| Next changeset 1:37887c2733a3 (2021-06-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97" |
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added:
hyphy_summary.xml macros.xml scripts/annotator.bf scripts/hyphy_summary.py 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-in2.nex test-data/busted-out1.json test-data/busted-out2-1.json test-data/busted-out2-2.json test-data/cfel-out1.json test-data/conv-in1.fa test-data/conv-out1.nex 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.nex test-data/relax-in2.nhx test-data/relax-out1.json test-data/relax-out2-1.json test-data/relax-out2-2.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 test-data/summary/ORF6-segment.json test-data/summary/ORF6-site.json test-data/summary/ORF6.FADE.json test-data/summary/ORF6.MEME-full.json test-data/summary/ORF6.SLAC.json test-data/summary/ORF6.combined.fas test-data/summary/ORF6.labels.json test-data/summary/merged-segment.json test-data/summary/merged-site.json test-data/summary/nsp7-segment.json test-data/summary/nsp7-site.json test-data/summary/nsp7.FADE.json test-data/summary/nsp7.MEME-full.json test-data/summary/nsp7.SLAC.json test-data/summary/nsp7.combined.fas test-data/summary/nsp7.labels.json test-data/summary/nsp8-segment.json test-data/summary/nsp8-site.json test-data/summary/nsp8.BUSTED.json test-data/summary/nsp8.CFEL.json test-data/summary/nsp8.FADE.json test-data/summary/nsp8.FEL.json test-data/summary/nsp8.MEME-full.json test-data/summary/nsp8.MEME.json test-data/summary/nsp8.PRIME.json test-data/summary/nsp8.RELAX.json test-data/summary/nsp8.SLAC.json test-data/summary/nsp8.combined.fas test-data/summary/nsp8.combined.fas.BGM.json test-data/summary/nsp8.labels.json |
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| diff -r 000000000000 -r f304c108aa1f hyphy_summary.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hyphy_summary.xml Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,198 @@\n+<?xml version="1.0"?>\n+<tool id="hyphy_summary" version="1.0.0" name="HyPhy-Summary" profile="21.01">\n+ <description>generate summary report of HyPhy analyses</description>\n+ <requirements>\n+ <requirement type="package" version="0.19.7">python-bioext</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ python \'$__tool_directory__/scripts/hyphy_summary.py\' \n+ --mode $mode_conditional.mode\n+ #if $mode_conditional.mode == \'summary\':\n+ --combined \'$mode_conditional.combined\'\n+ --pvalue $mode_conditional.pvalue\n+ --gene \'$mode_conditional.gene\'\n+ --labels \'$mode_conditional.labels\'\n+ --default-tag \'$mode_conditional.default_tag\'\n+ --name \'$mode_conditional.name\'\n+ #if $mode_conditional.relax:\n+ --relax \'$mode_conditional.relax\'\n+ #end if\n+ #if $mode_conditional.busted:\n+ --busted \'$mode_conditional.busted\'\n+ #end if\n+ #if $mode_conditional.slac:\n+ --slac \'$mode_conditional.slac\'\n+ #end if\n+ #if $mode_conditional.fel:\n+ --fel \'$mode_conditional.fel\'\n+ #end if\n+ #if $mode_conditional.cfel:\n+ --cfel \'$mode_conditional.cfel\'\n+ #end if\n+ #if $mode_conditional.meme:\n+ --meme \'$mode_conditional.meme\'\n+ #end if\n+ #if $mode_conditional.meme_full:\n+ --meme-full \'$mode_conditional.meme_full\'\n+ #end if\n+ #if $mode_conditional.prime:\n+ --prime \'$mode_conditional.prime\'\n+ #end if\n+ #if $mode_conditional.fade:\n+ --fade \'$mode_conditional.fade\'\n+ #end if\n+ #if $mode_conditional.bgm:\n+ --bgm \'$mode_conditional.bgm\'\n+ #end if\n+ #else:\n+ --annotation-inputs \'$mode_conditional.annotation_inputs\'\n+ --summary-inputs \'$mode_conditional.summary_inputs\'\n+ #end if\n+ --annotation-output \'$annotation\'\n+ --summary-output \'$summary\'\n+ ]]></command>\n+ <inputs>\n+ <conditional name="mode_conditional">\n+ <param argument="--mode" type="select" label="Mode">\n+ <option value="summary">Generate gene summary</option>\n+ <option value="merge">Merge gene summaries for clade analysis</option>\n+ </param>\n+ <when value="summary">\n+ <param argument="--combined" type="data" format="fasta" label="Combined reference and query alignments from TN93-Filter" />\n+ <param argument="--pvalue" type="float" min="0" max="1" value="0.05" label="p-value to use" />\n+ <param argument="--labels" type="data" format="json,hyphy_results.json" label="HyPhy-Annotate branche labels in JSON format" />\n+ <param argument="--gene" type="text" label="Name of the gene or sequence being analyzed">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="_" />\n+ <add value="-" />\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param argument="--default-tag" type="text" value="Reference" label="Default name for sequences that have no explicit label">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.ascii_letters,string.digits">\n+ <add value="_" />\n+ <add value="-" />\n+ </valid>\n+ </sanitizer>\n+ '..b' <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Site annotations" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="mode" value="summary" />\n+ <param name="name" value="epi_isl_1009769" />\n+ <param name="gene" value="nsp8" />\n+ <param name="combined" value="summary/nsp8.combined.fas" />\n+ <param name="fade" value="summary/nsp8.FADE.json" />\n+ <param name="prime" value="summary/nsp8.PRIME.json" />\n+ <param name="relax" value="summary/nsp8.RELAX.json" />\n+ <param name="meme" value="summary/nsp8.MEME.json" />\n+ <param name="meme_full" value="summary/nsp8.MEME-full.json" />\n+ <param name="labels" value="summary/nsp8.labels.json" />\n+ <param name="busted" value="summary/nsp8.BUSTED.json" />\n+ <param name="slac" value="summary/nsp8.SLAC.json" />\n+ <param name="fel" value="summary/nsp8.FEL.json" />\n+ <param name="cfel" value="summary/nsp8.CFEL.json" />\n+ <param name="bgm" value="summary/nsp8.combined.fas.BGM.json" />\n+ <output name="summary" file="summary/nsp8-segment.json" />\n+ <output name="annotation" file="summary/nsp8-site.json" />\n+ </test>\n+ <test>\n+ <param name="mode" value="summary" />\n+ <param name="name" value="epi_isl_1009769" />\n+ <param name="gene" value="ORF6" />\n+ <param name="combined" value="summary/ORF6.combined.fas" />\n+ <param name="fade" value="summary/ORF6.FADE.json" />\n+ <param name="meme_full" value="summary/ORF6.MEME-full.json" />\n+ <param name="labels" value="summary/ORF6.labels.json" />\n+ <param name="slac" value="summary/ORF6.SLAC.json" />\n+ <output name="summary" file="summary/ORF6-segment.json" />\n+ <output name="annotation" file="summary/ORF6-site.json" />\n+ </test>\n+ <test>\n+ <param name="mode" value="summary" />\n+ <param name="name" value="epi_isl_1009769" />\n+ <param name="gene" value="nsp7" />\n+ <param name="combined" value="summary/nsp7.combined.fas" />\n+ <param name="fade" value="summary/nsp7.FADE.json" />\n+ <param name="meme_full" value="summary/nsp7.MEME-full.json" />\n+ <param name="labels" value="summary/nsp7.labels.json" />\n+ <param name="slac" value="summary/nsp7.SLAC.json" />\n+ <output name="summary" file="summary/nsp7-segment.json" />\n+ <output name="annotation" file="summary/nsp7-site.json" />\n+ </test>\n+ <test>\n+ <param name="mode" value="merge" />\n+ <param name="summary_inputs" value="summary/nsp7-segment.json,summary/nsp8-segment.json,summary/ORF6-segment.json" />\n+ <param name="annotation_inputs" value="summary/nsp7-site.json,summary/nsp8-site.json,summary/ORF6-site.json" />\n+ <output name="summary" file="summary/merged-segment.json" />\n+ <output name="annotation" file="summary/merged-site.json" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+HyPhy-Summary\n+=============\n+\n+This tool has two operation modes, summary and merge.