nex test-data/meme-in1.fa test-data/meme-in1.nhx test-data/meme-out1.json test-data/params.json test-data/prime-in1.fa test-data/prime-in1.nhx test-data/prime-out1.json test-data/relax-in1.fa test-data/relax-in1.nhx test-data/relax-in2.nhx test-data/relax-out1.json test-data/slac-out1.json test-data/sm19-in1.nhx test-data/sm19-in2.nhx test-data/sm19-out1.json test-data/sm19-out2.json test-data/strike-ambigs-in1.fa test-data/strike-ambigs-in2.fa test-data/strike-ambigs-out1.fa test-data/strike-ambigs-out2.fa |
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| diff -r 000000000000 -r 7c86ceaf523c hyphy_strike_ambigs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hyphy_strike_ambigs.xml Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| @@ -0,0 +1,40 @@ +<?xml version="1.0"?> +<tool id="hyphy_strike_ambigs" name="Replace ambiguous codons" version="@VERSION@"> + <description>in a multiple alignment using HyPhy</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + hyphy '$__tool_directory__/scripts/strike-ambigs.bf' + --alignment '$alignment' --output '$output' + @ERRORS@ + ]]></command> + <inputs> + <param name="alignment" type="data" format="fasta" label="Input alignment" /> + </inputs> + <outputs> + <data name="output" format="fasta" /> + </outputs> + <tests> + <test> + <param name="alignment" ftype="fasta" value="strike-ambigs-in1.fa"/> + <output name="output" file="strike-ambigs-out1.fa" /> + </test> + <test> + <param name="alignment" ftype="fasta" value="strike-ambigs-in2.fa"/> + <output name="output" file="strike-ambigs-out2.fa" /> + </test> + </tests> + <help><![CDATA[ +HyPhy Strike-Ambigs +=================== + +Reads an alignment of coding sequences and replaces any ambiguous codons with ---. + +Note: The input fasta must be aligned along codon boundaries. +]]></help> + <expand macro="citations"> + <citation type="doi">10.1093/bioinformatics/bti079</citation> + </expand> +</tool> |
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| diff -r 000000000000 -r 7c86ceaf523c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Apr 20 10:27:46 2021 +0000 |
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| @@ -0,0 +1,144 @@ +<?xml version="1.0"?> +<macros> + <xml name="inputs"> + <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" /> + <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/> + </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 + for between-host HIV sequences</option> + <option value="HIVWm">HIVWm - Specialist empirical model + for within-host HIV sequences</option> + <option value="WAG">WAG - Generalist empirical model from + Whelan and Goldman (2001)</option> + <option value="JTT">JTT - Generalist empirical model from + Jones, Taylor, and Thornton (1996)</option> + <option value="JC69">JC69 - Generalist empirical model + from with equal exchangeability rates</option> + <option value="mtMet">mtMet - Specialist empirical model + for metazoan mitochondrial genomes</option> + <option value="mtVer">mtVer - Specialist empirical model + for vertebrate mitochondrial genomes</option> + <option value="mtInv">mtInv - Specialist empirical model + for invertebrate mitochondrial genomes</option> + <option value="gcpREV">gcpREV - Specialist empirical + model for green plant chloroplast genomes</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> + <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA + code</option> + <option value="Yeast-mtDNA">Yeast mitochondrial DNA + code</option> + <option value="Mold-Protozoan-mtDNA">Mold, Protozoan and + Coelenterate mt; Mycloplasma/Spiroplasma</option> + <option value="Invertebrate-mtDNA">Invertebrate mitochondrial + DNA code</option> + <option value="Ciliate-Nuclear">Ciliate, Dasycladacean and + Hexamita Nuclear code</option> + <option value="Echinoderm-mtDNA">Echinoderm mitochondrial DNA + code</option> + <option value="Euplotid-Nuclear">Euplotid Nuclear + code</option> + <option value="Alt-Yeast-Nuclear">Alternative Yeast Nuclear + code</option> + <option value="Ascidian-mtDNA">Ascidian mitochondrial DNA + code</option> + <option value="Flatworm-mtDNA">Flatworm mitochondrial DNA + code</option> + <option value="Blepharisma-Nuclear">Blepharisma Nuclear + code</option> + </param> + </xml> + + <xml name="branches"> + <param name="branches" type="select" label="Set of branches to test"> + <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> + </param> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/molbev/msz197</citation> + <yield/> + </citations> + </xml> + <token name="@VERSION@">2.5.31</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">hyphy</requirement> + <yield/> + </requirements> + </xml> + <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> + <token name="@CATCH_ERROR@"><![CDATA[ + EC=\$? ; + if [ \$EC -ne 0 ] ; then + if [ -f errors.log.mpinode0 ] ; then + cat errors.log.mpinode0 >&2 ; + else + cat errors.log >&2 ; + fi ; + fi ; + exit \$EC + ]]></token> + <token name="@HYPHY_ENVIRONMENT@"><![CDATA[ + export HYPHY=`which hyphy` && + export HYPHY_PATH=`dirname \$HYPHY` && + export HYPHY_LIB=`readlink -f \$HYPHY_PATH/../share/hyphy` &&]]></token> + <token name="@HYPHY_INVOCATION@"><![CDATA[ + @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB + ]]></token> + <token name="@SYMLINK_FILES@"><![CDATA[ + ln -s '$input_file' input.$input_file.extension && + ln -s '$@operation@_output' input.${input_file.extension}.@OPERATION@.json && + #set $input_file = 'input.%s' % $input_file.extension + #if $input_nhx: + ln -s '$input_nhx' input.nhx && + #end if + ]]></token> +</macros> |
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| diff -r 000000000000 -r 7c86ceaf523c scripts/annotator.bf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/annotator.bf Tue Apr 20 10:27:46 2021 +0000 |
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| @@ -0,0 +1,102 @@ +LoadFunctionLibrary ("libv3/tasks/trees.bf"); +LoadFunctionLibrary ("libv3/tasks/alignments.bf"); +LoadFunctionLibrary ("libv3/convenience/regexp.bf"); +LoadFunctionLibrary ("libv3/IOFunctions.bf"); + +tags = { + "^Node" : "Internal" +}; + + + + +tree = trees.LoadAnnotatedTopology (TRUE); +ts = tree[^"terms.trees.newick_with_lengths"]; +root_node = io.PromptUserForString ("Root on this node"); + + + +Topology T = ts; +ts = RerootTree (T, root_node); +ACCEPT_ROOTED_TREES = FALSE; +Topology T = ts; +ACCEPT_ROOTED_TREES = TRUE; +Topology TR = ts; + + +NORMALIZE_SEQUENCE_NAMES = FALSE; +SetDialogPrompt ("File with the sequences to label as the in-clade"); +DataSet query = ReadDataFile (PROMPT_FOR_FILE); +GetString (seqNames,query,-1); + +label = io.PromptUserForString ("Use this label"); + + +for (s;in;seqNames) { + tags [s && 6] = label; +} + +reg_exp = Rows (tags); + + +node_labels = {}; +for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (T,-1), reg_exp)) { + tag = tags[_regexp_]; + + if (tag != "Internal") { + + if (Abs (tag) == 0) { + tag = "Reference"; + } + + for (l; in; _leaves_) { + node_labels[l] = tag; + } + } +} + +node_labelsR = {}; +for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (TR,-1), reg_exp)) { + tag = tags[_regexp_]; + + if (tag != "Internal") { + + if (Abs (tag) == 0) { + tag = "Reference"; + } + + for (l; in; _leaves_) { + node_labelsR[l] = tag; + } + } +} + + +leaf_labels = node_labels; +node_labelsF = node_labels; +node_labels * ((trees.ParsimonyLabel ("T", node_labels))["labels"]); +node_labelsR * ((trees.ParsimonyLabel ("T", node_labelsR))["labels"]); +node_labelsF * ((trees.ParsimonyLabel ("T", node_labelsF))["labels"]); + +output_to = io.PromptUserForString ("Write output to this prefix"); + +fprintf (output_to + "labels.json", CLEAR_FILE, leaf_labels); +fprintf (output_to + "int.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate", "{}", FALSE)); +fprintf (output_to + "clade.nwk", CLEAR_FILE, tree.Annotate ("TR", "relabel_and_annotate_full", "{}", FALSE)); +fprintf (output_to + "full.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate_full", "{}", FALSE)); + +function relabel_and_annotate (node_name) { + _label = ""; + if (node_labels / node_name && leaf_labels / node_name == FALSE) { + _label = "{" + node_labels[node_name] + "}"; + } + return node_name + _label; +} + +function relabel_and_annotate_full (node_name) { + _label = ""; + if (node_labelsR / node_name) { + _label = "{" + node_labelsR[node_name] + "}"; + } + return node_name + _label; +} |
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| diff -r 000000000000 -r 7c86ceaf523c scripts/strike-ambigs.bf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/strike-ambigs.bf Tue Apr 20 10:27:46 2021 +0000 |
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| @@ -0,0 +1,83 @@ +RequireVersion ("2.5.20"); + +LoadFunctionLibrary ("libv3/tasks/alignments.bf"); +LoadFunctionLibrary ("libv3/tasks/trees.bf"); +LoadFunctionLibrary ("libv3/UtilityFunctions.bf"); +LoadFunctionLibrary ("libv3/IOFunctions.bf"); +LoadFunctionLibrary ("libv3/convenience/math.bf"); + + + +filter.analysis_description = {terms.io.info : + " + Read an alignment of coding sequences and replace any ambiguous codons with ---. Write results to a new file in FASTA format, and report changed sequences to stdout + ", + terms.io.version : "0.1", + terms.io.reference : "TBD", + terms.io.authors : "Sergei L Kosakovsky Pond", + terms.io.contact : "spond@temple.edu", + terms.io.requirements : "An MSA" + }; + + +io.DisplayAnalysisBanner (filter.analysis_description); + +utility.SetEnvVariable ("NORMALIZE_SEQUENCE_NAMES", FALSE); + +KeywordArgument ("code", "Which genetic code should be used", "Universal"); +KeywordArgument ("alignment", "An in-frame codon alignment in one of the formats supported by HyPhy"); + +filter.in = alignments.PromptForGeneticCodeAndAlignment ("filter.dataset", "filter.input"); + +KeywordArgument ("output", ".fasta for compressed data", None); +filter.out = io.PromptUserForFilePath(".fasta for filtered data"); +fprintf (filter.out, CLEAR_FILE, KEEP_OPEN); + +GetDataInfo (filter.site_patterns, filter.input); + +filter.patter2site = {}; + + +for (i,j,v; in; filter.site_patterns) { + index = i+j; + if (filter.patter2site / v == FALSE ) { + filter.patter2site [v] = {}; + } + filter.patter2site [v] + index; +} + +GET_DATA_INFO_RETURNS_ONLY_THE_INDEX = TRUE; +COUNT_GAPS_IN_FREQUENCIES = FALSE; +filter.unique_patterns = utility.Array1D (filter.input.site_freqs); + +for (seq = 0; seq < filter.input.species; seq += 1) { + io.ReportProgressBar ("filter","Processing sequence " + (1+seq)); + codons = {1, filter.input.sites}; + codons [0] = ""; + GetString (seq_name, filter.input, seq); + GetDataInfo (seq_chars, filter.input, seq); + + filter.ambigs = 0; + + for (pattern = 0; pattern < filter.unique_patterns; pattern += 1) { + GetDataInfo (pattern_info, filter.input, seq, pattern); + if (pattern_info >= 0) { + codon_start = (filter.patter2site[pattern])[0] * 3; + codon = seq_chars [codon_start][codon_start+2]; + } else { + codon = "---"; + filter.ambigs += Abs (filter.patter2site [pattern]) + } + for (c; in; filter.patter2site [pattern] ) { + codons[c] = codon; + } + } + if (filter.ambigs > 0) { + fprintf (stdout, "\nStriking ", filter.ambigs, " codons that are incompletely resolved from " + seq_name + "\n"); + } + fprintf (filter.out,">",seq_name,"\n",Join ("", codons), "\n"); +} + +fprintf (filter.out,CLOSE_FILE); + + |
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| diff -r 000000000000 -r 7c86ceaf523c test-data/absrel-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
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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 7c86ceaf523c test-data/absrel-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
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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 7c86ceaf523c test-data/absrel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,478 @@\n+{\n+ "analysis":{\n+ "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",\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. v2.2 adds support for multiple-hit models",\n+ "contact":"spond@temple.edu",\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+ "requirements":"in-frame codon alignment and a phylogenetic tree",\n+ "version":"2.2"\n+ },\n+ "branch attributes":{\n+ "0":{\n+ "Baboon":{\n+ "Baseline MG94xREV":0.001816807585564731,\n+ "Baseline MG94xREV omega ratio":0,\n+ "Corrected P-value":1,\n+ "Full adaptive model":0.001810407118394509,\n+ "LRT":0,\n+ "Nucleotide GTR":0.001678881906620672,\n+ "Rate Distributions": [\n+[0, 1] \n+ ],\n+ "Rate classes":1,\n+ "Uncorrected P-value":1,\n+ "original name":"Baboon",\n+ "rate at which 2 nucleotides are changed instantly within a single codon":0\n+ },\n+ "Cat":{\n+ "Baseline MG94xREV":0.2286001363527903,\n+ "Baseline MG94xREV omega ratio":1.403298474422089,\n+ "Corrected P-value":1,\n+ "Full adaptive model":0.1219386838393392,\n+ "LRT":1.644967676056694,\n+ "Nucleotide GTR":0.265904547400163,\n+ "Rate Distributions": [\n+[0.2130519766306851, 0.6352283641519592],\n+ [2.628217450705319, 0.3647716358480408] \n+ ],\n+ "Rate classes":2,\n+ "Uncorrected P-value":0.171730764045231,\n+ "original name":"Cat",\n+ "rate at which 2 nucleotides are changed instantly within a single codon":0\n+ },\n+ "Chimp":{\n+ "Baseline MG94xREV":0.001840311209746262,\n+ "Baseline MG94xREV omega ratio":10000000000,\n+ "Corrected P-value":1,\n+ "Full adaptive model":0.001841979303044237,\n+ "LRT":0.6159123786974305,\n+ "Nucleotide GTR":0.001816713800925801,\n+ "Rate Distributions": [\n+[10000000000, 1] \n+ ],\n+ "Rate classes":1,\n+ "Uncorrected P-value":0.3069983227523322,\n+ "original name":"Chimp",\n+ "rate at which 2 nucleotides are changed instantly within a single codon":0\n+ },\n+ "Cow":{\n+ "Baseline MG94xREV":0.2070244948790512,\n+ "Baseline MG94xREV omega ratio":2.153434974462683,\n+ "Corrected P-value":0.5006146299996015,\n+ "Full adaptive model":0.1241125417707662,\n+ "LRT":4.898194538953248,\n+ "Nucleotide GTR":0.2481512612523618,\n+ "Rate Distributions": [\n+[0, 0.52318726440949],\n+ [2.444056517734385, 0.47681273559051] \n+ ],\n+ "Rate classes":2,\n+ "Uncorrected P-value":0.03128841437497509,\n+ "original name":"Cow",\n+ "rate at which 2 nucleotides are changed instantly within a single codon":0\n+ },\n+ "Horse":{\n+ "Baseline MG94xREV":0.190365915457708,\n+ "Baseline MG94xREV omega ratio":1.182933895494305,\n+ "Corrected P-value":1,\n+ "Full adaptive model":0.0869489794025302,\n+ "LRT":2.047309801283518,\n+ "Nucleotide GTR":0.2090927256979082,\n+ "Rate Distributions": [\n+[0, 0.5397658078247131],\n+ [1.633257246666139, 0.4602341921752869] \n+ ],\n+ "Rate classes":2,\n+ "Uncorrected P-value":0.1382789032066179,\n+ "original name":"Horse",\n+ "rate at which 2 nucleotides are changed instantly within a single codon":0\n+ },\n+ "Human":{\n+ "Baseline MG94xREV":0,\n+ "Baseline MG94xREV omega ratio":1,\n+ "Corrected P-value":1,\n+ "Full adaptive model":0,\n+ "LRT":0,\n+ "Nucle'..b'\n+ [0.005501589790395056],\n+ [0.009655668202293983],\n+ [0.007888099278638223],\n+ [0.009797203904398108],\n+ [0.008223514024394991],\n+ [0.03326722643528176],\n+ [0.02717732003095303],\n+ [0.03375486749252685],\n+ [0.02833294365668738],\n+ [0.01236215156074466],\n+ [0.01009913314808799],\n+ [0.01254335971371867],\n+ [0.01052856463184265],\n+ [0.01292858539344675],\n+ [0.0105618754683007],\n+ [0.0131180965046964],\n+ [0.01101098350431497],\n+ [0.0193250328267319],\n+ [0.01578738770911659],\n+ [0.0196083049972345],\n+ [0.01645869298147252],\n+ [0.01962343746171723],\n+ [0.02045785777700414],\n+ [0.008926115885166477],\n+ [0.007292098982657142],\n+ [0.009056957588961733],\n+ [0.007602170831388156],\n+ [0.007626222986467745],\n+ [0.009471947420992787],\n+ [0.007950502328516303],\n+ [0.01395367801862353],\n+ [0.01139931439306339],\n+ [0.01415821524731906],\n+ [0.01188403168729233] \n+ ],\n+ "Log Likelihood":-3427.720059001285,\n+ "Rate Distributions":{\n+ "Per-branch delta":{\n+ "2.5%":0,\n+ "97.5%":12.07373117808175,\n+ "Mean":1.277646334033236,\n+ "Median":0.4551223038316586\n+ },\n+ "Per-branch omega":{\n+ "2.5%":0,\n+ "97.5%":2.153434974462683,\n+ "Mean":666666667.5119981,\n+ "Median":1\n+ }\n+ },\n+ "display order":1,\n+ "estimated parameters":62\n+ },\n+ "Full adaptive model":{\n+ "AIC-c":6972.859938351839,\n+ "Log Likelihood":-3415.824749853321,\n+ "Rate Distributions":{\n+ },\n+ "display order":2,\n+ "estimated parameters":68\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":7112.857317645923,\n+ "Equilibrium frequencies": [\n+[0.3592490842490842],\n+ [0.181959706959707],\n+ [0.240018315018315],\n+ [0.2187728937728937] \n+ ],\n+ "Log Likelihood":-3532.321228205235,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813,\n+ "Substitution rate from nucleotide C to nucleotide T":1.028960084526602,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399\n+ },\n+ "display order":0,\n+ "estimated parameters":24\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/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)Node3:0.08509899999999999,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+ "test results":{\n+ "P-value threshold":0.05,\n+ "positive test results":0,\n+ "tested":16\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node12":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node8":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Baseline model fitting":{\n+ "order":2,\n+ "timer":17\n+ },\n+ "Complexity analysis":{\n+ "order":3,\n+ "timer":110\n+ },\n+ "Full adaptive model fitting":{\n+ "order":4,\n+ "timer":20\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":259\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":0\n+ },\n+ "Testing for selection":{\n+ "order":5,\n+ "timer":112\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r 7c86ceaf523c test-data/annotate-in1.fa.gz |
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| Binary file test-data/annotate-in1.fa.gz has changed |
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| diff -r 000000000000 -r 7c86ceaf523c test-data/annotate-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1:0.000523,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021:0.000001):0.000001,REFERENCE:0.000262,(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4:0.001835,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3:0.000001,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1:0.000786,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1:0.000785,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021:0.823959):0.000001):0.000001):0.000262):0.000001); |
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| diff -r 000000000000 -r 7c86ceaf523c test-data/annotate-out1-clade.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-clade.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1{Annotated},epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated})Node2{Annotated},(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated},(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3{Annotated},(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated},(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated},epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated})Node11{Annotated})Node9{Annotated})Node7{Annotated})Node5{Annotated})Node1{Annotated},REFERENCE{Annotated})Node14 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/annotate-out1-full.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-full.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1{Annotated},epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated})Node2{Annotated},(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated},(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3{Annotated},(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated},(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated},epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated})Node11{Annotated})Node9{Annotated})Node7{Annotated})Node5{Annotated},REFERENCE{Annotated})Node1{Annotated} \ No newline at end of file |
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| diff -r 000000000000 -r 7c86ceaf523c test-data/annotate-out1-int.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-int.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021)Node2{Annotated},(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021)Node11{Annotated})Node9{Annotated})Node7{Annotated})Node5{Annotated},REFERENCE)Node1{Annotated} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/bgm-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,20 @@ +>Human +GCACAATTCAGAAAAGAGAAAGAGACTTTC +>Chimp +GCACAATTCAGAAAAGAGAAAGAGACTTTC +>Baboon +GCACAATTCAGAAAAGAGAAGGAGACTTTC +>RhMonkey +GCACAATTCAGAAAAGAGAAGGAGACTTTC +>Cow +GCACGAATAAAGAAAGATATGCCACTTCAC +>Pig +GCAGAATTTAAAAAAAACAAAGAAACTCAC +>Horse +GCAAAATTCAAAAATGGCAGTATGACTTTC +>Cat +GCGAGGTTCCAAATTAGCAACAAGCCTAAG +>Mouse +GCAGAGTTTAAAAGGAAGAAGCCACCTTTT +>Rat +GCCGAGTTTAAAAGGAAGATGAAGCCTTTT |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/bgm-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -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); |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/bgm-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| @@ -0,0 +1,168 @@ +{ + "MLE":{ + "content": [ +[2, 3, 0.02851572177464722, 0.01992394838090668, 0.04843967015555389, 4, 3, 1], + [2, 4, 0.2913031811286725, 0.1581095173619919, 0.4494126984906644, 4, 2, 2], + [2, 5, 0.04313828130286183, 0.09337388689236253, 0.1365121681952244, 4, 3, 2], + [2, 6, 0.05037434713194238, 0.07113225549859428, 0.1215066026305367, 4, 6, 3], + [2, 7, 0.2804886800096655, 0.2001828066808252, 0.4806714866904907, 4, 4, 3], + [2, 8, 0.07183821900324161, 0.1469389589305462, 0.2187771779337878, 4, 5, 3], + [2, 9, 0.03082407077478325, 0.09900473652454521, 0.1298288072993285, 4, 3, 2], + [2, 10, 0.02245776059232202, 0.02955557233236829, 0.05201333292469031, 4, 3, 1], + [3, 4, 0.03717045364745913, 0.02520976460488304, 0.06238021825234218, 3, 2, 0], + [3, 5, 0.02873335174526813, 0.03479214292405394, 0.06352549466932207, 3, 3, 1], + [3, 6, 0.1236923855363388, 0.2512471049857198, 0.3749394905220587, 3, 6, 3], + [3, 7, 0.01909635400892135, 0.02551889926711521, 0.04461525327603656, 3, 4, 1], + [3, 8, 0.02488014112561441, 0.05406148356625361, 0.07894162469186802, 3, 5, 2], + [3, 9, 0.08440837590482446, 0.2181470609147132, 0.3025554368195377, 3, 3, 2], + [3, 10, 0.1267967238159999, 0.1611592144212058, 0.2879559382372058, 3, 3, 2], + [4, 5, 0.03705892982325252, 0.07620033982326219, 0.1132592696465147, 2, 3, 1], + [4, 6, 0.01210885428759886, 0.04049276326654051, 0.05260161755413936, 2, 6, 1], + [4, 7, 0.03773982374178716, 0.04469577929352821, 0.08243560303531537, 2, 4, 1], + [4, 8, 0.02406357502679824, 0.04542327412998536, 0.06948684915678359, 2, 5, 1], + [4, 9, 0.04518375503528457, 0.08175199548949739, 0.126935750524782, 2, 3, 1], + [4, 10, 0.05271458150974553, 0.07030981080391227, 0.1230243923136578, 2, 3, 1], + [5, 6, 0.1359282078272841, 0.1540926795656895, 0.2900208873929736, 3, 6, 3], + [5, 7, 0.09099743539437326, 0.04199316180345154, 0.1329905971978248, 3, 4, 2], + [5, 8, 0.1895195673806065, 0.2930011407919719, 0.4825207081725784, 3, 5, 3], + [5, 9, 0.1148199627842869, 0.1105571269028783, 0.2253770896871652, 3, 3, 2], + [5, 10, 0.1270434887308012, 0.1100230063742557, 0.2370664951050569, 3, 3, 2], + [6, 7, 0.09069770755435493, 0.0484084497358865, 0.1391061572902414, 6, 4, 3], + [6, 8, 0.1325890592140632, 0.1385237411340729, 0.2711128003481361, 6, 5, 4], + [6, 9, 0.1237432424538594, 0.1610336810828299, 0.2847769235366894, 6, 3, 3], + [6, 10, 0.2074649804257667, 0.132053108013182, 0.3395180884389487, 6, 3, 3], + [7, 8, 0.0894441901425615, 0.1431622704391284, 0.2326064605816899, 4, 5, 3], + [7, 9, 0.06037024754303832, 0.114173814968622, 0.1745440625116604, 4, 3, 2], + [7, 10, 0.02455907863678367, 0.02700169365828593, 0.0515607722950696, 4, 3, 1], + [8, 9, 0.2356164682007381, 0.275411073609017, 0.5110275418097552, 5, 3, 3], + [8, 10, 0.05927356969559661, 0.02598780235339034, 0.08526137204898694, 5, 3, 2], + [9, 10, 0.1776480482199785, 0.09671451255218226, 0.2743625607721607, 3, 3, 2] + ], + "headers": [ +["Site 1", "Index of site 1"], + ["Site 2", "Index of site 2"], + ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"], + ["P [Site 2 –> Site 1]", "Probability that site 1 is conditionally dependent on site 2"], + ["P [Site 1 <–> Site 2]", "Probability that sites 1 and 2 are not conditionally independent"], + ["Site 1 subs", "Substitution counts inferred for Site 1"], + ["Site 2 subs", "Substitution counts inferred for Site 2"], + ["Shared subs", "Substitutions shared by both sites"] + ] + }, + "analysis":{ + "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond", + "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950", + "contact":"apoon42@uwo.ca", + "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data. Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"1.1" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Cat":{ + "models.codon.MG_REV.ModelDescription":0.8288168941011919 + }, + "Chimp":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Cow":{ + "models.codon.MG_REV.ModelDescription":0.8164924147537205 + }, + "Horse":{ + "models.codon.MG_REV.ModelDescription":0.2841592907567805 + }, + "Human":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Mouse":{ + "models.codon.MG_REV.ModelDescription":0.1035113121392619 + }, + "Node1":{ + "models.codon.MG_REV.ModelDescription":0.5236339695213962 + }, + "Node12":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node2":{ + "models.codon.MG_REV.ModelDescription":0.08766202644314423 + }, + "Node3":{ + "models.codon.MG_REV.ModelDescription":0.2629569437833751 + }, + "Node8":{ + "models.codon.MG_REV.ModelDescription":0.07018254851044582 + }, + "Node9":{ + "models.codon.MG_REV.ModelDescription":0.03334231749233734 + }, + "Pig":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Rat":{ + "models.codon.MG_REV.ModelDescription":0.1018034850081214 + }, + "RhMonkey":{ + "models.codon.MG_REV.ModelDescription":0 + } + }, + "attributes":{ + "models.codon.MG_REV.ModelDescription":{ + "attribute type":"branch length", + "display order":0 + } + } + }, + "data partitions":{ + "0":{ + "coverage": [ +[0, 1, 2, 3, 4, 5, 6, 7, 8, 9] + ], + "name":"bgm.filter.default" + } + }, + "fits":{ + "models.codon.MG_REV.ModelDescription":{ + "AIC-c":508.3788244913426, + "Log Likelihood":-208.6011769515537, + "Rate Distributions":null, + "display order":0, + "estimated parameters":31 + } + }, + "input":{ + "datatype":"codon", + "file name":"/tmp/tmp_Fhyr9/job_working_directory/000/3/working/./bgm_input.fa", + "number of sequences":10, + "number of sites":10, + "trees":{ + "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,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)" + } + }, + "settings":{ + "burn-in":10000, + "data-type":"codon", + "max-parents":1, + "min-subs":1, + "samples":100, + "steps":100000, + "threshold":0.5 + }, + "tested":0, + "timers":{ + "Baseline fit":{ + "order":1, + "timer":3 + }, + "Network inference":{ + "order":2, + "timer":0 + }, + "Overall":{ + "order":0, + "timer":3 + } + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/busted-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,394 @@\n+{\n+ "Evidence Ratios":{\n+ "constrained": [\n+[1.766356514902524, 0.9484374805763239, 0.9571091930814299, 1.845676838710576, 1.513819401189324, 2.11256226458989, 7.366103227625151, 3.937756516229049, 2.586067836907899, 0.722379841928909, 0.3151239046214458, 1.502917468627881, 0.6499879033472316, 1.047489715978757, 1.060206108705189, 0.5038296392390414, 0.8532658611088545, 1.114374823999701, 0.5611409841208096, 0.6702870396165613, 0.4604115167079821, 0.3988433224622866, 2.47019807349414, 