\n+\n+Summary\n+-------\n+\n+Given a combined and filtered alignment from TN93-Filter, along with the\n+appropriate HyPhy analysis outputs, this mode will return two JSON files, one \n+with segment annotations and the other with site annotations.\n+\n+Analyses required for this mode:\n+\n+- FADE\n+- PRIME\n+- RELAX\n+- MEME\n+- MEME-Full\n+- Annotate, with the labels in JSON format\n+- BUSTED\n+- SLAC\n+- FEL\n+- CFEL\n+- BGM\n+\n+Merge\n+-----\n+\n+This mode takes a set of segment and site annotations, one each per gene that\n+was analyzed, and returns a merged set of site and segment annotations.\n+\n+]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/bti079</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r f304c108aa1f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jun 09 07:03:54 2021 +0000 |
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| b'@@ -0,0 +1,198 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <xml name="inputs">\n+\t <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" />\n+ <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>\n+ </xml>\n+ <xml name="substitution">\n+ <param name="model" type="select" label="Substitution model">\n+ <option value="GTR">GTR - General time reversible\n+ model</option>\n+ <option value="LG">LG - Generalist empirical model from\n+ Le and Gascuel (2008)</option>\n+ <option value="HIVBm">HIVBm - Specialist empirical model\n+ for between-host HIV sequences</option>\n+ <option value="HIVWm">HIVWm - Specialist empirical model\n+ for within-host HIV sequences</option>\n+ <option value="WAG">WAG - Generalist empirical model from\n+ Whelan and Goldman (2001)</option>\n+ <option value="JTT">JTT - Generalist empirical model from\n+ Jones, Taylor, and Thornton (1996)</option>\n+ <option value="JC69">JC69 - Generalist empirical model\n+ from with equal exchangeability rates</option>\n+ <option value="mtMet">mtMet - Specialist empirical model\n+ for metazoan mitochondrial genomes</option>\n+ <option value="mtVer">mtVer - Specialist empirical model\n+ for vertebrate mitochondrial genomes</option>\n+ <option value="mtInv">mtInv - Specialist empirical model\n+ for invertebrate mitochondrial genomes</option>\n+ <option value="gcpREV">gcpREV - Specialist empirical\n+ model for green plant chloroplast genomes</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="conditional_posteriorEstimationMethod">\n+ <conditional name="posteriorEstimationMethod">\n+ <param argument="--method" type="select" label="Posterior estimation method">\n+ <option value="Variational-Bayes">0-th order Variational Bayes approximation</option>\n+ <option value="Metropolis-Hastings">Full Metropolis-Hastings MCMC algorithm</option>\n+ <option value="Collapsed-Gibbs">Collapsed Gibbs sampler</option>\n+ </param>\n+ <when value="Variational-Bayes">\n+ </when>\n+ <when value="Metropolis-Hastings">\n+ <expand macro="mcmc_options" />\n+ </when>\n+ <when value="Collapsed-Gibbs">\n+ <expand macro="mcmc_options" />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <token name="@posteriorEstimationMethod_cmd@">\n+ #if $posteriorEstimationMethod.method != "Variational-Bayes"\n+ --chains \'$posteriorEstimationMethod.chains\'\n+ --chain-length \'$posteriorEstimationMethod.chain_length\'\n+ --burn-in \'$posteriorEstimationMethod.samples\'\n+ --samples \'$posteriorEstimationMethod.samples_per_chain\'\n+ #end if\n+ </token>\n+\n+ <xml name="mcmc_options">\n+ <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />\n+ <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />\n+ <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />\n+ <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />\n+ </xml>\n+\n+ <xml name="gencode">\n+ <param name="gencodeid" type="select" label="Genetic code">\n+ <option value="Universal">Universal code</option>\n+ <option value="Vertebrate-'..b'eger" min="1" max="10" value="3" label="Alpha rate classes to include in the model" />\n+ <param argument="--rates" type="integer" min="2" max="10" value="3" label="Omega rate classes to include in the model" />\n+ <param argument="--srv" type="boolean" truevalue="Yes" falsevalue="No" label="Include synonymous rate variation" />\n+ <param name="save_alternative_model" type="boolean" label="Save alternative model fit" />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="branches">\n+ <conditional name="branch_cond">\n+ <param name="branch_sel" type="select" label="Set of branches to test">\n+ <option value="All">All branches</option>\n+ <option value="Internal">Internal branches</option>\n+ <option value="Leaves">Leaf branches</option>\n+ <option value="\'Unlabeled-branches\'">Unlabeled branches</option>\n+ <option value="specify">Enter a branch label</option>\n+ </param>\n+ <when value="specify">\n+ <param name="branch_label" type="text" value="Test" optional="false" label="Branch label">\n+ <sanitizer invalid_char="">\n+ <valid initial="default" />\n+ </sanitizer>\n+ </param>\n+ </when>\n+ <when value="All" />\n+ <when value="Internal" />\n+ <when value="Leaves" />\n+ <when value="\'Unlabeled-branches\'" />\n+ </conditional>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/molbev/msz197</citation>\n+ <yield/>\n+ </citations>\n+ </xml>\n+ <token name="@VERSION@">2.5.31</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">hyphy</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <xml name="alternative_model_output">\n+ <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json">\n+ <filter>advanced[\'save_alternative_model\']</filter>\n+ </data>\n+ </xml>\n+ <token name="@INPUT_TREE@"><![CDATA[\n+ #if $input_nhx:\n+ --tree input.nhx\n+ #end if\n+ ]]>\n+ </token>\n+ <token name="@branch_options@"><![CDATA[\n+ #if $branch_cond.branch_sel == \'specify\':\n+ --branches \'$branch_cond.branch_label\'\n+ #else:\n+ --branches $branch_cond.branch_sel\n+ #end if\n+ ]]>\n+ </token>\n+ <token name="@advanced_options@"><![CDATA[\n+ #if $advanced.srv_options == \'specify\':\n+ --grid-size $advanced.grid_size\n+ --starting-points $advanced.starting_points\n+ --syn-rates $advanced.syn_rates\n+ --rates $advanced.rates\n+ --srv $advanced.srv\n+ #if $advanced.save_alternative_model:\n+ --save-fit alternative_model.json\n+ #end if\n+ #end if\n+ ]]></token>\n+ <token name="@HYPHYMPI@">\\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\\${TMPDIR:-.}" -np \\${GALAXY_SLOTS:-1}} HYPHYMPI</token>\n+ <token name="@ERRORS@"><![CDATA[\n+ ; EC=\\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \\$EC\n+ ]]></token>\n+ <token name="@HYPHY_ENVIRONMENT@"><![CDATA[\n+ export HYPHY=`which hyphy` &&\n+ export HYPHY_PATH=`dirname \\$HYPHY` &&\n+ export HYPHY_LIB=`readlink -f \\$HYPHY_PATH/../share/hyphy` &&]]></token>\n+ <token name="@HYPHY_INVOCATION@"><![CDATA[\n+ @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\\$HYPHY_LIB\n+ ]]></token>\n+ <token name="@SYMLINK_FILES@"><![CDATA[\n+ #if $input_nhx is not None:\n+ ln -s \'$input_nhx\' input.nhx &&\n+ #end if\n+ ln -s \'$input_file\' input.$input_file.extension &&\n+ #set $input_file = \'input.%s\' % $input_file.extension\n+ ]]></token>\n+</macros>\n' |