0.9858342091732886, 1.106653406611749, 1.067348070135177, 1.77412165088655, 1.321424873505688, 1.90457149631063, 0.7888758683589224, 0.7229203540914775, 0.8813401886687667, 0.6954297746421804, 4.613654710605887, 0.4975309466317643, 1.84565076502724, 0.6214894235132998, 0.9480915704528677, 0.9669462933548731, 1.488081789562878, 1.368539685217942, 1.726522735566884, 1.222915324989829, 0.7085094082639855, 0.3168181005885327, 2.290014391709923, 0.6343005734674315, 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0.9211859677702382, 2.195241379859611, 1.767535349740496, 1.225677095999665, 1.347676192394215, 1.671173168407676, 1.179430472478473, 1.873629958128968, 1.972321068578892, 1.863249013159319, 1.501711930393218, 2.85458165498371, 0.5332817404709185, 0.7514817421990073, 0.2887801591578705, 1.93925520496415, 0.2163710715496819, 2.457406602553581, 0.4895227461773333, 2.731573653164397, 0.8923840424261161, 0.6288736610053396, 3.562511382204229, 0.8043427141817341, 2.97831687935463, 3.021636055180988, 1.919432168129229, 1.231674183402057, 3.382911261347008, 1.455440822286478, 1.714894279904311, 0.4763853457361669, 0.907985271671091, 0.9191891327337078, 0.8704988461364657, 0.4660185191281315, 0.6176233729242167, 0.9987767701341157] \n+ ],\n+ "optimized null": [\n+[1.118923161648219, 0.9980202548897937, 0.9997654691276022, 1.028326548692021, 0.7919741374095479, 0.6742163346738066, 0.9701775068012184, 1.781350909123149, 2.014615609490285, 0.9375026657270238, 0.6503469909372603, 1.467509823797021, 1.009616470968526, 1.168421464905222, 0.59'..b'371867],\n+ [0.01052856463184265],\n+ [0.01292858539344675],\n+ [0.0105618754683007],\n+ [0.0131180965046964],\n+ [0.01101098350431497],\n+ [0.0193250328267319],\n+ [0.01578738770911659],\n+ [0.0196083049972345],\n+ [0.01645869298147252],\n+ [0.01962343746171723],\n+ [0.02045785777700414],\n+ [0.008926115885166477],\n+ [0.007292098982657142],\n+ [0.009056957588961733],\n+ [0.007602170831388156],\n+ [0.007626222986467745],\n+ [0.009471947420992787],\n+ [0.007950502328516303],\n+ [0.01395367801862353],\n+ [0.01139931439306339],\n+ [0.01415821524731906],\n+ [0.01188403168729233] \n+ ],\n+ "Log Likelihood":-3467.004808147542,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.9950576192409499, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":31\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":7112.85745601076,\n+ "Equilibrium frequencies": [\n+[0.3592490842490842],\n+ [0.181959706959707],\n+ [0.240018315018315],\n+ [0.2187728937728937] \n+ ],\n+ "Log Likelihood":-3532.321297387654,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.264666902964203,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098,\n+ "Substitution rate from nucleotide C to nucleotide T":1.027924764411573,\n+ "Substitution rate from nucleotide G to nucleotide T":0.304615404570875\n+ },\n+ "display order":0,\n+ "estimated parameters":24\n+ },\n+ "Unconstrained model":{\n+ "AIC-c":6910.766610587704,\n+ "Log Likelihood":-3414.486640449675,\n+ "Rate Distributions":{\n+ "Synonymous site-to-site rates":{\n+ "0":{\n+ "proportion":0.2645541257391169,\n+ "rate":0.2747941124675511\n+ },\n+ "1":{\n+ "proportion":0.6325830460054784,\n+ "rate":0.9734675888351726\n+ },\n+ "2":{\n+ "proportion":0.1028628282554047,\n+ "rate":3.028333913894314\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.04809457608200497\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.3410012743721951\n+ },\n+ "2":{\n+ "omega":1.89363684081788,\n+ "proportion":0.6109041495458\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":40\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_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)Node3:0.08509899999999999,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+ "test results":{\n+ "LRT":10.17362366082671,\n+ "p-value":0.003088842014430382\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node12":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node8":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Constrained BUSTED model fitting":{\n+ "order":3,\n+ "timer":62\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":228\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "Unconstrained BUSTED model fitting":{\n+ "order":2,\n+ "timer":161\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/cfel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cfel-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,457 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0.06119510183854701, 89.89195279268617, 0.0004623763636215286, 1, 0, 0.02604337408104318, 0.811685158859179, -1, 63.5934805540066],\n+ [0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 30.68649872459121, 0, 4, 0.09420783493835005, 0.60747810805074, -1, 17.97424403638481],\n+ [4.002735462744614, 1.681163962819147, 1.228805177498639, 2, 1, 0.8623362362181146, 1, -1, 3.706931649150397],\n+ [3.050065014123722, 3.059937797506153, 2.418613924712312, 4, 3, 0.8197206876541498, 1, -1, 4.950806946880908],\n+ [0, 24.69410076903886, 2.602816011187676, 6, 0, 0.2048204536099466, 0.7226683929256608, -1, 18.98662250194162],\n+ [0.7973929595981712, 0.56976393636776, 6.448137478127731, 2, 3, 0.06745323839043926, 0.5733525263187338, -1, 4.538073888148586],\n+ [0, 1.220294976236213, 1.931034796125328, 2, 1, 0.6817876981968, 1, -1, 1.993993062285827],\n+ [0, 0.7273121045548806, 0, 1, 0, 0.261419115100697, 0.7638339769348492, -1, 0.5143075999810249],\n+ [1.621724997367116, 0, 0, 1, 1, 0.9121485865111767, 1, -1, 0.7286149415473206],\n+ [0.5060806624687831, 1.999902075014571, 0, 3, 1, 0.0321757051476228, 0.752107107825683, -1, 1.641573976803133],\n+ [0.9420105153372681, 0.7146285434777966, 0, 2, 1, 0.2644815118797826, 0.7381797421122291, -1, 0.9285687782746239],\n+ [0, 1.987391099359683, 0, 3, 0, 0.3529798862703204, 0.7253542717862628, -1, 1.405353135379039],\n+ [8.244286695269041, 1.185994719868233, 0.6569566762624601, 3, 1, 0.6286360235526834, 1, -1, 4.927487703059774],\n+ [0.9500757632276707, 0, 0.5124208919340753, 1, 1, 0.2013061949629433, 0.7239280472705847, -1, 0.726998065759856],\n+ [0, 0.5627658928917045, 0, 1, 0, 0.268228707078901, 0.7376289444669777, -1, 0.3979512700416927],\n+ [0, 0.4711115774899237, 0.6829037036151366, 1, 1, 0.7990116922248531, 1, -1, 0.7331418792667797],\n+ [0.4167417817571659, 0, 0, 0, 1, 0.9206940254260957, 1, -1, 0.1872353755712544],\n+ [0, 0, 0.5212303676872864, 0, 1, 0.1996277088955986, 0.731968265950528, -1, 0.3053043591603385],\n+ [0.8675634762363731, 0, 0, 0, 1, 0.9661066726954236, 1, -1, 0.3897823074521307],\n+ [0.7210654427571777, 0, 0, 1, 0, 0.9836163243596738, 1, -1, 0.3239630987246734],\n+ [1.427522329748797, 1.811321397351979, 2.047657099183609, 3, 2, 0.9153591138659802, 1, -1, 3.121601237885459],\n+ [0, 1.169550303774839, 0, 2, 0, 0.1240860099621399, 0.6106337858663201, -1, 0.8270295599708779],\n+ [0, 0.5199246087354797, 0.6609898247714937, 1, 1, 0.8711034612935368, 1, -1, 0.7548234772115322],\n+ [15.62849382074995, 0.8354792436567606, 0.3568193143210429, 2, 1, 0.692201812400887, 1, -1, 7.821429665659478],\n+ [0, 2.048844622077364, 0.7034505168953565, 2, 1, 0.3378069542919415, 0.7097741623886861, -1, 1.86084665052398],\n+ [0, 1.700054129075257, 0, 2, 0, 0.04433653641539281, 0.5922094506913184, -1, 1.202167203717357],\n+ [1.996997597242381, 4.191343395708055, 0, 4, 1, 0.1469200405479562, 0.6541439900587571, -1, 3.861063080915803],\n+ [2.905972734304771, 0.5690151548622607, 0.8753525229497926, 2, 2, 0.7870098322033844, 1, -1, 2.22070423298495],\n+ [59.02352946734126, 0.9878963984643503, 0, 2, 2, 0.106227812438751, 0.6207687789389512, -1, 27.21689766175553],\n+ [0, 0.493823010263051, 0.5992185198004483, 1, 1, 0.8822938448128469, 1, -1, 0.700184340303363],\n+ [0.151693667651528, 0, 1.145340845562134, 0, 1, 0.1082039933982597, 0.6131559625901383, -1, 0.7390230172493181],\n+ [0, 2.787986645749746, 1.784950467476681, 4, 2, 0.6411055012556299, 1, -1, 3.01699506099285],\n+ [0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [385.3762662337238, 5.564044480778701, 0, 6, 1, 0.02371410328251622, 0.8869074627661065, -1, 177.0778829569787],\n+ [2.573452429663424, 0.5220696742903632, 0.713573878301312, 2, 1, 0.8351273640659775, 1, -1, 1.943351558242732],\n+ [0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 1, 1, '..b'5003],\n+ [0.01837636270304883],\n+ [0.01541821854326533],\n+ [0.01892910005547028],\n+ [0.01545910240515689],\n+ [0.01921445878706794],\n+ [0.01612140169177368],\n+ [0.02829747763884322],\n+ [0.02311011106415996],\n+ [0.02872406592369408],\n+ [0.02410019507229243],\n+ [0.01663805943190806],\n+ [0.01358804506433061],\n+ [0.01688888041768248],\n+ [0.01417018446135155],\n+ [0.006177213955434187],\n+ [0.005044834822351987],\n+ [0.006270336287397383],\n+ [0.00526096577332031],\n+ [0.006458939937330408],\n+ [0.005274916061901906],\n+ [0.006556309326397028],\n+ [0.005500904159606446],\n+ [0.009655594186286731],\n+ [0.007885574003572761],\n+ [0.009801153568494354],\n+ [0.008223407979974132],\n+ [0.03327785448210915],\n+ [0.02717750758119989],\n+ [0.03377952261833742],\n+ [0.02834184710178207],\n+ [0.01235507229404208],\n+ [0.01009019590244688],\n+ [0.01254132667213156],\n+ [0.01052248035033209],\n+ [0.01291855364640413],\n+ [0.01055038238273567],\n+ [0.01311330258173711],\n+ [0.01100238215235291],\n+ [0.01931219560697892],\n+ [0.0157719705998612],\n+ [0.01960332955558842],\n+ [0.01644767379420349],\n+ [0.01965132601881859],\n+ [0.02049322866376102],\n+ [0.008933621043463411],\n+ [0.007295949736387736],\n+ [0.009068296583349953],\n+ [0.007608523013862737],\n+ [0.007628698224327205],\n+ [0.009481877006094248],\n+ [0.00795552712159237],\n+ [0.01396413011303752],\n+ [0.01140428846505027],\n+ [0.01417464125436193],\n+ [0.01189287130232129] \n+ ],\n+ "Log Likelihood":-3463.018342931476,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *internal*": [\n+[0.6757243377045866, 1] \n+ ],\n+ "non-synonymous/synonymous rate ratio for *leaf*": [\n+[1.251739840537981, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":32\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":7112.857310169033,\n+ "Equilibrium frequencies": [\n+[0.3592490842490842],\n+ [0.181959706959707],\n+ [0.240018315018315],\n+ [0.2187728937728937] \n+ ],\n+ "Log Likelihood":-3532.32122446679,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,\n+ "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,\n+ "Substitution rate from nucleotide G to nucleotide T":0.304509117524575\n+ },\n+ "display order":0,\n+ "estimated parameters":24\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmp29yw9zzo/job_working_directory/000/3/working/cfel_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)Node3:0.08509899999999999,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+ "tested":{\n+ "0":{\n+ "Baboon":"leaf",\n+ "Cat":"leaf",\n+ "Chimp":"leaf",\n+ "Cow":"leaf",\n+ "Horse":"leaf",\n+ "Human":"leaf",\n+ "Mouse":"leaf",\n+ "Node1":"internal",\n+ "Node12":"internal",\n+ "Node2":"internal",\n+ "Node3":"internal",\n+ "Node8":"internal",\n+ "Node9":"internal",\n+ "Pig":"leaf",\n+ "Rat":"leaf",\n+ "RhMonkey":"leaf"\n+ }\n+ },\n+ "timers":{\n+ "FEL analysis":{\n+ "order":2,\n+ "timer":180\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":13\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":193\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/conv-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conv-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| b'@@ -0,0 +1,22 @@\n+>epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGACG\n+>epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021\n+------------------------------------------'..b'ATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+\n+>REFERENCE\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/conv-out1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conv-out1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| b"@@ -0,0 +1,27 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 8;\n+\tTAXLABELS\n+\t\t'epi_isl_1041406_hCoV_19_USA_NY_PRL_2021_02_08_05H12_2021' 'epi_isl_1041403_hCoV_19_USA_NY_PRL_2021_02_08_05H08_2021' 'gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4' 'gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1' 'gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3' 'gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1' 'gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1' 'REFERENCE' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 1273;\n+\tFORMAT\n+\t\tDATATYPE = PROTEIN\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t\tNOLABELS\n+\t;\n+\n+MATRIX\n+ ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ET\n+ ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????\n+ LVFFFVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGLSPTKLNDLCFTNVYADSFVI"..b'DPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n+ MLVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFYNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n+ MLVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTLFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNHPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n+ MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT;\n+END;\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/fade-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,50 @@ +>Human +KEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTY +KLFKNGTLKIKH-LKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVS +CPEKGLD +>Chimp +EEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTY +KLFKNGTLKIKH-LKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVS +CPEKGLD +>Baboon +KEIRNALETWGALGQDIDLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFEEKDAY +KLFKNGTLKIKH-LKIHDQDSYKVSIYDTKGKNVLEKTFDLKIQERVSEPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESRMETVS +CPEKGLD +>RhMonkey +KEIRNALETWGALGQDIDLDIPSFQMSDDIDDIRWEKTSDKKKIAQFRKEKETFEEKDAY +KLFKNGTLKXKH-LKIHDQDSYKVSIYDTKGKNVLEKTFDLKIQERVSEPKISWTCINTT +LTCEVMNGTXPELNLYQDGKHVK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESRMETVS +CPEKGLD +>Cow +----ESIVVWGALDHDLNLDIPGFPRSDIVADIKWNR--NKNKIARIKKDMPLHNEMDKY +DMFTNGTLKIKT-LMRNDSGLYEVEVYDSNGVNLLSKKFDLKIQEMLSGPEINWICTNRT +VSCKVENGSNPKLQLFLNTTRVKQDHGKLITYTWNTRWNKTFKCVASNHVDSKVSIEIAV +CPDEGLD +>Pig +-----TEVVWGIVDQDINLDIPELSKHDNVDHIRWQK--NENKIAEFKKNKETHPVKDTY +MMLPNGTLRIKD-LKRDDEGIYKVTVYATDGKHMLERKFDLPILDGVSKPVISWSCADKT +VTCEVAEGSDPKLKLYVNKSTAREGRQKVILWKWNTKWSTLFKCVASNNASEQISMVTIS +CTGQGLD +>Horse +----KNITILGALERDINLDIPAFQMSEHVEDIQWSK--GKTKIAKFKNGSMTFQKDKTY +EVLKNGTLKIKH-LERIHEGTYKVDAYDSDGKNVLEETFHLSLLEMVSKPNISWSCTNTT +LTCEVTKGTDFELKLYLNGRMIQKSPRKVIVYKRASNQIASFKCTANNTVSEESSSVVIR +CTEKGLD +>Cat +---ANDDIVWGTLGQDINLDIPDSQ-GINIDDIHWEK--GKKKVARFQISNKPKNPDEKY +NVSMNGTLKIKH-LMLEDCDTYKVVIYDKDGKNVLDKTFQLKIQEKVSTPNIDWNCINKT +LVCKVSNGTDPELKLYVNGTSIKPVSSKFSTYRFINKQKILVNCTAENKVSKESDVKMIT +CSEKGLD +>Mouse +---RDNETIWGVLGHGITLNIPNFQMTDDIDEVRWVR--RGTLVAEFKRKKPPFLISETY +EVLANGSLKIKKPMMRNDSGTYNVMVYGTNGMTRLEKDLDVRILERVSKPMIHWECPNTT +LTCAVLQGTDFELKLYQGETLLNSLPQKNMSYQW-TNLNAPFKCEAINPVSKESKMEVVN +CPEKGLS +>Rat +---RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWER--GSTLVAEFKRKMKPFLKSGAF +EILANGDLKIKN-LTRDDSGTYNVTVYSTNGTRILDKALDLRILEMVSKPMIYWECSNAT +LTCEVLEGTDVELKLYQGKEHLRSLRQKTMSYQW-TNLRAPFKCKAVNRVSQESEMEVVN +CPEKGLP |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/fade-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -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):0.1,Mouse:0.097950); |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/fade-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,4281 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "A":{\n+ "0": [\n+[11.51603702583788, 5.631258087856319, 0.9499945736517019, 1.039547845181838],\n+ [1.097681549705998, 5.630570600846716, 0.947706309872091, 0.9916649771782264],\n+ [1.539775545261955, 5.630630056322405, 0.9478739114757647, 0.9950294283968122],\n+ [1.667724788704626, 5.630719725601435, 0.9499994157127767, 1.039653814109997],\n+ [1.25847739711632, 5.630686152901463, 0.949999717667571, 1.039660423096818],\n+ [4.185910849001634, 5.630654866793391, 0.9499999990566257, 1.039666582026189],\n+ [17.36207569658563, 5.630654762177219, 0.9499999999975496, 1.039666602620866],\n+ [1.24218514731028, 5.630683377853925, 0.9499997426265079, 1.039660969385093],\n+ [1.024191826188649, 5.630715314989586, 0.9499994553820734, 1.039654682360772],\n+ [1.014004796667106, 5.632607163746273, 0.9499824399855789, 1.039282388967598],\n+ [0.4740621651395832, 5.627503581943447, 0.9444437370511891, 0.9302154716674949],\n+ [0.9140592541745473, 5.630730160151203, 0.9499993218638363, 1.039651760022723],\n+ [0.7567550781917379, 5.633990183409649, 0.949970001027206, 1.039010387334885],\n+ [0.9228460004688066, 5.631089594644688, 0.9499960890893352, 1.039581008459963],\n+ [0.7121146981259312, 5.630928767310179, 0.9499975355796291, 1.03961266479502],\n+ [0.6095796503565455, 5.637045393913153, 0.9499425222882696, 1.038409991274629],\n+ [0.6605558065143393, 5.63554887505476, 0.9499559820649285, 1.0387039979643],\n+ [0.7334618546894945, 5.631584447719907, 0.9499916383523238, 1.039483615889978],\n+ [0.504224974984698, 5.628287880610704, 0.945085891537364, 0.9417330997713343],\n+ [0.5854212568599715, 5.637914315759457, 0.949934707155223, 1.038239355084906],\n+ [0.4134221795168672, 5.624771969338814, 0.9425950877828698, 0.8984969502868022],\n+ [0.3904522005816345, 5.623504918093849, 0.9417960395092443, 0.8854107996422699],\n+ [2.212335991763995, 5.630654963724663, 0.9499999981848204, 1.039666562944362],\n+ [0.9394451709609548, 5.631043490270708, 0.9499965037547257, 1.039590083194665],\n+ [0.662131332286878, 5.63206552947176, 0.9499873114753865, 1.039388950286528],\n+ [0.6265288978761459, 5.632604714967718, 0.9499824620100337, 1.039282870694441],\n+ [0.8073383340999795, 5.630800914362855, 0.9499986854963882, 1.039637831946584],\n+ [0.7792544736123335, 5.63140929379169, 0.9499932136968249, 1.039518086142237],\n+ [1.454921870901184, 5.630658037203366, 0.9499999705417759, 1.039665957901579],\n+ [0.8187160463016893, 5.631238578773209, 0.949994749117517, 1.039551684908112],\n+ [0.7579513217946872, 5.631482189124849, 0.9499925580720074, 1.039503740093819],\n+ [0.7197156570640451, 5.631648897767064, 0.9499910586848941, 1.039470932682291],\n+ [0.6214790654256428, 5.636571110701319, 0.9499467880187472, 1.038503152027503],\n+ [1.057135219780293, 5.630660196325318, 0.9499999511225089, 1.039665532858806],\n+ [0.6108370616594117, 5.629852062445075, 0.9466008848231501, 0.9700035810798537],\n+ [1.302972523179607, 5.630665076132612, 0.9499999072332416, 1.039664572225623],\n+ [0.6199990540154902, 5.632759480958808, 0.9499810700358113, 1.039252425764596],\n+ [1.201664187292616, 5.630591693857761, 0.9477598036683865, 0.992736471372866],\n+ [1.125320876061587, 5.630581829699935, 0.947731859108226, 0.9921764611988656],\n+ [1.663131794636887, 5.630679928739902, 0.9499997736480377, 1.039661648369019],\n+ [1.373376890533494, 5.630675820666751, 0.949999810596284, 1.039662457075089],\n+ [1.009621807867757, 5.630729047751628, 0.9499993318688219, 1.03965197900313],\n+ [0.7922677004712597, 5.631579600918412, 0.9499916819447352, 1.039484569710167],\n+ [0.8020493394401262, 5.631282254381984, 0.9499943562965806, 1.039543088827367],\n+ [0.3617783815235022, 5.6211737'..b'T7", "T->E(1)K(1)R(1)S(1)"],\n+ ["H11,L1,M1,R2,S1,T1", "H->L(1)M(1)R(1)S(1), R->T(1)"],\n+ ["A1,I4,L10,V2", "I->A(1)V(1), L->I(1)V(1)"],\n+ ["K12,N1,Q1,R3", "K->Q(1)R(1), R->K(1)N(1)"],\n+ ["E4,K1,P1,Q1,S3", "E->K(1)P(1)Q(1), S->E(1)"],\n+ ["D1,G2,L12,S1,V1", "G->D(1), L->G(1)S(1)V(1)"],\n+ ["H1,P3,R2,S11", "P->R(1)S(1), S->H(1)P(1)R(1)"],\n+ ["G1,Q14,R1,S1", "Q->G(1)R(1)S(1)"],\n+ ["K10,R7", "K->R(1)"],\n+ ["F1,L1,N1,T2,V12", "T->N(1)V(1), V->F(1)L(1)"],\n+ ["I13,M3,S1", "I->S(1), M->I(1)"],\n+ ["L1,S3,T12,V1", "S->T(1), T->L(1)V(1)"],\n+ ["H7,W1,Y9", "Y->H(1)W(1)"],\n+ ["K12,Q3,R1,T1", "K->R(1)T(1), Q->K(1)"],\n+ ["F1,R1,W15", "W->F(1)R(1)"],\n+ ["A4,I1,N3,T7", "A->I(1)N(1)T(1)"],\n+ ["N1,S1,T15", "T->N(1)S(1)"],\n+ ["K3,N6,R1,S7", "K->R(1), N->K(2)S(1)"],\n+ ["L11,Q3,W3", "L->Q(1), Q->W(1)"],\n+ ["I1,K1,N2,R2,S11", "R->N(1)S(1), S->I(1)K(1)N(1)"],\n+ ["A13,I1,K1,T2", "A->I(1)T(1), T->K(1)"],\n+ ["K7,L2,P3,S1,T4", "P->T(1), T->K(1)L(2)S(1)"],\n+ ["F16,V1", "F->V(1)"],\n+ ["K16,N1", "K->N(1)"],\n+ ["C17", ""],\n+ ["E1,K2,T11,V3", "K->E(1)T(1), T->V(1)"],\n+ ["A17", ""],\n+ ["E1,G7,I2,N1,S5,V1", "I->S(1)V(1), S->E(1)G(1)N(1)"],\n+ ["N17", ""],\n+ ["H1,K10,N2,P1,R2,T1", "K->N(1)T(1), N->H(1), R->K(1)P(1)"],\n+ ["A1,V16", "V->A(1)"],\n+ ["D1,S16", "S->D(1)"],\n+ ["E3,K12,Q1,S1", "E->S(1), K->E(2)Q(1)"],\n+ ["E15,K1,Q1", "E->K(1)Q(1)"],\n+ ["I2,S14,V1", "I->V(1), S->I(1)"],\n+ ["D1,E2,K1,R3,S10", "E->K(1)S(1), S->D(1)R(1)"],\n+ ["I1,M11,S1,V4", "M->I(1)S(1)V(2)"],\n+ ["E14,K1,V2", "E->K(1)V(2)"],\n+ ["I1,M1,P3,T5,V7", "T->P(1), V->I(1)M(1)T(2)"],\n+ ["A1,I5,V11", "I->A(1), V->I(1)"],\n+ ["N3,R1,S11,T1,V1", "N->S(1), S->R(1)T(1)V(1)"],\n+ ["C17", ""],\n+ ["P14,S1,T2", "P->S(1)T(2)"],\n+ ["D1,E15,G1", "E->D(1)G(1)"],\n+ ["E1,K15,Q1", "K->E(1)Q(1)"],\n+ ["G17", ""],\n+ ["L17", ""],\n+ ["D14,P1,S2", "S->D(1)P(1)"] \n+ ]\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node10":"test",\n+ "Node13":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node4":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Baseline Fit":{\n+ "order":1,\n+ "timer":88\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":121\n+ },\n+ "Residue A analysis":{\n+ "order":2,\n+ "timer":2\n+ },\n+ "Residue C analysis":{\n+ "order":3,\n+ "timer":1\n+ },\n+ "Residue D analysis":{\n+ "order":4,\n+ "timer":1\n+ },\n+ "Residue E analysis":{\n+ "order":5,\n+ "timer":1\n+ },\n+ "Residue F analysis":{\n+ "order":6,\n+ "timer":2\n+ },\n+ "Residue G analysis":{\n+ "order":7,\n+ "timer":1\n+ },\n+ "Residue H analysis":{\n+ "order":8,\n+ "timer":2\n+ },\n+ "Residue I analysis":{\n+ "order":9,\n+ "timer":1\n+ },\n+ "Residue K analysis":{\n+ "order":10,\n+ "timer":2\n+ },\n+ "Residue L analysis":{\n+ "order":11,\n+ "timer":1\n+ },\n+ "Residue M analysis":{\n+ "order":12,\n+ "timer":2\n+ },\n+ "Residue N analysis":{\n+ "order":13,\n+ "timer":2\n+ },\n+ "Residue P analysis":{\n+ "order":14,\n+ "timer":1\n+ },\n+ "Residue Q analysis":{\n+ "order":15,\n+ "timer":2\n+ },\n+ "Residue R analysis":{\n+ "order":16,\n+ "timer":2\n+ },\n+ "Residue S analysis":{\n+ "order":17,\n+ "timer":2\n+ },\n+ "Residue T analysis":{\n+ "order":18,\n+ "timer":2\n+ },\n+ "Residue V analysis":{\n+ "order":19,\n+ "timer":2\n+ },\n+ "Residue W analysis":{\n+ "order":20,\n+ "timer":2\n+ },\n+ "Residue Y analysis":{\n+ "order":21,\n+ "timer":2\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/fel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fel-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| 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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0.3554421959431151, 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 7c86ceaf523c test-data/fubar-in1.fa.gz |
| b |
| Binary file test-data/fubar-in1.fa.gz has changed |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/fubar-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
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| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/fubar-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,4234 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[2.358303696561651, 0.2466171873692551, -2.111686509192396, 0.8210197338138971, 0.142087457564682, 0.3966878876600468, 0, 0],\n+ [1.326584461663443, 0.6866899518991865, -0.6398945097642563, 0.6688273802220104, 0.2636275007897265, 0.8574905953981414, 0, 0],\n+ [0.7044422164661149, 0.6750500349130593, -0.02939218155305567, 0.4326692199559115, 0.5033349164743647, 2.427334580981709, 0, 0],\n+ [1.364044071446117, 0.7245533194421999, -0.6394907520039169, 0.659200973014336, 0.2700465050330634, 0.8860935649345238, 0, 0],\n+ [0.8832572277883376, 0.324055205187422, -0.5592020226009156, 0.6938860968986269, 0.2516249096259696, 0.8053237779146634, 0, 0],\n+ [0.8480568188667065, 0.3001964190676413, -0.5478603997990652, 0.7028888613991836, 0.2417160286876891, 0.7635013130968795, 0, 0],\n+ [0.6407145320808335, 0.4049432206602815, -0.235771311420552, 0.5905083476225061, 0.346254278491581, 1.268593561124676, 0, 0],\n+ [0.9072661993050892, 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| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/gard-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
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| @@ -0,0 +1,120 @@ +>BRO1_1 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO2 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACCCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTGCATAAAGCCATTTACCGTACATA +GCACATTATA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO3_1 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG 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| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/gard-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,318 @@\n+{\n+ "analysis":{\n+ "authors":"Sergei L Kosakovsky Pond",\n+ "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891\xe2\x80\x931901",\n+ "contact":"spond@temple.edu",\n+ "info":"GARD : Genetic Algorithms for Recombination Detection. Implements a heuristic\\n approach to screening alignments of sequences for recombination, by using the CHC genetic algorithm to search for phylogenetic\\n incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the\\n placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc\\n tests run to distinguish topological incongruence from rate-variation.",\n+ "requirements":"A sequence alignment.",\n+ "version":"0.1"\n+ },\n+ "baselineScore":8884.998566352424,\n+ "breakpointData":{\n+ "0":{\n+ "bps": [\n+[1, 461] \n+ ],\n+ 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"newickString":"((((((TREESPARROW_HENAN_1_2004:0,TREESPARROW_HENAN_3_2004:0.01064277225673711)Node5:0.00531987705161906,TREESPARROW_HENAN_2_2004:0)Node4:0.005231591103466107,CHICKEN_HEBEI_326_2005:0.05043188754547531)Node3:0.005435427857192481,CK_HK_WF157_2003:0)Node2:0.005367407450692448,((TREESPARROW_HENAN_4_2004:0.005403333058615208,(((CHICKEN_HONGKONG_915_97:0,(GOOSE_HONGKONG_W355_97:0,DUCK_HONGKONG_Y283_97:0)Node18:0.005303893633648769)Node16:0,HONGKONG_97_98:0)Node15:0,HONGKONG_538_97:0)Node14:0.0160450339521957)Node12:0.01065583332597595,((DUCK_GUANGZHOU_20_2005:0.02156617952480121,GOOSE_SHANTOU_2216_2005:0.005315754078746889)Node24:0,PEREGRINEFALCON_HK_D0028_2004:0.005310132566451705)Node23:0)Node11:0.005324661683629481)Node1:0.01075596871747344,(SWINE_ANHUI_2004:0.01612941661930485,DUCK_VIETNAM_272_2005:0.005332918418299072)Node28:0.005343017103483476,((HUMAN_VIETNAM_CL105_2005:0.01615610619083483,DUCK_VIETNAM_376_2005:0.01622595235090508)Node32:0.005403715853761346,(VIETNAM_3062_2004:0,(MALLARD_VIETNAM_16_2003:0.01066500623689393,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0)Node37:0.005316372444723995)Node35:0)Node31:0)"\n+ },\n+ "2":{\n+ "newickString":"(((((((TREESPARROW_HENAN_1_2004:0.001954008187578416,TREESPARROW_HENAN_3_2004:0.003896316686452931)Node6:0.001938506890703636,TREESPARROW_HENAN_4_2004:0)Node5:0.005890390504717593,((CHICKEN_HEBEI_326_2005:0.0118071209154035,(SWINE_ANHUI_2004:0,TREESPARROW_HENAN_2_2004:0.001939618450410721)Node13:0.01383276182388132)Node11:0.009974147725569997,((CHICKEN_HONGKONG_915_97:0,GOOSE_HONGKONG_W355_97:0)Node17:0.001941847153562197,((DUCK_HONGKONG_Y283_97:0,HONGKONG_538_97:0)Node21:0,HONGKONG_97_98:0.005840445012127324)Node20:0.001942715072940801)Node16:0.01987446960589405)Node10:0.005913850464875198)Node4:0.005886750382502456,(((DUCK_GUANGZHOU_20_2005:0.003893604042162395,GOOSE_SHANTOU_2216_2005:0.003905435534305824)Node27:0.001941929040845811,PEREGRINEFALCON_HK_D0028_2004:0.003899037680959845)Node26:0.001951590047476092,CK_HK_WF157_2003:0.005864286435734769)Node25:0.001925781157666145)Node3:0.009803928769016717,DUCK_VIETNAM_272_2005:0.01580156952635168)Node2:0,CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.003890598353658968)Node1:0,((HUMAN_VIETNAM_CL105_2005:0.003905371265795895,DUCK_VIETNAM_376_2005:0.0137665342243657)Node35:0.001932867193851192,MALLARD_VIETNAM_16_2003:0.003887459835724038)Node34:0,VIETNAM_3062_2004:0.00194102772512571)"\n+ },\n+ "3":{\n+ "newickString":"(TREESPARROW_HENAN_1_2004:0,((TREESPARROW_HENAN_3_2004:0.005713571370335148,TREESPARROW_HENAN_4_2004:0)Node3:0.00189607429178233,(CHICKEN_HEBEI_326_2005:0.005712316903324198,(SWINE_ANHUI_2004:0.005701998731046575,(((CHICKEN_HONGKONG_915_97:0,HONGKONG_97_98:0)Node12:0.001895621658683188,(GOOSE_HONGKONG_W355_97:0,HONGKONG_538_97:0)Node15:0)Node11:0.01534803500036186,((DUCK_HONGKONG_Y283_97:0.0001941011375241317,(((HUMAN_VIETNAM_CL105_2005:0.001928158212296621,DUCK_VIETNAM_376_2005:0.003824815472812549)Node23:0.001900556734363341,(VIETNAM_3062_2004:0.001945118440015516,MALLARD_VIETNAM_16_2003:0)Node26:0)Node22:0,(CHICKEN_THAILAND_KANCHANABURI_CK_160_2005:0.00380825293990655,DUCK_VIETNAM_272_2005:0.005749159769097136)Node29:0.001884324589239026)Node21:0.006136201619836659)Node19:0.006956231732180768,(((DUCK_GUANGZHOU_20_2005:0.003782134609270667,GOOSE_SHANTOU_2216_2005:0.005745814969410696)Node34:0.005728903718080784,PEREGRINEFALCON_HK_D0028_2004:0)Node33:0.001883474579815808,CK_HK_WF157_2003:0.005783922057126199)Node32:0.003686703559509533)Node18:0.002359028413665987)Node10:0.003781653021946557)Node8:0.003836413220384994)Node6:0.001894177236914572)Node2:0,TREESPARROW_HENAN_2_2004:0.00767492225272676)"\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/meme-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| b'@@ -0,0 +1,1 @@\n+>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>MALLARD_VIETNAM_16_2003\rATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAAT\rTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG\rACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT\rCCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGAATATGAAGAATT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGCA\rTGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTGT\rCAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA\rACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG\rGCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGG\rGACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCA\rAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAA\rCCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA\rATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG\rAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG\rATAAACTCTAGTATGCCATTCCACAATATACACCCCCTCACCATCGGGGA\rATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCA\rGAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGA\rGCTATAGCAGGTTTTATAGAGGGAGGATGGCAAGGAATGGTAGATGGTTG\rGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACA\rAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG\rATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA\rCAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT\rTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT\rGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA\rGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT\rTCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC\rGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA\rGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT\rCAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT\rGGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGA---\r>CHICKEN_CK_160_2005\rATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA\rTCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACA\rCAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA\rAAGACACACAACGGGAAGCTCTGTGATCTAGATGGAGTGAAGCCTCTAAT\rTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTTGGAAACCCAATGTGTG\rATGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT\rCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATT\rGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC\rCCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGAGT'..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 000000000000 -r 7c86ceaf523c test-data/meme-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((((((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 000000000000 -r 7c86ceaf523c test-data/meme-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,2535 @@\n+{\n+ "MLE":{\n+ "content":{\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, 3.477431520841965, 1, 0, 0.6666666666666666, 0, 0.1244820193331403],\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, 3.741010141509965, 1, 0, 0.6666666666666666, 0, 0.1339173737771157],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 0, 3.515256679835982, 1, 0, 0.6666666666666666, 0, 0.1258360509351867],\n+ [0, 0, 0, 2.551430028273134, 1, 0, 0.6666666666666666, 0, 0.09133383654087057],\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, 0.09433309141367374, 3.23711069521408, 0.9056669085863263, 0.5595133528189606, 0.4135250593893275, 0, 0.1049479822225346],\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, 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[0.01271990463804815],\n+ [0.01352184453103644],\n+ [0.01479548113102975],\n+ [0.008898103672735205],\n+ [0.005323560008197935],\n+ [0.005659189501089015],\n+ [0.006192234446128948],\n+ [0.010061425331433],\n+ [0.006019552422614294],\n+ [0.006399061496227086],\n+ [0.007001795754005012],\n+ [0.01338015932252603],\n+ [0.008005085543223482],\n+ [0.008509774660521757],\n+ [0.009311319186526256],\n+ [0.04013232935583105],\n+ [0.02401038147590574],\n+ [0.02552414146855538],\n+ [0.02792828690027832],\n+ [0.01679626299677307],\n+ [0.01004887302569606],\n+ [0.0106824148947738],\n+ [0.01168860266413242],\n+ [0.01899217543474583],\n+ [0.01136264414662781],\n+ [0.01207901411089265],\n+ [0.0132167490129733],\n+ [0.02525669324448205],\n+ [0.01511058165209229],\n+ [0.0160632443156804],\n+ [0.01757625800461362],\n+ [0.02112670632168297],\n+ [0.02457406668036405],\n+ [0.01477901198657192],\n+ [0.008841991514828857],\n+ [0.009399444257673735],\n+ [0.01028478768834936],\n+ [0.009997977173519282],\n+ [0.01062831025955897],\n+ [0.01162940185705429],\n+ [0.02222333457585675],\n+ [0.01329578296096281],\n+ [0.01413402971424556],\n+ [0.01546532867335853] \n+ ],\n+ "Log Likelihood":-2978.298667783946,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.2932353608697501, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":27\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":6152.529196194525,\n+ "Equilibrium frequencies": [\n+[0.3478363400542389],\n+ [0.184883858035609],\n+ [0.2307510906732697],\n+ [0.2365287112368824] \n+ ],\n+ "Log Likelihood":-3056.215005465311,\n+ "Rate Distributions":{\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":0.08708610799393901,\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":20\n+ }\n+ },\n+ "input":{\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:-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+ "CK_HK_WF157_2003":"test",\n+ "MALLARD_VIETNAM_16_2003":"test",\n+ "Node11":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node4":"test",\n+ "Node5":"test",\n+ "Node7":"test",\n+ "Node9":"test",\n+ "SWINE_ANHUI_1_2004":"test"\n+ }\n+ },\n+ "timers":{\n+ "MEME analysis":{\n+ "order":2,\n+ "timer":437\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":4\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":442\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/params.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/params.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| 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": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):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_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):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)",\n+ "goodtree": 0,\n+ "sequences": 21,\n+ "sites": 566,\n+ "partitions": 1,\n+ "analysis_type": "1",\n+ "gencodeid": 0,\n+ "datatype": 0,\n+ "_id": "5446bc0d355080301f18a8c7",\n+ "created": "2014-10-21T20:03:25.803Z",\n+ "sequence_info": [\n+ {\n+ "seqindex": 0,\n+ "name": "TREESPARROW_HENAN_1_2004",\n+ "_id": "5446bc0d355080301f18a8c8"\n+ },\n+ {\n+ "seqindex": 1,\n+ "name": "HUMAN_VIETNAM_CL105_2005",\n+ "_id": "5446bc0d355080301f18a8c9"\n+ },\n+ {\n+ "seqindex": 2,\n+ "name": "TREESPARROW_HENAN_4_2004",\n+ "_id": "5446bc0d355080301f18a8ca"\n+ },\n+ {\n+ "seqindex": 3,\n+ "name": "CHICKEN_HEBEI_326_2005",\n+ "_id": "5446bc0d355080301f18a8cb"\n+ },\n+ {\n+ "seqindex": 4,\n+ "name": "CHICKEN_HONGKONG_915_97",\n+ "_id": "5446bc0d355080301f18a8cc"\n+ },\n+ {\n+ "seqindex": 5,\n+ "name": "HUMAN_VIETNAM_3062_2004",\n+ "_id": "5446bc0d355080301f18a8cd"\n+ },\n+ {\n+ "seqindex": 6,\n+ "name": "GOOSE_HONGKONG_W355_97",\n+ "_id": "5446bc0d355080301f18a8ce"\n+ },\n+ {\n+ "seqindex": 7,\n+ "name": "DUCK_HONGKONG_Y283_97",\n+ "_id": "5446bc0d355080301f18a8cf"\n+ },\n+ {\n+ "seqindex": 8,\n+ "name": "DUCK_VIETNAM_376_2005",\n+ "_id": "5446bc0d355080301f18a8d0"\n+ },\n+ {\n+ "seqindex": 9,\n+ "name": "MALLARD_VIETNAM_16_2003",\n+ "_id": "5446bc0d355080301f18a8d1"\n+ },\n+ {\n+ "seqindex": 10,\n+ "name": "CHICKEN_CK_160_2005",\n+ "_id": "5446bc0d355080301f18a8d2"\n+ },\n+ {\n+ "seqindex": 11,\n+ '..b'ex": 10\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d3",\n+ "name": "DUCK_GUANGZHOU_20_2005",\n+ "seqindex": 11\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d4",\n+ "name": "CK_HK_WF157_2003",\n+ "seqindex": 12\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d5",\n+ "name": "SWINE_ANHUI_1_2004",\n+ "seqindex": 13\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d6",\n+ "name": "DUCK_VIETNAM_272_2005",\n+ "seqindex": 14\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d7",\n+ "name": "HONGKONG_1_97_98",\n+ "seqindex": 15\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d8",\n+ "name": "GOOSE_SHANTOU_2216_2005",\n+ "seqindex": 16\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8d9",\n+ "name": "TREESPARROW_HENAN_3_2004",\n+ "seqindex": 17\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8da",\n+ "name": "PEREGRINEFALCON_HK_D0028_2004",\n+ "seqindex": 18\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8db",\n+ "name": "TREESPARROW_HENAN_2_2004",\n+ "seqindex": 19\n+ },\n+ {\n+ "_id": "5446bc0d355080301f18a8dc",\n+ "name": "HONGKONG_1_538_97",\n+ "seqindex": 20\n+ }\n+ ],\n+ "created": "2014-10-21T20:03:25.803Z",\n+ "_id": "5446bc0d355080301f18a8c7",\n+ "datatype": 0,\n+ "gencodeid": 0,\n+ "partitions": 1,\n+ "sites": 566,\n+ "sequences": 21,\n+ "goodtree": 0,\n+ "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):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_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):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)",\n+ "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 7c86ceaf523c test-data/prime-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +>HUMAN_VIETNAM_CL105_2005 ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CHICKEN_HEBEI_326_2005 ATGGAGAGAATAGTGCTTCTTCTTGCAATAATCGGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAG >CHICKEN_HONGKONG_915_97 ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >HUMAN_VIETNAM_3062_2004 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >GOOSE_HONGKONG_W355_97 ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >MALLARD_VIETNAM_16_2003 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CHICKEN_CK_160_2005 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CK_HK_WF157_2003 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >SWINE_ANHUI_1_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGA TCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAA >HONGKONG_1_97_98 ------------------------------------------------GA CCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGATA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >GOOSE_SHANTOU_2216_2005 ATGGAGAAAATAGTGCTTCTTCTTGCAATAATCAGCCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >PEREGRINEFALCON_HK_D0028_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >HONGKONG_1_538_97 ------------------------------------------------GA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/prime-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +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) |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/prime-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,391 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 4.123712641737602, 511.6499971244988, -5.608842688620929, -7.031699805798055, 1, 3.180962375542725, 1, -5.599238755695894, 0.7828049218517579, 1, -5.608352884924835, -2.115291881920681, 1, -5.604784076919627, -5.404956845857691, 1, -5.615111503355894, 2.462902938936584, 1, -5.607953657572869],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 4.849174446703908, 0.2440623951294166, -7.530855366772653, -8.547881040478554, 1, 8.833984038052169, 1, -7.53445935473729, 1.725573110573239, 1, -7.53079217870133, -0.2671292981572289, 1, -7.530980113687253, -0.4804669617756561, 1, -7.530833122267245, -0.1532486612226931, 1, -7.530868793694735],\n+ [10.63135649145974, 0, 0.7502380884715356, -7.750335490678291, -7.750335610925491, 1, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839, -0.06122935182163709, 1, -7.750335490675839],\n+ [0, 2.202981274414969, 0.397462976308795, -6.144243972107117, -7.361850215781605, 1, -2.763157788623757, 1, -6.146863972828472, -0.02286865932396898, 1, -6.141696705195292, 2.56489740323532, 1, -6.144140070703968, 3.673465169891661, 1, -6.162164086824393, -0.3782299185469108, 