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| diff -r 000000000000 -r f304c108aa1f scripts/annotator.bf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/annotator.bf Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| @@ -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 f304c108aa1f scripts/hyphy_summary.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/hyphy_summary.py Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b"@@ -0,0 +1,668 @@\n+import argparse\n+import json\n+import re\n+from collections import defaultdict\n+\n+import BioExt\n+from Bio import SeqIO\n+from Bio.Seq import Seq\n+from Bio.SeqRecord import SeqRecord\n+from BioExt.uds import _align_par\n+\n+\n+class HyPhySummary(object):\n+\n+ def __init__(self, arguments, summary_json=None, annotation_json=None):\n+ self.arguments = arguments\n+ self.ref_map = ''\n+ self.summary_json = {}\n+ self.annotation_json = {}\n+ self.include_in_annotation = {}\n+ self.test_map = {}\n+ self.site_reports = {}\n+ self.labels = {}\n+ self.ref_seq_map = []\n+ self.cfel = {}\n+ self.relax = {}\n+ self.busted = {}\n+ self.slac = {}\n+ self.fel = {}\n+ self.meme = {}\n+ self.meme_full = {}\n+ self.prime = {}\n+ self.fade = {}\n+ self.bgm = {}\n+ self.ref_genes = [\n+ ['genome', 'ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGG"..b" return generate_error(char_index)\n+ current_node_annotation += current_char\n+ except Exception:\n+ return generate_error(char_index)\n+\n+ if (len(clade_stack) != 1):\n+ return generate_error(len(nwk_str) - 1)\n+\n+ if (len(current_node_name)):\n+ tree_json['name'] = current_node_name\n+\n+ return {\n+ 'json': tree_json,\n+ 'error': None\n+ }\n+\n+\n+if __name__ == '__main__':\n+ parser = argparse.ArgumentParser(description='Summarize selection analysis results.')\n+ parser.add_argument('--combined', help='Combined reference and query alignment from TN-93', required=False, type=str)\n+ parser.add_argument('--pvalue', help='p-value to use', required=False, type=float, default=0.05)\n+ parser.add_argument('--gene', help='Name of the gene or sequence being analyzed', required=False, type=str)\n+ parser.add_argument('--labels', help='JSON file with labels', required=False, type=str)\n+ parser.add_argument('--annotation-output', help='Write a JSON file with site annotations', required=True, type=str)\n+ parser.add_argument('--summary-output', help='Write a JSON file here segment annotations', required=True, type=str)\n+ parser.add_argument('--annotation-inputs', help='Comma-separated list of site annotation files to merge', required=False, type=str)\n+ parser.add_argument('--summary-inputs', help='Comma-separated list of segment annotation files to merge', required=False, type=str)\n+ parser.add_argument('--default-tag', help='Default name for sequences that have no explicit label', required=False, type=str, default='Reference')\n+ parser.add_argument('--name', help='The sequence ID to highlight', required=False, default='MN908947')\n+ parser.add_argument('--mode', help='Operation mode, generate a summary or merge multiple summaries', type=str, choices=['summary', 'merge'], default='summary')\n+ parser.add_argument('--relax', help='Path to RELAX.json file', required=False, type=str)\n+ parser.add_argument('--busted', help='Path to BUSTED.json file', required=False, type=str)\n+ parser.add_argument('--slac', help='Path to SLAC.json file', required=False, type=str)\n+ parser.add_argument('--fel', help='Path to FEL.json file', required=False, type=str)\n+ parser.add_argument('--cfel', help='Path to CFEL.json file', required=False, type=str)\n+ parser.add_argument('--meme', help='Path to MEME.json file', required=False, type=str)\n+ parser.add_argument('--meme-full', help='Path to MEME-full.json file', dest='meme_full', required=False, type=str)\n+ parser.add_argument('--prime', help='Path to PRIME.json file', required=False, type=str)\n+ parser.add_argument('--fade', help='Path to FADE.json file', required=False, type=str)\n+ parser.add_argument('--bgm', help='Path to BGM.json file', required=False, type=str)\n+ arguments = parser.parse_args()\n+ if arguments.mode == 'summary':\n+ analyzer = HyPhySummary(arguments)\n+ annotation_json, summary_json = analyzer.summary()\n+ if annotation_json is not None:\n+ with open(arguments.annotation_output, 'w') as fh:\n+ json.dump(annotation_json, fh, indent=1)\n+ if summary_json is not None:\n+ with open(arguments.summary_output, 'w') as fh:\n+ json.dump(summary_json, fh, indent=1)\n+ else:\n+ summary = {}\n+ annotation = {}\n+ for filename in arguments.annotation_inputs.split(','):\n+ with open(filename, 'r') as fh:\n+ annotation.update(json.load(fh))\n+ for filename in arguments.summary_inputs.split(','):\n+ with open(filename, 'r') as fh:\n+ summary.update(json.load(fh))\n+ with open(arguments.annotation_output, 'w') as fh:\n+ json.dump(annotation, fh, indent=1)\n+ with open(arguments.summary_output, 'w') as fh:\n+ json.dump(summary, fh, indent=1)\n+ exit(0)\n" |
| b |
| diff -r 000000000000 -r f304c108aa1f scripts/strike-ambigs.bf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/strike-ambigs.bf Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| @@ -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); + + |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/absrel-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/absrel-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.nhx Wed Jun 09 07:03:54 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); \ No newline at end of file |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/absrel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-out1.json Wed Jun 09 07:03:54 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 f304c108aa1f 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 f304c108aa1f test-data/annotate-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-in1.nhx Wed Jun 09 07:03:54 2021 +0000 |
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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/annotate-out1-clade.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-clade.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/annotate-out1-full.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-full.nhx Wed Jun 09 07:03:54 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 |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/annotate-out1-int.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-int.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/bgm-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/bgm-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/bgm-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-out1.json Wed Jun 09 07:03:54 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 f304c108aa1f test-data/busted-in2.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-in2.nex Wed Jun 09 07:03:54 2021 +0000 |