1, -6.140399389962398],\n+ [0, 6.509531966707992, 0.7279903564537584, -7.452295439546786, -8.507460649598423, 1, 6.763405786911178, 1, -7.454926555248795, 0.6678772051425989, 1, -7.451746683657063, -0.5798067642619018, 1, -7.452771449125621, -0.2211171350169704, 1, -7.452165845137638, 0.1663073214171773, 1, 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-0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021, -0.06122935182163709, 1, -5.863592599386021],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 2.699658477079707, 0.4801615193392039, -5.903524182207455, -6.898872136243598, 1, -0.8716130556024849, 1, -5.903538930457988, -0.4627800379305517, 1, -5.903694932983693, 3.044105631862708, 1, -5.908943461477226, -0.07628230444039112, 1, -5.903502621374115, 0.3057953308962, 1, -5.903488680659473],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, '..b' [0.0116874925496928],\n+ [0.01921743321791434],\n+ [0.00769695150511784],\n+ [0.004704463089092132],\n+ [0.005592004637968804],\n+ [0.00919478452948895],\n+ [0.03431876246786721],\n+ [0.02097601254029597],\n+ [0.02493333610872543],\n+ [0.04099722156245031],\n+ [0.006131000492593795],\n+ [0.01198292502502543],\n+ [0.004198752217504174],\n+ [0.002566324448628536],\n+ [0.003050485878513492],\n+ [0.005015832814718212],\n+ [0.001227885122343091],\n+ [0.001459537288103269],\n+ [0.002399878352343215],\n+ [0.008957344771016727],\n+ [0.00547482958980595],\n+ [0.006507708080284218],\n+ [0.01070045135026252] \n+ ],\n+ "Log Likelihood":-277.7176481414617,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.4074296362572946, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":43\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":658.4548031196325,\n+ "Equilibrium frequencies": [\n+[0.3543689320388349],\n+ [0.1790722761596548],\n+ [0.2076591154261057],\n+ [0.2588996763754045] \n+ ],\n+ "Log Likelihood":-292.5311130078037,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0,\n+ "Substitution rate from nucleotide C to nucleotide G":0,\n+ "Substitution rate from nucleotide C to nucleotide T":1.816257034982832,\n+ "Substitution rate from nucleotide G to nucleotide T":0\n+ },\n+ "display order":0,\n+ "estimated parameters":36\n+ }\n+ },\n+ "input":{\n+ "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa",\n+ "number of sequences":13,\n+ "number of sites":50,\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+ }\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+ "Model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "PRIME analysis":{\n+ "order":2,\n+ "timer":86\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":89\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/relax-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/relax-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Horse{TEST}:0.165787,Cat{TEST}: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:0.09795) \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/relax-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nhx Tue Apr 20 10:27:46 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}:0.058611,((RhMonkey{REFERENCE}:0.002015,Baboon{REFERENCE}:0.003108){REFERENCE}:0.022733,(Human{REFERENCE}:0.004349,Chimp{REFERENCE}:0.000799):0.011873){REFERENCE}:0.101856){REFERENCE}:0.340802,Rat{REFERENCE}:0.050958,Mouse{REFERENCE}:0.09795) |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/relax-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,499 @@\n+{\n+ "analysis":{\n+ "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of \'Test\' branches evolves under relaxed selection relative to a set of \'Reference\' branches (R), as measured by the relaxation parameter (K).\\n Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems",\n+ "version":"2.1",\n+ "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832",\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, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"\n+ },\n+ "input":{\n+ "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_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":-3531.964032193222,\n+ "estimated parameters":24,\n+ "AIC-c":7112.142925621896,\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":0.5465757107930838,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.264131123736109,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388,\n+ "Substitution rate from nucleotide C to nucleotide T":1.017887589835735,\n+ "Substitution rate from nucleotide G to nucleotide T":0.3021773696987065\n+ },\n+ "display order":0\n+ },\n+ "MG94xREV with separate rates for branch sets":{\n+ "Log Likelihood":-3460.931903299487,\n+ "estimated parameters":32,\n+ "AIC-c":6987.013507197776,\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+ [0.009982861811889655],\n+ [0.008390428826966174],\n+ [0.03287895020631181],\n+ [0.02687490503171972],\n+ [0.033269810543681],\n+ [0.0279627207822247],\n+ [0.01248470225271473],\n+ [0.01020486315060615],\n+ [0.01263311863778268],\n+ [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+ [0.0091760343267108'..b',\n+ "k (general descriptive)":0.2294495132372282,\n+ "RELAX alternative":0.1341640738853253,\n+ "RELAX null":0.1483938193994467,\n+ "RELAX partitioned descriptive":0.1476318125310598\n+ },\n+ "Rat":{\n+ "original name":"Rat",\n+ "Nucleotide GTR":0.06669544716210057,\n+ "MG94xREV with separate rates for branch sets":0.06725647453745125,\n+ "General descriptive":0.07175915155128718,\n+ "k (general descriptive)":0.5208088414555363,\n+ "RELAX alternative":0.0724007498013708,\n+ "RELAX null":0.07365614414375878,\n+ "RELAX partitioned descriptive":0.07568744563050285\n+ },\n+ "Node1":{\n+ "Nucleotide GTR":0.2771601504028877,\n+ "MG94xREV with separate rates for branch sets":0.286127507474972,\n+ "General descriptive":0.3532216661512288,\n+ "k (general descriptive)":0.2199586786715634,\n+ "RELAX alternative":0.3833004811985787,\n+ "RELAX null":0.4576044234710181,\n+ "RELAX partitioned descriptive":0.4360897576025625\n+ },\n+ "Node12":{\n+ "Nucleotide GTR":0.01783222754921504,\n+ "MG94xREV with separate rates for branch sets":0.01799298835381691,\n+ "General descriptive":0.01771170858901891,\n+ "k (general descriptive)":0.1560499010177516,\n+ "RELAX alternative":0.01833338832069913,\n+ "RELAX null":0.01828012634520382,\n+ "RELAX partitioned descriptive":0.01877701767421286\n+ },\n+ "Node2":{\n+ "Nucleotide GTR":0.06619118337434968,\n+ "MG94xREV with separate rates for branch sets":0.06192085035608558,\n+ "General descriptive":0.05843310574046084,\n+ "k (general descriptive)":0.2816499194095207,\n+ "RELAX alternative":0.05469841675490748,\n+ "RELAX null":0.06219694236954142,\n+ "RELAX partitioned descriptive":0.06011281230238084\n+ },\n+ "Node3":{\n+ "Nucleotide GTR":0.09883746945145887,\n+ "MG94xREV with separate rates for branch sets":0.09744342239018626,\n+ "General descriptive":0.1340338084149808,\n+ "k (general descriptive)":0.8358980179450297,\n+ "RELAX alternative":0.1164056814082033,\n+ "RELAX null":0.1282588343299434,\n+ "RELAX partitioned descriptive":0.1194563668460339\n+ },\n+ "Node8":{\n+ "Nucleotide GTR":0.106110061225871,\n+ "MG94xREV with separate rates for branch sets":0.1090208137603471,\n+ "General descriptive":0.1401594332730181,\n+ "k (general descriptive)":0.9135621448569878,\n+ "RELAX alternative":0.1275155316795084,\n+ "RELAX null":0.1346842719904758,\n+ "RELAX partitioned descriptive":0.1358683972849559\n+ },\n+ "Node9":{\n+ "Nucleotide GTR":0.02567391471029082,\n+ "MG94xREV with separate rates for branch sets":0.02582385148170195,\n+ "General descriptive":0.02665352479510937,\n+ "k (general descriptive)":0.1089752436854629,\n+ "RELAX alternative":0.02681134359856903,\n+ "RELAX null":0.02759760291393045,\n+ "RELAX partitioned descriptive":0.02746061131173372\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+ "MG94xREV with separate rates for branch sets":{\n+ "attribute type":"branch length",\n+ "display order":1\n+ },\n+ "General descriptive":{\n+ "attribute type":"branch length",\n+ "display order":4\n+ },\n+ "k (general descriptive)":{\n+ "attribute type":"branch label",\n+ "display order":4\n+ },\n+ "RELAX alternative":{\n+ "attribute type":"branch length",\n+ "display order":2\n+ },\n+ "RELAX null":{\n+ "attribute type":"branch length",\n+ "display order":3\n+ },\n+ "RELAX partitioned descriptive":{\n+ "attribute type":"branch length",\n+ "display order":5\n+ }\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/slac-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slac-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| b'@@ -0,0 +1,2076 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0":{\n+ "by-branch":{\n+ "AVERAGED": [\n+[131.3409038539508, 387.3032052553191, 18.83333333333334, 62.16666666666666, 0.2532389774551154, 0.1433927495601502, 0.1605116245440958, 0.009922319377965909, 0.3896479078188506, 0.7050801922163503, 0.190671339253091],\n+ [129.582341679606, 390.2657462377136, 20.16666666666666, 84.83333333333334, 0.2492696322088151, 0.1556282006118473, 0.2173732492568301, 0.03578822166983051, 0.1057124571474986, 0.9315947329811959, 0.2526189686412594],\n+ [133.5634277511288, 389.0892183853288, 9, 31, 0.255549127586847, 0.06738371537431539, 0.07967324339812369, 0.007123167975176309, 0.4078805639677862, 0.7273413969784412, 0.100661445687484],\n+ [136.3001744404261, 388.2752414674823, 20.66666666666666, 73.33333333333334, 0.2598295122247097, 0.1516261204471138, 0.1888694552250377, 0.02158671423873519, 0.2256328450945964, 0.8402434326037131, 0.2128981270938909],\n+ [133.8191805302023, 389.2442828476442, 23, 92, 0.2558373694580443, 0.1718737172718601, 0.2363554303917937, 0.03737442747928117, 0.1006659765808149, 0.9336498751512877, 0.270986057489719],\n+ [140.2315863698817, 396.7622548627548, 7.5, 18.5, 0.2611418895382275, 0.05348295768556476, 0.0466274192498462, -0.003973557954650256, 0.7090493474259939, 0.4503697460596697, 0.0674227399326417],\n+ [134.7817325168444, 392.4918226549124, 0, 3, 0.2556201258243265, 0, 0.007643471345994557, 0.004430253969516925, 0.4124619282373314, 1, 0.003845100000905624],\n+ [136.1184811420076, 397.1417020142569, 1, 0, 0.255257162341183, 0.007346540981137861, 0, -0.004258149323861931, 1, 0.255257162341183, 0.001710698008755675],\n+ [136.5467837843545, 396.817130340981, 6, 8, 0.2560105402111387, 0.04394098369593, 0.02016041997260975, -0.01378351956376455, 0.9568131059753749, 0.1225532921657104, 0.0261290773391622],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [136.6003799486803, 396.6078513587676, 0, 1, 0.2561858049597822, 0, 0.002521382258505542, 0.001461425477216891, 0.7438141950402177, 1, 0.001852173963769908],\n+ [136.9415154360939, 396.3923665097976, 4.5, 4.5, 0.2567650773216525, 0.03286074340326692, 0.01135238813911109, -0.01246651841466516, 0.9670681040365207, 0.116490042971819, 0.01816964082591924],\n+ [138.8593313638795, 397.772580198107, 9, 39, 0.2587608533374368, 0.06481379329427697, 0.09804597385917452, 0.01926179784012569, 0.1682548120106906, 0.905709700565171, 0.1081901197733327],\n+ [143.8068579584112, 396.4414008640307, 42.50000000000001, 70.5, 0.2661866199659049, 0.295535279772895, 0.1778320827399651, -0.06822228177164953, 0.9959804586708396, 0.007098480560500553, 0.28199060274564],\n+ [145.8733144714348, 394.7876057082412, 10, 23, 0.2698055454478885, 0.06855263442963876, 0.05825917447113987, -0.005966221338044341, 0.7401529271181795, 0.3966272436071658, 0.06785010407729926],\n+ [145.261732918168, 395.7720178098857, 21, 35, 0.2684892258989267, 0.1445666355352526, 0.08843475138460322, -0.03253475957690278, 0.9711633315400029, 0.05307382915791914, 0.1202934609265267] \n+ ],\n+ "NAMES": [\n+["Pig"],\n+ ["Cow"],\n+ ["Node3"],\n+ ["Horse"],\n+ ["Cat"],\n+ ["Node2"],\n+ ["RhMonkey"],\n+ ["Baboon"],\n+ ["Node9"],\n+ ["Human"],\n+ ["Chimp"],\n+ ["Node12"],\n+ ["Node8"],\n+ ["Node1"],\n+ ["Rat"],\n+ ["Mouse"] \n+ ],\n+ "RESOLVED": [\n+[131.3409038539508, 387.3032052553191, 18.83333333333334, 62.16666666666666, 0.2532389774551154, 0.1433927495601502, 0.1605116245440958, 0.009922319377965909, 0.3896479078188506, 0.7050801922163503, 0.190671339253091],\n+ [129.582341679606, 390.2657462377136, 20.16666666666666, 84.83333333333334, 0.2492696322088151, 0.1556282006118473, 0.2173732492568301, 0.035788221669'..b'0, 0, 0.1387249812240129, 0, 0, 0, 1, 1, 1.725289655759397],\n+ [0.6659596192381536, 2.256767693355746, 2.5, 6, 0.2284450217013008, 3.443359136114996, 2.639155331188279, -0.367350344747201, 0.7673619164483392, 0.5300792745888832, 1.725289655759397],\n+ [1, 2, 0, 1, 0.3333333333333333, 0, 0.4999999999999999, 0.2898064092199763, 0.6666666666666667, 1, 1.725289655759397],\n+ [0.459387925258634, 2.540612074741366, 1, 2, 0.1531293084195447, 2.176809500243183, 0.7872118769661439, -0.8054285949250646, 0.9368355759475115, 0.3926328355868177, 1.725289655759397],\n+ [0.68260572574677, 2.182710391950513, 0, 5.416666666666666, 0.238230511995077, 0, 2.477393204043783, 1.327736424808056, 0.2565180128752361, 1, 1.725289655759397],\n+ [0.6209312921230391, 2.230235398735714, 1, 2, 0.2177814766543932, 1.610484143230854, 0.8967663239197839, -0.4136799968217064, 0.8783719010971742, 0.5213872231511146, 1.725289655759397],\n+ [0.7803173801516352, 2.212772241130693, 1, 5, 0.2603123363353145, 1.31349237295003, 2.302026965721967, 0.5631982273065281, 0.5099524183271413, 0.8358889331635316, 1.725289655759397],\n+ [0.5250516553536253, 2.45302813924145, 1, 6, 0.1763054355717879, 1.930849168777699, 2.513667229467984, 0.5454049260406475, 0.5662130073449929, 0.777561508830334, 1.725289655759397],\n+ [0.203181127576837, 2.790309709539656, 1, 6, 0.06787431084056803, 4.92171695238688, 2.150298936167153, -1.606349407456378, 0.9230321845151072, 0.3886057635842186, 1.725289655759397],\n+ [0.7145233834068655, 2.170085079520931, 1, 3, 0.2477020339466259, 1.399534323470248, 1.382434277951112, -0.00991140557879785, 0.7421530662286839, 0.6796980736658556, 1.725289655759397],\n+ [0.8025307113169092, 2.197469288683092, 1, 6, 0.2675102371056363, 1.246058232910557, 2.730413585709635, 0.860351389602304, 0.4023716041625731, 0.8868613698058293, 1.725289655759397],\n+ [0.886960160336796, 2.113039839663204, 1, 4, 0.295653386778932, 1.127446355223306, 1.867415205641442, 0.4068397961730323, 0.5572071130808076, 0.8144379212000086, 1.725289655759397],\n+ [0.5840734718676881, 2.415926528132312, 2.5, 5.5, 0.1946911572892293, 4.175355120340121, 2.27655929762562, -0.9098022780654729, 0.8340495404636969, 0.3957525961476541, 1.725289655759397],\n+ [0.5268550139960962, 2.205618688973626, 0, 0, 0.1928124737023075, 0, 0, 0, 1, 1, 1.725289655759397],\n+ [1, 1.954150177116668, 1, 3, 0.3385068260057204, 0.9999999999999998, 1.535194190871489, 0.3102054133837139, 0.5833958240116991, 0.8085296778030449, 1.725289655759397],\n+ [0.7013114701420603, 2.186058834646364, 0, 2, 0.2428893408576666, 0, 0.9148884596802435, 0.530281078673453, 0.5732165501869386, 1, 1.725289655759397],\n+ [0.6103766338418385, 2.230395005807139, 1, 2, 0.2148629707938298, 1.638332702393587, 0.8967021513197104, -0.4298585739491048, 0.8813404805118064, 0.5160100083098675, 1.725289655759397],\n+ [1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 1.725289655759397],\n+ [1.416174943672039, 1.583825056327961, 0, 0, 0.4720583145573463, 0, 0, 0, 1, 1, 1.725289655759397],\n+ [0.566048512190645, 2.41804757094315, 2, 3, 0.1896884337572, 3.533266066295039, 1.240670380537576, -1.333516642795554, 0.9504034442939914, 0.2397204872545077, 1.725289655759397] \n+ ]\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"test",\n+ "Cat":"test",\n+ "Chimp":"test",\n+ "Cow":"test",\n+ "Horse":"test",\n+ "Human":"test",\n+ "Mouse":"test",\n+ "Node1":"test",\n+ "Node12":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node8":"test",\n+ "Node9":"test",\n+ "Pig":"test",\n+ "Rat":"test",\n+ "RhMonkey":"test"\n+ }\n+ },\n+ "timers":{\n+ "Ancestor sampling analysis":{\n+ "order":3,\n+ "timer":12\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":1\n+ },\n+ "Primary SLAC analysis":{\n+ "order":2,\n+ "timer":1\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":14\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/sm19-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in1.nhx Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| @@ -0,0 +1,152 @@ +#NEXUS +begin taxa; + dimensions ntax=50; + taxlabels + C019-B2_10_1[&!color=#ff0000] + C019-B2_13_1[&!color=#ff0000] + C019-B2_16_1[&!color=#ff0000] + C019-B2_17_3[&!color=#ff0000] + C019-B2_18_1[&!color=#ff0000] + C019-B2_1_2[&!color=#ff0000] + C019-B2_24_1[&!color=#ff0000] + C019-B2_28_1[&!color=#ff0000] + C019-B2_29_1[&!color=#ff0000] + C019-B2_31_1[&!color=#ff0000] + C019-B2_32_1[&!color=#ff0000] + C019-B2_34_1[&!color=#ff0000] + C019-B2_35_1[&!color=#ff0000] + C019-B2_42_2[&!color=#ff0000] + C019-B2_43_2[&!color=#ff0000] + C019-B2_45_1[&!color=#ff0000] + C019-B2_46_2[&!color=#ff0000] + C019-B2_47_3[&!color=#ff0000] + C019-B2_4_1[&!color=#ff0000] + C019-B2_52_1[&!color=#ff0000] + C019-B2_53_1[&!color=#ff0000] + C019-B2_54_1[&!color=#ff0000] + C019-B2_5_1[&!color=#ff0000] + C019-B2_6_3[&!color=#ff0000] + C019-B2_9_1[&!color=#ff0000] + C019-S2_10_1[&!color=#0000ff] + C019-S2_11_1[&!color=#0000ff] + C019-S2_12_2[&!color=#0000ff] + C019-S2_13_1[&!color=#0000ff] + C019-S2_14_1[&!color=#0000ff] + C019-S2_15_4[&!color=#0000ff] + C019-S2_16_1[&!color=#0000ff] + C019-S2_17_1[&!color=#0000ff] + C019-S2_18_2[&!color=#0000ff] + C019-S2_19_1[&!color=#0000ff] + C019-S2_1_1[&!color=#0000ff] + C019-S2_20_2[&!color=#0000ff] + C019-S2_21_1[&!color=#0000ff] + C019-S2_22_1[&!color=#0000ff] + C019-S2_23_2[&!color=#0000ff] + C019-S2_24_1[&!color=#0000ff] + C019-S2_25_2[&!color=#0000ff] + C019-S2_2_1[&!color=#0000ff] + C019-S2_3_1[&!color=#0000ff] + C019-S2_4_1[&!color=#0000ff] + C019-S2_5_1[&!color=#0000ff] + C019-S2_6_1[&!color=#0000ff] + C019-S2_7_1[&!color=#0000ff] + C019-S2_8_1[&!color=#0000ff] + C019-S2_9_1[&!color=#0000ff] +; +end; + +begin trees; + tree tree_1 = [&R] ((((((C019-B2_35_1:0.005858,C019-B2_52_1:0.001773):9.4E-4,((((((C019-B2_28_1:0.002896,C019-B2_29_1:9.09E-4):0.004372,C019-B2_31_1:0.003387):0.001252,C019-S2_9_1:0.001965):4.28E-4,C019-B2_34_1:0.003365):0.00173,C019-S2_2_1:0.011763):5.94E-4,((((C019-B2_4_1:0.002924,C019-B2_6_3:8.81E-4):0.001821,C019-B2_5_1:0.001994):0.006052,C019-S2_1_1:0.011533):0.002707,((C019-S2_4_1:0.006447,C019-S2_6_1:0.00696):0.001115,C019-S2_7_1:0.004624):0.003256):0.001452):0.002006):3.96E-4,((C019-S2_10_1:0.005429,C019-S2_12_2:3.52E-4):9.31E-4,C019-B2_42_2:9.87E-4):6.51E-4):5.28E-4,(C019-B2_53_1:0.002654,C019-B2_54_1:0.001151):0.002202):3.98E-4,((((((C019-B2_9_1:0.003599,C019-B2_10_1:0.002149):0.003701,C019-B2_1_2:0.011845):0.001658,C019-S2_3_1:0.009874):1.58E-4,C019-S2_5_1:0.009998):2.67E-4,(((C019-B2_17_3:0.0,C019-S2_22_1:0.0):6.76E-4,C019-B2_16_1:0.003129):2.62E-4,(((((C019-B2_18_1:0.0,C019-S2_25_2:0.0):3.0E-5,C019-S2_24_1:-3.0E-5):7.69E-4,C019-S2_23_2:0.003047):4.93E-4,(((((C019-B2_24_1:0.004304,C019-S2_19_1:-0.002103):0.00459,C019-S2_17_1:0.00129):0.002822,C019-S2_18_2:0.004477):8.52E-4,C019-S2_21_1:0.001446):8.3E-4,C019-S2_20_2:0.003028):0.002252):0.001275,C019-B2_13_1:0.006181):9.2E-4):0.003349):0.001411,C019-S2_13_1:-4.68E-4):0.001963):3.46E-4,(((C019-B2_45_1:8.37E-4,C019-S2_8_1:0.006794):0.001393,C019-S2_14_1:5.17E-4):3.77E-4,(((C019-B2_32_1:0.005635,C019-B2_43_2:0.001995):9.13E-4,C019-S2_11_1:0.002993):5.52E-4,(((C019-B2_46_2:0.0,C019-S2_15_4:0.0):0.001576,C019-S2_16_1:0.002229):0.001073,C019-B2_47_3:8.77E-4):8.62E-4):7.32E-4):3.46E-4); +end; + +begin figtree; + set appearance.backgroundColorAttribute="Default"; + set appearance.backgroundColour=#ffffff; + set appearance.branchColorAttribute="User selection"; + set appearance.branchColorGradient=false; + set appearance.branchLineWidth=1.0; + set appearance.branchMinLineWidth=0.0; + set appearance.branchWidthAttribute="Fixed"; + set appearance.foregroundColour=#000000; + set appearance.hilightingGradient=false; + set appearance.selectionColour=#2d3680; + set branchLabels.colorAttribute="User selection"; + set branchLabels.displayAttribute="Branch times"; + set branchLabels.fontName="sansserif"; + set branchLabels.fontSize=8; + set branchLabels.fontStyle=0; + set branchLabels.isShown=false; + set branchLabels.significantDigits=4; + set layout.expansion=0; + set layout.layoutType="RECTILINEAR"; + set layout.zoom=0; + set legend.attribute=null; + set legend.fontSize=10.0; + set legend.isShown=false; + set legend.significantDigits=4; + set nodeBars.barWidth=4.0; + set nodeBars.displayAttribute=null; + set nodeBars.isShown=false; + set nodeLabels.colorAttribute="User selection"; + set nodeLabels.displayAttribute="Node ages"; + set nodeLabels.fontName="sansserif"; + set nodeLabels.fontSize=8; + set nodeLabels.fontStyle=0; + set nodeLabels.isShown=false; + set nodeLabels.significantDigits=4; + set nodeShapeExternal.colourAttribute="User selection"; + set nodeShapeExternal.isShown=false; + set nodeShapeExternal.minSize=10.0; + set nodeShapeExternal.scaleType=Width; + set nodeShapeExternal.shapeType=Circle; + set nodeShapeExternal.size=4.0; + set nodeShapeExternal.sizeAttribute="Fixed"; + set nodeShapeInternal.colourAttribute="User selection"; + set nodeShapeInternal.isShown=false; + set nodeShapeInternal.minSize=10.0; + set nodeShapeInternal.scaleType=Width; + set nodeShapeInternal.shapeType=Circle; + set nodeShapeInternal.size=4.0; + set nodeShapeInternal.sizeAttribute="Fixed"; + set polarLayout.alignTipLabels=false; + set polarLayout.angularRange=0; + set polarLayout.rootAngle=0; + set polarLayout.rootLength=100; + set polarLayout.showRoot=true; + set radialLayout.spread=0.0; + set rectilinearLayout.alignTipLabels=false; + set rectilinearLayout.curvature=0; + set rectilinearLayout.rootLength=100; + set scale.offsetAge=0.0; + set scale.rootAge=1.0; + set scale.scaleFactor=1.0; + set scale.scaleRoot=false; + set scaleAxis.automaticScale=true; + set scaleAxis.fontSize=8.0; + set scaleAxis.isShown=false; + set scaleAxis.lineWidth=1.0; + set scaleAxis.majorTicks=1.0; + set scaleAxis.minorTicks=0.5; + set scaleAxis.origin=0.0; + set scaleAxis.reverseAxis=false; + set scaleAxis.showGrid=true; + set scaleBar.automaticScale=true; + set scaleBar.fontSize=10.0; + set scaleBar.isShown=true; + set scaleBar.lineWidth=1.0; + set scaleBar.scaleRange=0.0; + set tipLabels.colorAttribute="User selection"; + set tipLabels.displayAttribute="Names"; + set tipLabels.fontName="sansserif"; + set tipLabels.fontSize=8; + set tipLabels.fontStyle=0; + set tipLabels.isShown=true; + set tipLabels.significantDigits=4; + set trees.order=false; + set trees.orderType="increasing"; + set trees.rooting=false; + set trees.rootingType="User Selection"; + set trees.transform=false; + set trees.transformType="cladogram"; +end; + |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/sm19-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in2.nhx Tue Apr 20 10:27:46 2021 +0000 |
| [ |
| @@ -0,0 +1,166 @@ +#NEXUS +begin taxa; + dimensions ntax=64; + taxlabels + C019-B3_103_1[&!color=#ff0000] + C019-B3_10_1[&!color=#ff0000] + C019-B3_121_1[&!color=#ff0000] + C019-B3_122_4[&!color=#ff0000] + C019-B3_125_1[&!color=#ff0000] + C019-B3_132_1[&!color=#ff0000] + C019-B3_140_2[&!color=#ff0000] + C019-B3_144_1[&!color=#ff0000] + C019-B3_147_1[&!color=#ff0000] + C019-B3_154_1[&!color=#ff0000] + C019-B3_162_1[&!color=#ff0000] + C019-B3_164_1[&!color=#ff0000] + C019-B3_173_1[&!color=#ff0000] + C019-B3_179_1[&!color=#ff0000] + C019-B3_180_1[&!color=#ff0000] + C019-B3_18_1[&!color=#ff0000] + C019-B3_1_1[&!color=#ff0000] + C019-B3_201_1[&!color=#ff0000] + C019-B3_211_4[&!color=#ff0000] + C019-B3_26_6[&!color=#ff0000] + C019-B3_27_1[&!color=#ff0000] + C019-B3_32_1[&!color=#ff0000] + C019-B3_37_1[&!color=#ff0000] + C019-B3_3_2[&!color=#ff0000] + C019-B3_57_1[&!color=#ff0000] + C019-B3_59_1[&!color=#ff0000] + C019-B3_61_3[&!color=#ff0000] + C019-B3_63_1[&!color=#ff0000] + C019-B3_84_1[&!color=#ff0000] + C019-B3_87_1[&!color=#ff0000] + C019-B3_94_1[&!color=#ff0000] + C019-B3_98_1[&!color=#ff0000] + C019-S3_10_3[&!color=#0000ff] + C019-S3_11_1[&!color=#0000ff] + C019-S3_12_1[&!color=#0000ff] + C019-S3_13_1[&!color=#0000ff] + C019-S3_14_1[&!color=#0000ff] + C019-S3_15_1[&!color=#0000ff] + C019-S3_16_1[&!color=#0000ff] + C019-S3_17_1[&!color=#0000ff] + C019-S3_18_1[&!color=#0000ff] + C019-S3_19_2[&!color=#0000ff] + C019-S3_1_3[&!color=#0000ff] + C019-S3_20_1[&!color=#0000ff] + C019-S3_21_1[&!color=#0000ff] + C019-S3_22_2[&!color=#0000ff] + C019-S3_23_6[&!color=#0000ff] + C019-S3_24_1[&!color=#0000ff] + C019-S3_25_1[&!color=#0000ff] + C019-S3_26_1[&!color=#0000ff] + C019-S3_27_1[&!color=#0000ff] + C019-S3_28_1[&!color=#0000ff] + C019-S3_29_1[&!color=#0000ff] + C019-S3_2_1[&!color=#0000ff] + C019-S3_30_5[&!color=#0000ff] + C019-S3_31_1[&!color=#0000ff] + C019-S3_32_1[&!color=#0000ff] + C019-S3_3_1[&!color=#0000ff] + C019-S3_4_1[&!color=#0000ff] + C019-S3_5_1[&!color=#0000ff] + C019-S3_6_1[&!color=#0000ff] + C019-S3_7_44[&!color=#0000ff] + C019-S3_8_1[&!color=#0000ff] + C019-S3_9_1[&!color=#0000ff] +; +end; + +begin trees; + tree tree_1 = [&R] (((((((C019-S3_30_5:0.001628,C019-S3_29_1:0.006003):0.00113,(C019-B3_173_1:0.001171,C019-S3_28_1:0.002634):0.001744):8.3E-4,C019-B3_132_1:0.014016):5.86E-4,((C019-S3_25_1:0.002323,C019-S3_26_1:0.001482):9.35E-4,C019-B3_144_1:0.004793):0.001476):5.2E-4,((C019-B3_140_2:0.005006,C019-B3_211_4:7.09E-4):0.005792,C019-S3_24_1:0.003793):6.51E-4):3.29E-4,((((((C019-B3_180_1:0.007012,C019-S3_12_1:0.002539):0.001059,C019-B3_164_1:0.004685):0.001059,C019-B3_201_1:0.002755):4.7E-4,C019-S3_27_1:0.004308):5.29E-4,(C019-B3_179_1:0.00111,C019-B3_162_1:0.006521):0.001397):4.5E-4,(((C019-B3_98_1:0.00603,C019-B3_84_1:0.011255):0.001462,C019-B3_3_2:0.01022):0.004778,(((((C019-B3_122_4:-1.5E-5,C019-B3_121_1:0.003821):1.07E-4,(((C019-S3_6_1:3.19E-4,C019-S3_5_1:0.003493):2.06E-4,C019-S3_4_1:0.003609):1.56E-4,C019-S3_7_44:-1.63E-4):0.001868):8.3E-5,C019-S3_2_1:0.003743):9.49E-4,C019-S3_3_1:9.47E-4):1.32E-4,((((((C019-B3_87_1:0.004026,C019-B3_94_1:0.003649):0.001868,C019-S3_9_1:0.001947):5.6E-5,C019-S3_8_1:0.001847):0.002662,C019-S3_10_3:0.003074):0.001087,C019-B3_103_1:0.002733):2.29E-4,(C019-S3_1_3:0.003978,C019-B3_125_1:0.003697):9.13E-4):4.97E-4):0.006645):7.82E-4):8.25E-4):5.47E-4,((((C019-S3_22_2:9.84E-4,C019-S3_23_6:0.005041):0.001644,(((((((((C019-B3_32_1:0.001955,C019-S3_15_1:-5.5E-5):9.11E-4,C019-B3_37_1:9.97E-4):0.001209,C019-B3_57_1:0.002666):0.001047,C019-B3_59_1:0.001825):0.001321,(C019-B3_26_6:-2.4E-5,C019-B3_27_1:2.4E-5):0.006853):0.001793,C019-B3_10_1:0.009272):0.001166,((C019-S3_19_2:7.58E-4,C019-S3_17_1:0.003048):0.001952,C019-S3_11_1:0.007625):0.001734):0.001109,C019-B3_147_1:0.00437):0.001515,(((C019-S3_32_1:0.009024,C019-S3_31_1:0.002453):0.007605,C019-B3_1_1:0.014729):0.003341,(C019-S3_14_1:0.002908,C019-S3_13_1:0.004722):0.006888):0.001642):0.00149):2.85E-4,(((C019-S3_20_1:4.17E-4,C019-S3_21_1:0.001505):0.001098,C019-S3_16_1:0.00369):0.00156,((C019-B3_61_3:7.33E-4,C019-B3_63_1:0.006898):0.003303,C019-B3_18_1:0.0063):0.00288):7.85E-4):1.97E-4,(C019-S3_18_1:3.32E-4,C019-B3_154_1:0.00368):0.001664):5.47E-4); +end; + +begin figtree; + set appearance.backgroundColorAttribute="Default"; + set appearance.backgroundColour=#ffffff; + set appearance.branchColorAttribute="User selection"; + set appearance.branchColorGradient=false; + set appearance.branchLineWidth=1.0; + set appearance.branchMinLineWidth=0.0; + set appearance.branchWidthAttribute="Fixed"; + set appearance.foregroundColour=#000000; + set appearance.hilightingGradient=false; + set appearance.selectionColour=#2d3680; + set branchLabels.colorAttribute="User selection"; + set branchLabels.displayAttribute="Branch times"; + set branchLabels.fontName="sansserif"; + set branchLabels.fontSize=8; + set branchLabels.fontStyle=0; + set