| b |
| b"@@ -0,0 +1,30 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 8;\n+\tTAXLABELS\n+\t\t'B_FR_83_HXB2' 'B_US_83_RF' 'B_US_86_JRFL' 'B_US_90_WEAU160' 'D_CD_83_ELI' 'D_CD_83_NDK' 'D_CD_84_84ZR085' 'D_UG_94_94UG114' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 1320;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t;\n+\n+MATRIX\n+\t'B_FR_83_HXB2' CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC\n+\t'B_US_83_RF' CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCATTGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTAAAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCACAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAATCTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATAAAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACCGGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAGCTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAAACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCATAATAGGAGCAGAAACTTTC\n+\t'B_US_86_JRFL' CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCGCAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCAAAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGTGTATTATGACCCATCAAAAGAC"..b"ACTCCAATATTTGCCATAAAGAAAAAAGACAGTACCAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGATTTCTGGGAGGTTCAATTAGGAATACCGCATCCTGCAGGGCTGAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTCTCAGTTCCCTTAGATGAAGATTTTAGGAAATATACCGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTCCCACAGGGATGGAAAGGATCACCGGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCCTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAATTAAGAGAACATCTATTGAGGTGGGGATTTACCACACCAGATAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAAACCTGCCAGAAAAAGAAAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGGAAATTAAACTGGGCAAGCCAGATTTATGCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAATTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAACTACAGAAACAAGGGGACGGCCAATGGACATACCAAATTTATCAAGAACCATTTAAAAATCTAAAAACAGGAAAGTATGCAAGAACGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAGCCACAGAAAGCATAGTGATATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAGGAAACATGGGAAACATGGTGGATAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGTCAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCATAATAGGAGCAGAAACTTTC\n+\t'D_CD_84_84ZR085' CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGATATGGAAAAGGAAGGAAAAATTTCAAGAATTGGGCCTGAAAATCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGACAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCTGCAGGATTAAAGAAGAAAAAGTCAATAACAGTACTGGATGTGGGCGATGCATATTTTTCAATTCCCTTATGTGAAGACTTTAGGAAGTACACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTACTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGATAAAAATCTTAGAGCCCTTTAGAAAACAAAATCCAGAAGTAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGACAGCATAGAGCAAAAATAGAGAAATTAAGAGAACATCTGTTGAGGTGGGGGCTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAGTGGACAGTACAGTCTATAACACTGCCAGAGAAAGAAAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGCCAGATTTATCCAGGAATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAGGCACTAACAGAGGTAATACCACTAACAGAAGAAGCAGAATTAGAACTGGCAGAAAACAGGGAGATTCTAAAGGAACCAATGCATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAATTACAGAAACAAGGGCAAGGTCAATGGACATATCAAATTTATCAAGAACCATTTAAAAATCTGAAAACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAGTTAACAGAGGCAGTGCAAAAAATAGCCATAGAAAGCATAGTGATATGGGGAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACATGGTGGATAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGTCAATACCCCTCCTTTAGTAAAATTATGGTACCAGTTAGAGAAGGAACCCATAATAGGAGCAGAAACTTTC\n+\t'D_UG_94_94UG114' CCAATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGGATGGATGGCCCAAAAGTTAAACAATGGCCGTTGACAGAAGAAAAAATAAAAGCACTAATAGAAATTTGTTCAGAACTAGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAACCCATACAATACTCCAATATTTGCCATAAAGAAAAAAGACAGTACTAAGTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTTTGGGAAGTTCAACTAGGAATACCACATCCTGCAGGGCTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGACGCATATTTTTCAGTTCCCTTACATGAAGACTTTAGAAAATATACCGCATTCACCATACCTAGTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCACAAGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAACCTTTTAGAAAACAAAATCCAGAAATGATTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAATAAAAATAGAGGAATTAAGGGGACACCTCTTGAAGTGGGGATTTACCACACCAGACAAAAAGTATCAGAAAGAACCCCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAGTGGACAGTACAGCCTATACATCTGCCAGAAAAGGAAAGCTGGACTGTCAATGATATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGCCAGATTTATCCAGGAATTAAAGTAAGACAATTATGCAAATGCCTTAGGGGAGCCAAAGCACTGACAGAAGTAATACCACTGACAGCAGAAGCAGAATTAGAACTGGCAGAAAACAGGGAAATACTAAAAGAACCAGTACATGGAGCGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAACAAGGGCAAGATCAATGGACATATCAAATATATCAAGAACAATATAAAAATCTGAAAACAGGAAAGTATGCGAAAATGAGGGGTACCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAGAAAATAGCCCAAGAATGTATAGTAATATGGGGAAAGACTCCTAAATTTAGACTACCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAGGCCACCTGGATTCCTGAGTGGGAGTATGTCAACACCCCTCCTTTAGTTAAATTATGGTATCAGTTAGAGAAGGAACCCATAGTAGGAGCAGAAACTTTC;\n+END;\n+\n+BEGIN TREES;\n+\tTREE tree = ((((D_CD_83_ELI,D_CD_83_NDK),D_UG_94_94UG114),D_CD_84_84ZR085),B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL),B_US_90_WEAU160));\n+END;\n" |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/busted-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out1.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,394 @@\n+{\n+ "Evidence Ratios":{\n+ "constrained": [\n+[1.751697313438667, 0.9490151622254345, 0.9575938099872893, 1.827482077500528, 1.505094606485015, 2.088346790071941, 7.070051504373732, 3.867967952992799, 2.545750919582881, 0.7247660693488289, 0.3196737937441124, 1.489449650902744, 0.6530151351740718, 1.04337285373284, 1.058333334239147, 0.5088801718500566, 0.8550055907613735, 1.110381942461004, 0.565683766000719, 0.6740763008813015, 0.4649952970969699, 0.4036426325687712, 2.442336342315371, 0.9859501295040206, 1.104892115806872, 1.062417300927637, 1.753888646580218, 1.31233150141181, 1.885518048500539, 0.7894296553774935, 0.723576644239061, 0.8827532839004689, 0.6984548336173313, 4.520258616283331, 0.501963856483453, 1.807812329244406, 0.6240669422720765, 0.9486848826066486, 0.9673516986934556, 1.479968294590536, 1.364799619489093, 1.709865961585205, 1.218557239747954, 0.7108467425303473, 0.3215450048962207, 2.271412336163041, 0.6355183534074139, 0.8839058954441763, 1.497501825835906, 2.637709102972778, 1.711470421506773, 3.027431470913309, 1.57278424917318, 3.277990564747366, 6.926286311855851, 3.784092751645639, 3.146955337815139, 1.955427417762355, 2.022694964562529, 0.666396825353515, 3.560060598929708, 1.666971860419219, 1.738637096007019, 3.220829375167113, 0.3447106216301303, 0.4881402535027675, 1.387141991322175, 0.5556476307196163, 0.6310295884570762, 0.4580705327203016, 0.4272583872429177, 2.901848650844198, 0.9999999999999991, 1.027519028508734, 2.915165037860989, 2.8354880840935, 1.858569677080054, 0.4521292148676688, 3.009136246768449, 0.705314987368983, 2.743480940643173, 0.3932432097494273, 0.9370673501878248, 0.4620247121091633, 2.83829096947346, 0.9007779218604833, 0.3302046680129435, 1.07627096358673, 1.391320542790854, 1.521972158264955, 0.4323783230969274, 2.334048026570822, 2.149795581008433, 3.074008352247498, 0.4499660997382409, 1.699461664815503, 0.8463586773204229, 2.696688856522739, 0.5804226171984278, 1.135876829610681, 0.8103519829402507, 2.896966803514224, 0.8351241901463535, 1.602690102144888, 0.7282588483860968, 2.78698806913424, 0.9149220061406503, 0.6214951247464974, 1.819052515045006, 0.2353728426618933, 2.441495991316177, 0.4689975029575301, 6.36479070098702, 0.501963856483453, 1.155173566804371, 0.3029791752249296, 3.710694239289469, 0.7371667962152887, 1.911346283016054, 0.3691203298834842, 1.027711744192628, 1.502724363578014, 0.3011502503588185, 0.9854850481813123, 0.3756291290353144, 4.112619261559145, 2.95680467264194, 0.4290868700547413, 0.4685206821924932, 0.4059560116267469, 2.50268310954176, 0.5227540827634783, 0.4671119113495291, 0.9338453011500626, 0.5571522059019809, 0.5886144003589358, 1.839204151926823, 1.060599026952742, 3.125234562282934, 2.54439731915596, 5.066889740057174, 2.915048895304102, 1.905524097635808, 2.212264991895895, 3.738815510070657, 2.074128973780481, 3.31083714843465, 0.6408491718084866, 3.068722634962862, 0.9229478196348808, 2.172843296216792, 1.750529904876356, 1.222415748191823, 1.340180507105605, 1.65676234501901, 1.177884311452671, 1.853985207061093, 1.949028686126, 1.848056555892881, 1.490331787720329, 2.808897643683787, 0.5370047325763545, 0.754447735175597, 0.292920631250886, 1.922199953975427, 0.2194780669088011, 2.411432550287456, 0.4936742969382611, 2.687417056073211, 0.8937719293629136, 0.630203462304753, 3.500554848762429, 0.8047116371904648, 2.9258711565943, 2.978602987543041, 1.892870394871532, 1.224886235480212, 3.334368853761007, 1.443700495825233, 1.7051887541283, 0.480593393899601, 0.907604501104216, 0.9198540076829841, 0.8702783448030316, 0.4699917745647508, 0.6213048344098008, 0.9960464828596589] \n+ ],\n+ "optimized null": [\n+[1.115754847329475, 0.9981043798375602, 0.9996678649277134, 1.027524895296611, 0.7950614097315224, 0.6815044886735678, 0.9660630441693723, 1.768207537367336, 1.995453831253169, 0.9376497008654193, 0.6553491413144868, 1.461081981960806, 1.013114798606584, 1.166859848568389, 0.60149018717580'..b'3156],\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":-3467.012706765863,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.9959842858928788, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":31\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+ "Unconstrained model":{\n+ "AIC-c":6910.776988890891,\n+ "Log Likelihood":-3414.491829601268,\n+ "Rate Distributions":{\n+ "Synonymous site-to-site rates":{\n+ "0":{\n+ "proportion":0.2655037162058198,\n+ "rate":0.2749303122566129\n+ },\n+ "1":{\n+ "proportion":0.6321791898264187,\n+ "rate":0.9740711294478059\n+ },\n+ "2":{\n+ "proportion":0.1023170939677615,\n+ "rate":3.041695877803997\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.386646389823596\n+ },\n+ "1":{\n+ "omega":0.9964438830494696,\n+ "proportion":0\n+ },\n+ "2":{\n+ "omega":1.876622752045829,\n+ "proportion":0.613353610176404\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":40\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/3/working/./input.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)Node3:0.08509899999999999,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":10.17667489929045,\n+ "p-value":0.003084133210483175\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":70\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":451\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":10\n+ },\n+ "Unconstrained BUSTED model fitting":{\n+ "order":2,\n+ "timer":370\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/busted-out2-1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out2-1.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,338 @@\n+{\n+ "Evidence Ratios":{\n+ "constrained": [\n+[0.935557169656361, 0.9478485707814517, 0.9365713272643597, 0.9348516866501475, 0.9478485707814517, 0.9470782825238451, 0.9404255507056813, 0.9445269614625446, 0.9357171171944089, 0.9445269614625446, 0.951038343352286, 0.9642191069363555, 0.9509681609268663, 0.9357171171944089, 0.9365508162861411, 0.9330337048596494, 0.9453769311406178, 0.9354507653189286, 0.9357171171944089, 0.951038343352286, 0.944959794342383, 0.951038343352286, 0.9554450473318812, 0.957741198595587, 0.9357223141306646, 0.9635859922205572, 0.9400812190552175, 0.9471227276423632, 0.9471155585144405, 0.951038343352286, 0.9425085292914046, 0.951038343352286, 0.9382075921692818, 0.9681439336221066, 9.055411306947674, 0.9467899324264936, 0.9478485707814517, 0.9398061397692539, 1.097085569751409, 1.371682580705311, 1.704754646360477, 0.9467899324264936, 0.9509681609268663, 0.9467899324264936, 0.9364415899930733, 0.951038343352286, 0.9478485707814517, 0.9525827524658199, 1.146813959542357, 0.9478485707814517, 0.9362276370626634, 0.9348516866501475, 0.9467899324264936, 0.9486832156560699, 0.9357171171944089, 0.9541686971206805, 0.9484511531422709, 0.9404255507056813, 0.9357171171944089, 1.072863229391129, 0.947891315956519, 0.938167627826613, 0.9425085292914046, 0.9509681609268663, 0.951038343352286, 0.9514408733975561, 0.9395660064639854, 0.9365128450433999, 0.9404014893688138, 0.9514344449206511, 0.957741198595587, 0.9388792918800136, 0.951038343352286, 0.9642191069363555, 0.9445269614625446, 0.9453769311406178, 0.9418928080136506, 0.9388792918800136, 0.9467899324264936, 0.9399880829471382, 0.9484511531422709, 0.9509681609268663, 1.153990916133998, 0.9404255507056813, 0.9554450473318812, 0.9412338215355154, 0.942333955072914, 0.957741198595587, 0.9470815762343416, 0.9449667231570663, 0.9557119925844111, 0.9676532717080474, 0.9365050172103501, 0.9425085292914046, 0.9357012899378949, 0.9407207493748144, 0.9348483936808639, 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0.9407207493748144, 0.9390630876730207,'..b'6807635995],\n+ [0.01505600521072376],\n+ [0.002882972930821469],\n+ [0.005825499564956559],\n+ [0.005903516300053625],\n+ [0.02274367484777162],\n+ [0.004355032959661065],\n+ [0.008800028033786655],\n+ [0.008917880494044083],\n+ [0.06143704799998004],\n+ [0.01176416611541591],\n+ [0.0237713451467977],\n+ [0.0240896977132239],\n+ [0.0262463496652457],\n+ [0.005025736545566795],\n+ [0.01015528996016046],\n+ [0.01029129247081581],\n+ [0.02256567087217255],\n+ [0.004320948178469224],\n+ [0.008731154380523415],\n+ [0.00884808446536876],\n+ [0.034087812394816],\n+ [0.006527245376826684],\n+ [0.01318932435908579],\n+ [0.01336595951511979],\n+ [0.01178447449308153],\n+ [0.02413128354890585],\n+ [0.0262916585104385],\n+ [0.005034412430862358],\n+ [0.01017282094890981],\n+ [0.01030905823951665],\n+ [0.004328407393735399],\n+ [0.008746226896405704],\n+ [0.008863358836639712],\n+ [0.03414665788893068],\n+ [0.006538513303760755],\n+ [0.0132120929750345],\n+ [0.01338903305480236] \n+ ],\n+ "Log Likelihood":-3176.217093030587,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *test*": [\n+[0.231720664913378, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":28\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":6683.094244259512,\n+ "Equilibrium frequencies": [\n+[0.4044507575757576],\n+ [0.1662878787878788],\n+ [0.2095643939393939],\n+ [0.2196969696969697] \n+ ],\n+ "Log Likelihood":-3320.503280793639,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.1815218119292989,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.08433479296165451,\n+ "Substitution rate from nucleotide C to nucleotide G":0.1775869374255926,\n+ "Substitution rate from nucleotide C to nucleotide T":1.184827038118431,\n+ "Substitution rate from nucleotide G to nucleotide T":0.04288318031815568\n+ },\n+ "display order":0,\n+ "estimated parameters":21\n+ },\n+ "Unconstrained model":{\n+ "AIC-c":6391.938375474656,\n+ "Log Likelihood":-3163.666348620609,\n+ "Rate Distributions":{\n+ "Test":{\n+ "0":{\n+ "omega":0.1490485393860332,\n+ "proportion":0.02658974082564446\n+ },\n+ "1":{\n+ "omega":0.169565784922581,\n+ "proportion":0.9641001770967245\n+ },\n+ "2":{\n+ "omega":15.09387961636913,\n+ "proportion":0.009310082077631076\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":32\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpfqvtss8b/job_working_directory/000/5/working/./input.nex",\n+ "number of sequences":8,\n+ "number of sites":440,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9)"\n+ }\n+ },\n+ "test results":{\n+ "LRT":8.711160142067456,\n+ "p-value":0.006417496108925114\n+ },\n+ "tested":{\n+ "0":{\n+ "B_FR_83_HXB2":"test",\n+ "B_US_83_RF":"test",\n+ "B_US_86_JRFL":"test",\n+ "B_US_90_WEAU160":"test",\n+ "D_CD_83_ELI":"test",\n+ "D_CD_83_NDK":"test",\n+ "D_CD_84_84ZR085":"test",\n+ "D_UG_94_94UG114":"test",\n+ "Node1":"test",\n+ "Node10":"test",\n+ "Node2":"test",\n+ "Node3":"test",\n+ "Node9":"test"\n+ }\n+ },\n+ "timers":{\n+ "Constrained BUSTED model fitting":{\n+ "order":3,\n+ "timer":23\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":133\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":4\n+ },\n+ "Unconstrained BUSTED model fitting":{\n+ "order":2,\n+ "timer":105\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/busted-out2-2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out2-2.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b"@@ -0,0 +1,1730 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 8;\n+\tTAXLABELS\n+\t\t'B_FR_83_HXB2' 'B_US_83_RF' 'B_US_86_JRFL' 'B_US_90_WEAU160' 'D_CD_83_ELI' 'D_CD_83_NDK' 'D_CD_84_84ZR085' 'D_UG_94_94UG114' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 1320;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t;\n+\n+MATRIX\n+\t'B_FR_83_HXB2' CCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC\n+\t'B_US_83_RF' CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAGGAAAAAATAAAAGCATTGGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCCAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAGTTAGGAATACCACATCCTGCAGGGTTAAAAAAGAAGAAATCAGTAACAGTATTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGAGTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAAACACCACGGATTAGATATCAGTACAATGTGCTTCCACAAGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGTATGACAAAAATCTTAGAGCCTTTTAAAAAACAAAATCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGATTTAGAAATAGGGCAGCATAGAATAAAAATAGAGGAACTGAGAGAACATCTGTTAAAGTGGGGGTTTACCACACCGGACAAGAAACATCAGAAAGAACCTCCATTTCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACAACTAACAAAAGAAGCAGAGCTAGAACTGGCAGAAAATAGGGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATACCAAATTTATCAAGAGCCATTTAAAAACCTGAAAACAGGAAAGTATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTACAAAAAGTAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAGGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTAAAATTGTGGTACCAGTTAGAAAAAGAACCCATAATAGGAGCAGAAACTTTC\n+\t'B_US_86_JRFL' CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTCAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAGAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAATATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCGCAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAATTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAGCAAAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGGTTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGACAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTAAATTGGGCAAGTCAGATTTACGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAGCCAGTACATGGAGTGTATTATGACCCATCAAAAGACT"..b'nt_3[60][31]:=0.1712746635706107*t*busted.test.theta_CT*busted.test.omega3;\n+busted.test_Q_component_3[60][47]:=0.2567033972679326*t*busted.test.theta_GT*busted.test.omega3;\n+busted.test_Q_component_3[60][49]:=0.4256503784977386*t*busted.test.theta_AT*busted.test.omega3;\n+busted.test_Q_component_3[60][53]:=0.1818409092376876*t*busted.test.theta_CT*busted.test.omega3;\n+busted.test_Q_component_3[60][56]:=0.1563402972714242*t*busted.test.theta_GT*busted.test.omega3;\n+busted.test_Q_component_3[60][57]:=0.5074830879161225*t*busted.test.theta_AT*busted.test.omega3;\n+busted.test_Q_component_3[60][58]:=0.09717451507454297*t*busted.test.theta_CT;\n+busted.test_Q_component_3[60][59]:=0.1963563685387479*t*busted.test.theta_GT*busted.test.omega3;\n+\n+\n+busted.test_pi={\n+{0.07535940345366139} \n+{0.01443006409728228} \n+{0.02915821068672351} \n+{0.02954870567752823} \n+{0.03219408024958758} \n+{0.006164627375802654} \n+{0.01245659774045292} \n+{0.01262342001471309} \n+{0.0276793164843978} \n+{0.005300125700761717} \n+{0.01070973633984303} \n+{0.01085316415297191} \n+{0.0418125103783387} \n+{0.008006395714089126} \n+{0.01617817990958604} \n+{0.0163948426631036} \n+{0.0409913146415633} \n+{0.007849150478922548} \n+{0.01586044121725868} \n+{0.01607284872448998} \n+{0.01751178502783737} \n+{0.003353213651232053} \n+{0.006775694789785172} \n+{0.006866436807635995} \n+{0.01505600521072376} \n+{0.002882972930821469} \n+{0.005825499564956559} \n+{0.005903516300053625} \n+{0.02274367484777162} \n+{0.004355032959661065} \n+{0.008800028033786655} \n+{0.008917880494044083} \n+{0.06143704799998004} \n+{0.01176416611541591} \n+{0.0237713451467977} \n+{0.0240896977132239} \n+{0.0262463496652457} \n+{0.005025736545566795} \n+{0.01015528996016046} \n+{0.01029129247081581} \n+{0.02256567087217255} \n+{0.004320948178469224} \n+{0.008731154380523415} \n+{0.00884808446536876} \n+{0.034087812394816} \n+{0.006527245376826684} \n+{0.01318932435908579} \n+{0.01336595951511979} \n+{0.01178447449308153} \n+{0.02413128354890585} \n+{0.0262916585104385} \n+{0.005034412430862358} \n+{0.01017282094890981} \n+{0.01030905823951665} \n+{0.004328407393735399} \n+{0.008746226896405704} \n+{0.008863358836639712} \n+{0.03414665788893068} \n+{0.006538513303760755} \n+{0.0132120929750345} \n+{0.01338903305480236} \n+};\n+Model busted.test=(\'Exp(busted.test_Q_component_1)*1*busted.test.bsrel_mixture_aux_0+Exp(busted.test_Q_component_2)*1*(1-busted.test.bsrel_mixture_aux_0)*busted.test.bsrel_mixture_aux_1+Exp(busted.test_Q_component_3)*1*(1-busted.test.bsrel_mixture_aux_0)*(1-busted.test.bsrel_mixture_aux_1)\',busted.test_pi,EXPLICIT_FORM_MATRIX_EXPONENTIAL);\n+TRY_NUMERIC_SEQUENCE_MATCH=0;\n+ACCEPT_ROOTED_TREES=0;\n+\n+UseModel (busted.test);\n+Tree