branchLabels.isShown=false; + set branchLabels.significantDigits=4; + set layout.expansion=0; + set layout.layoutType="RECTILINEAR"; + set layout.zoom=0; + set legend.attribute=null; + set legend.fontSize=10.0; + set legend.isShown=false; + set legend.significantDigits=4; + set nodeBars.barWidth=4.0; + set nodeBars.displayAttribute=null; + set nodeBars.isShown=false; + set nodeLabels.colorAttribute="User selection"; + set nodeLabels.displayAttribute="Node ages"; + set nodeLabels.fontName="sansserif"; + set nodeLabels.fontSize=8; + set nodeLabels.fontStyle=0; + set nodeLabels.isShown=false; + set nodeLabels.significantDigits=4; + set nodeShapeExternal.colourAttribute="User selection"; + set nodeShapeExternal.isShown=false; + set nodeShapeExternal.minSize=10.0; + set nodeShapeExternal.scaleType=Width; + set nodeShapeExternal.shapeType=Circle; + set nodeShapeExternal.size=4.0; + set nodeShapeExternal.sizeAttribute="Fixed"; + set nodeShapeInternal.colourAttribute="User selection"; + set nodeShapeInternal.isShown=false; + set nodeShapeInternal.minSize=10.0; + set nodeShapeInternal.scaleType=Width; + set nodeShapeInternal.shapeType=Circle; + set nodeShapeInternal.size=4.0; + set nodeShapeInternal.sizeAttribute="Fixed"; + set polarLayout.alignTipLabels=false; + set polarLayout.angularRange=0; + set polarLayout.rootAngle=0; + set polarLayout.rootLength=100; + set polarLayout.showRoot=true; + set radialLayout.spread=0.0; + set rectilinearLayout.alignTipLabels=false; + set rectilinearLayout.curvature=0; + set rectilinearLayout.rootLength=100; + set scale.offsetAge=0.0; + set scale.rootAge=1.0; + set scale.scaleFactor=1.0; + set scale.scaleRoot=false; + set scaleAxis.automaticScale=true; + set scaleAxis.fontSize=8.0; + set scaleAxis.isShown=false; + set scaleAxis.lineWidth=1.0; + set scaleAxis.majorTicks=1.0; + set scaleAxis.minorTicks=0.5; + set scaleAxis.origin=0.0; + set scaleAxis.reverseAxis=false; + set scaleAxis.showGrid=true; + set scaleBar.automaticScale=true; + set scaleBar.fontSize=10.0; + set scaleBar.isShown=true; + set scaleBar.lineWidth=1.0; + set scaleBar.scaleRange=0.0; + set tipLabels.colorAttribute="User selection"; + set tipLabels.displayAttribute="Names"; + set tipLabels.fontName="sansserif"; + set tipLabels.fontSize=8; + set tipLabels.fontStyle=0; + set tipLabels.isShown=true; + set tipLabels.significantDigits=4; + set trees.order=false; + set trees.orderType="increasing"; + set trees.rooting=false; + set trees.rootingType="User Selection"; + set trees.transform=false; + set trees.transformType="cladogram"; +end; + |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/sm19-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out1.json Tue Apr 20 10:27:46 2021 +0000 |
| b |
| b'@@ -0,0 +1,2606 @@\n+{\n+ "compartments":2,\n+ "events":{\n+ "C019-B2_18_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_24_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_45_1":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_46_2":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-B2_47_3":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "C019-S2_1_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_22_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_2_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "C019-S2_9_1":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node2":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node28":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node34":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node45":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node52":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ },\n+ "Node59":{\n+ "from":"Blood",\n+ "to":"Semen"\n+ },\n+ "Node88":{\n+ "from":"Semen",\n+ "to":"Blood"\n+ }\n+ },\n+ "leaf-count":50,\n+ "migrations":16,\n+ "node-migrations":{\n+ "Node10":1,\n+ "Node11":1,\n+ "Node12":0,\n+ "Node13":0,\n+ "Node2":6,\n+ "Node20":2,\n+ "Node21":1,\n+ "Node22":0,\n+ "Node23":0,\n+ "Node28":1,\n+ "Node29":0,\n+ "Node3":5,\n+ "Node33":1,\n+ "Node34":1,\n+ "Node38":0,\n+ "Node4":4,\n+ "Node41":6,\n+ "Node42":6,\n+ "Node43":1,\n+ "Node44":1,\n+ "Node45":1,\n+ "Node46":0,\n+ "Node5":0,\n+ "Node52":5,\n+ "Node53":1,\n+ "Node54":1,\n+ "Node58":3,\n+ "Node59":3,\n+ "Node60":1,\n+ "Node61":1,\n+ "Node62":1,\n+ "Node67":1,\n+ "Node68":1,\n+ "Node69":1,\n+ "Node70":1,\n+ "Node71":1,\n+ "Node79":16,\n+ "Node8":4,\n+ "Node80":4,\n+ "Node81":1,\n+ "Node82":1,\n+ "Node86":3,\n+ "Node87":1,\n+ "Node88":1,\n+ "Node9":2,\n+ "Node92":2,\n+ "Node93":1,\n+ "Node94":1\n+ },\n+ "node-p-value":{\n+ "panmictic":{\n+ "Node10":0.3866133866133866,\n+ "Node11":0.6103896103896104,\n+ "Node12":0.1568431568431568,\n+ "Node13":0.3486513486513487,\n+ "Node2":0.4045954045954046,\n+ 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/sm19-out2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out2.json Tue Apr 20 10:27:46 2021 +0000 |
| b |
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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/strike-ambigs-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-in1.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| b'@@ -0,0 +1,260 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---------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+--------------------------------------A\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/strike-ambigs-in2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-in2.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| b'@@ -0,0 +1,455 @@\n+>NC_045512.2:21563-25384\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC\n+AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC\n+AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC\n+AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT\n+AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA\n+ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT\n+AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT\n+TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT\n+TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA\n+GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT\n+TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT\n+TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT\n+TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT\n+GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT\n+GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG\n+TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC\n+CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA\n+GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC\n+TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT\n+GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT\n+GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT\n+TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT\n+CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT\n+CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT\n+AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT\n+AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA\n+CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT\n+TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG\n+CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG\n+ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA\n+GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTC\n+CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT\n+AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT\n+GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT\n+CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT\n+GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT\n+AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG\n+TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT\n+ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA\n+GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT\n+AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT\n+CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC\n+CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT\n+TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT\n+ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG\n+CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA\n+AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC\n+ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC\n+ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC\n+CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA\n+CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT\n+TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT\n+GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA\n+GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC\n+ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA\n+CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA\n+TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT\n+TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA\n+TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA\n+AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC\n+CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT\n+ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC\n+TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC\n+TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>gb_MW5'..b'_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1\n+ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC\n+AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC\n+AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC\n+AATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT\n+AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA\n+ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT\n+AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTT\n+TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT\n+TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA\n+GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT\n+TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT\n+TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT\n+TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT\n+GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT\n+GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG\n+TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC\n+CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA\n+GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC\n+TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT\n+GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT\n+GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT\n+TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT\n+CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT\n+CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT\n+AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT\n+AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA\n+CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT\n+TTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG\n+CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG\n+ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA\n+GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTC\n+CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT\n+AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT\n+GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT\n+CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT\n+GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT\n+AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG\n+TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT\n+ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA\n+GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT\n+AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT\n+CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC\n+CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT\n+TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT\n+ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG\n+CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA\n+AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC\n+ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC\n+ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC\n+CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA\n+CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT\n+TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT\n+GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA\n+GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC\n+ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA\n+CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA\n+TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT\n+TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA\n+TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA\n+AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC\n+CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT\n+ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC\n+TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC\n+TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/strike-ambigs-out1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-out1.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| b'@@ -0,0 +1,8 @@\n+>NC_045512.2:21563-25384\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021\n+----------------------------------------------------------------------------'..b'----------------------------------------------------------------------------------------------------------------------\n+>epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n' |
| b |
| diff -r 000000000000 -r 7c86ceaf523c test-data/strike-ambigs-out2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-out2.fa Tue Apr 20 10:27:46 2021 +0000 |
| b |
| b'@@ -0,0 +1,14 @@\n+>NC_045512.2:21563-25384\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_nu'..b'CTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1\n+ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n' |