cuWdXMfP.tree_id_0=((((D_CD_83_ELI,D_CD_83_NDK)Node3,D_UG_94_94UG114)Node2,D_CD_84_84ZR085)Node1,B_US_83_RF,((B_FR_83_HXB2,B_US_86_JRFL)Node10,B_US_90_WEAU160)Node9);\n+\n+cuWdXMfP.tree_id_0.D_CD_83_ELI.t=0.1377903766097694;\n+cuWdXMfP.tree_id_0.D_CD_83_NDK.t=0.06607109645594529;\n+cuWdXMfP.tree_id_0.Node3.t=0.0890081009446355;\n+cuWdXMfP.tree_id_0.D_UG_94_94UG114.t=0.4322474154485661;\n+cuWdXMfP.tree_id_0.Node2.t=0.01436667144151429;\n+cuWdXMfP.tree_id_0.D_CD_84_84ZR085.t=0.2152052309993384;\n+cuWdXMfP.tree_id_0.Node1.t=0.1867555551194544;\n+cuWdXMfP.tree_id_0.B_US_83_RF.t=0.2093873697545922;\n+cuWdXMfP.tree_id_0.B_FR_83_HXB2.t=0.08552069057797769;\n+cuWdXMfP.tree_id_0.B_US_86_JRFL.t=0.1313117411090917;\n+cuWdXMfP.tree_id_0.Node10.t=0.01181372524396516;\n+cuWdXMfP.tree_id_0.B_US_90_WEAU160.t=0.1600546391700751;\n+cuWdXMfP.tree_id_0.Node9.t=0.03506352054252541;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);\n+SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);\n+\n+DataSet busted.codon_data = ReadDataFile(USE_NEXUS_FILE_DATA);\n+DataSetFilter busted.filter.default = CreateFilter(busted.codon_data,3,"0-1319","4,5,7,6,1,0,2,3","TAA,TAG,TGA");\n+ASSUME_REVERSIBLE_MODELS=1;\n+USE_LAST_RESULTS=0;\n+LikelihoodFunction cuWdXMfP.likelihoodFunction = (busted.filter.default,cuWdXMfP.tree_id_0);\n+\n+END;\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/cfel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cfel-out1.json Wed Jun 09 07:03:54 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 f304c108aa1f test-data/conv-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conv-in1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/conv-out1.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conv-out1.nex Wed Jun 09 07:03:54 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 f304c108aa1f test-data/fade-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/fade-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/fade-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-out1.json Wed Jun 09 07:03:54 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, 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["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 f304c108aa1f test-data/fel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fel-out1.json Wed Jun 09 07:03:54 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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0.03121207319557584, 0.8597680862487451, 3.015865008244778],\n+ [3.805655301370652, 0, 0.7005303037771143, 11.62838958327228, 0.0006495276635800629, 1.696119588919385],\n+ [3.173406516538895, 2.860065663238961, 2.926441853316894, 0.003891888657044262, 0.9502562372040178, 5.080474489659786],\n+ [0, 0, 0, 0, 1, 0],\n+ [2.194271257132928, 4.019627316522699, 3.237226152191341, 0.09176983643381931, 0.7619391181878015, 6.130458650322728],\n+ [0, 0.2994174888128062, 0.1834705090468997, 0.9675444779876443, 0.3252933434590788, 0.3838044222970849],\n+ [1.737488918246139, 0.4263169813102716, 0.5705211950188817, 0.9504457433159637, 0.3296058631975952, 1.320839860569391],\n+ [9.491047642026737e-16, 2.201411562959478, 1.602398780540194, 2.916382754860905, 0.08768422447478674, 2.82185084281439],\n+ [1.033236674389839, 0.5673779129005597, 0.6682462878144323, 0.1916420169326862, 0.6615534805841186, 1.187783044398971],\n+ [0.6633763440867723, 2.065196310532788, 1.40713862608088, 0.9931353495817845, 0.318977273245592, 2.942901296371888],\n+ [3.88753619664278e-15, 1.779262169776622, 1.549159808629328, 1.288480285336618, 0.2563282037478503, 2.280724121673174],\n+ [137.6200023666397, 1.712312972734741, 2.612335663828599, 4.571254357285468, 0.03251275075427451, 63.52993609974021],\n+ [0.9069803858948896, 1.008331374883533, 0.9795641413367016, 0.006632998551161506, 0.9350894763840309, 1.696743112350582],\n+ [1.250218074119796, 2.685270528336648, 2.279331033581541, 0.4656302199387952, 0.4950043706394306, 3.99928134132692],\n+ [0.5981237480607854, 1.191515517605649, 0.9684057167421628, 0.3651500230254783, 0.5456598635374844, 1.793902873797072],\n+ [5.567356236371868, 1.655977785625157, 2.134648959148231, 0.8514639837247273, 0.3561385136046764, 4.60397510129604],\n+ [0, 0, 0, 0, 1, 0],\n+ [0.5915176036957202, 0.7772525687759813, 0.7215979531128016, 0.05398776775817282, 0.8162640993312603, 1.259941036310695],\n+ [0, 0.543676760549953, 0.4362855008937696, 0.8539326132569869, 0.3554421959431151, 0.6969049998601837],\n+ [1.00226665989553, 0.6268338660673796, 0.7169253651929272, 0.1172739583266811, 0.7320101172431673, 1.250193047146509],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [2.797676857161142, 0.824684447244541, 1.167394064072366, 1.285234262338761, 0.2569280765461694, 2.303990803636788]\n+ ]\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/fubar-in1.fa.gz |
| b |
| Binary file test-data/fubar-in1.fa.gz has changed |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/fubar-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-in1.nhx Wed Jun 09 07:03:54 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +((KF790010:0.001247,CY147300:0.000623):0.0,((CY168239:0.001872,(CY171039:0.001874,KF790389:0.000623):0.000624):0.0,((CY141224:0.001247,(CY147305:0.0,KF790037:0.000623):0.000623):0.0,(((KF790403:0.000623,KF761507:0.001876):0.0,KC526205:0.000623):0.0,((CY169303:0.0,(KF789585:0.000623,CY141202:0.000623):0.000623):0.000623,(((KJ667974:0.002501,KJ938675:0.001873):0.000623,CY134876:0.0):0.000623,((KF790414:0.001248,(KF790384:0.001245,KF790408:0.00125):0.0):0.0,((KF886352:0.001882,(KF790438:0.000623,CY134996:0.001873):0.000623):0.001875,(KF789591:0.001879,((KF790049:0.001255,(CY134956:0.000624,CY183153:0.000624):0.000626):0.001249,((CY168407:0.004394,CY183065:0.003128):0.0,(KF598733:0.002501,((KC892174:0.0,(KF685747:0.000624,CY168471:0.000625):0.00375):0.000624,(((KC892685:0.000624,KC892641:0.0):0.001874,KC893110:0.001249):0.0,(KC892480:0.0,(JX913043:0.001249,(KF551075:0.00125,((CY114509:0.0,(KC892889:0.0,KC893018:0.002498):0.005006):0.001877,(((KC892519:0.0,KC892498:0.000624):0.002497,KC892266:0.000623):0.001026,((KC892156:0.003756,(JX978746:0.001256,KC892407:0.001883):0.001875):0.00355,((KC535402:0.000623,(KC882488:0.002498,KC535387:0.001247):0.001872):0.0,(KC535363:0.000623,((KC535396:0.000623,(KC882883:0.0,KC882867:0.000623):0.003124):0.0,((KC535378:0.001872,KC535375:0.002498):0.0,(GQ385891:0.001248,((EU779522:0.001251,(CY037727:0.0,FJ179354:0.003124):0.0):0.000623,((GQ385889:0.005007,(FJ686933:0.001243,FJ179356:0.003117):0.0):0.000622,(CY173095:0.001245,(((CY173191:0.0,CY037703:0.001247):0.000622,CY035062:0.00249):0.0,((CY173255:0.001871,(CY044748:0.0,GQ385846:0.001247):0.000623):0.0,((CY027075:0.000623,(EU199367:0.0,CY172823:0.000623):0.0):0.000623,(((CY172847:0.000623,CY025643:0.0):0.000623,CY172839:0.000623):0.001247,(((CY026251:0.002497,CY092241:0.00125):0.000624,CY026019:0.000623):0.0,((CY025341:0.002502,(CY172775:0.001247,CY172903:0.000623):0.001248):0.000622,(EU199255:0.003134,(CY172431:0.000621,((CY172223:0.003127,(CY172191:0.001254,CY020069:0.000628):0.000621):0.0,((CY092217:0.003119,(CY025485:0.001283,EU516019:0.00059):0.008843):0.001868,(CY002080:0.000622,((CY002064:0.001873,(CY002456:0.000626,CY002048:0.002491):0.001243):0.003763,(AB434109:0.006307,(((CY088198:0.001245,CY088475:0.000621):0.0,CY000257:0.000621):0.002494,((CY112957:0.003135,CY006859:0.001253):0.000616,((CY000721:0.001243,(CY114493:0.0,CY090885:0.002483):0.002488):0.0,((CY001792:0.000621,(CY001600:0.00062,CY002368:0.001865):0.0):0.0,((CY002304:0.002489,(CY006163:0.001242,CY003632:0.00062):0.0):0.00062,(CY001920:0.003739,(CY001912:0.002498,((CY001504:0.0,CY006060:0.001241):0.00062,((CY001744:0.0,CY002136:0.00124):0.00062,((CY114309:0.003746,(CY006899:0.001874,CY112901:0.001863):0.002496):0.000618,(((CY006579:0.001245,CY006283:0.000621):0.001244,CY007979:0.001864):0.0,((CY006499:0.001241,(CY006491:0.001863,CY006635:0.00124):0.0):0.00062,(((CY036847:0.002495,CY010004:0.001867):0.000621,CY012200:0.000621):0.0,(((CY010028:0.001242,CY009732:0.001242):0.0,CY010012:0.002484):0.001875,(((CY010020:0.002497,CY011416:0.001237):0.001252,CY009484:0.00062):0.005658,((CY010036:0.0,(CY039879:0.002489,CY039880:0.000621):0.002487):0.003109,((CY010628:0.000619,(CY010716:0.002485,CY010516:0.001239):0.0):0.000619,((CY012728:0.0,CY013701:0.000621):0.001243,(((CY012760:0.001239,CY013200:0.001239):0.0,CY011888:0.005614):0.0,((CY013693:0.000619,(CY012184:0.002484,CY013669:0.00124):0.00124):0.0,((CY112669:0.004353,(CY112556:0.001861,CY011896:0.000619):0.00186):0.0,(CY112605:0.001243,(CY012224:0.006953,((CY012512:0.000619,(CY012896:0.00062,CY012232:0.00062):0.000621):0.0,(CY011848:0.0,(((CY011328:0.0,CY114221:0.000619):0.001241,CY011560:0.00124):0.0,((CY012456:0.000619,CY011824:0.00124):0.0,CY017283:0.000619):0.0):0.0):0.0):0.002439):0.008263):0.000618):0.0):0.0):0.000617):0.012609):0.000619):0.001215):0.003782):0.000613):0.006878):0.0):0.001862):0.0):0.0):0.001863):0.001862):0.001245):0.0):0.001241):0.021084):0.000623):0.00065):0.003713):0.002495):0.0):0.005637):0.00313):0.002515):0.001876):0.0):0.000623):0.0):0.003749):0.0):0.0):0.000623):0.000623):0.001872):0.002503):0.0):0.0):0.000623):0.001468):0.00189):0.002721):0.002524):0.0):0.000624):0.0):0.0):0.0):0.000623):0.001248):0.001255):0.000619):0.0):0.0):0.0):0.000623):0.0):0.0):0.0):0.0; |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/fubar-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fubar-out1.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
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"Node84":"test",\n+ "Node85":"test",\n+ "Node86":"test",\n+ "Node90":"test",\n+ "Node91":"test",\n+ "Node93":"test",\n+ "Node96":"test",\n+ "Node97":"test",\n+ "Node99":"test"\n+ }\n+ },\n+ "timers":{\n+ "Grid Calculations":{\n+ "order":2,\n+ "timer":81\n+ },\n+ "Nucleotide Fit":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":87\n+ },\n+ "Posterior estimation":{\n+ "order":3,\n+ "timer":1\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/gard-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-in1.fa Wed Jun 09 07:03:54 2021 +0000 |
| b |
| @@ -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 +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAGCTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO4 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCATACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO5 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO6 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAATACATAAAAACCC-AATTC--ACACCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO7_1 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO8 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGAATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO9 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACAT +CAATTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO10 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +CACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCC +CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGCACATAAAGCCATTTATCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO11_1 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGAC +TACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCTGCC +CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTGTCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGCACATAAAGTCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC +>BRO12 +ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGG +TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC +ATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGAC +TACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCTC +CC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACAT +CAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAAC +CTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATA +GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC \ No newline at end of file |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/gard-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-out1.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| @@ -0,0 +1,55 @@ +{ + "analysis":{ + "authors":"Sergei L Kosakovsky Pond", + "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901", + "contact":"spond@temple.edu", + "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. v0.2 adds and spooling results to JSON after each breakpoint search conclusion", + "requirements":"A sequence alignment.", + "version":"0.2" + }, + "baselineScore":1450.968340148184, + "bestModelAICc":1450.968340148184, + "breakpointData":{ + "bps": [ +[1, 428] + ], + "tree":"((BRO1_1:0,BRO2:0.007408926175080497)Node1:0,(BRO3_1:0.002455524404855022,BRO4:0.002457415365886074)Node4:0,(((BRO5:0.002464479112430666,(BRO6:0.004940850926103086,BRO7_1:0)Node11:0)Node9:0.002460542727794925,(BRO9:0.004931390913247289,((BRO10:0.002933649980980302,BRO11_1:0.01453409151831228)Node17:0.002436921831192641,BRO12:0.006987081661112447)Node16:0.005417113782285573)Node14:0)Node8:0,BRO8:0.002462026756884335)Node7:0)" + }, + "input":{ + "file name":"/tmp/tmpht3ax8lq/job_working_directory/000/2/working/./input.fasta", + "number of sequences":12, + "number of sites":428, + "partition count":1 + }, + "potentialBreakpoints":21, + "singleTreeAICc":1450.968340686507, + "siteBreakPointSupport":{ + "130":7.71938316947624e-08, + "150":7.49872016582054e-06, + "158":4.898720800158644e-06, + "175":0.0001152764571690805, + "176":0.000624401895637527, + "183":8.845949780426112e-06, + "196":5.17454230945286e-06, + "197":5.9168232845333e-06, + "198":4.436819044306368e-05, + "227":2.830236103715775e-06, + "233":9.74236872039044e-06, + "241":1.802640814372882e-05, + "245":1.305334911931824e-05, + "252":8.580180939514955e-06, + "253":2.317805781298633e-05, + "260":1.77855732841814e-06, + "287":4.449903505856628e-07, + "325":6.636014843884652e-09, + "326":2.134836027957093e-09, + "334":7.302354343864046e-09, + "341":1.678880851117679e-09, + "358":6.863087158511391e-14 + }, + "timeElapsed":8, + "totalModelCount":209, + "trees":{ + "newickString":"((BRO1_1:0,BRO2:0.007408926175080497)Node1:0,(BRO3_1:0.002455524404855022,BRO4:0.002457415365886074)Node4:0,(((BRO5:0.002464479112430666,(BRO6:0.004940850926103086,BRO7_1:0)Node11:0)Node9:0.002460542727794925,(BRO9:0.004931390913247289,((BRO10:0.002933649980980302,BRO11_1:0.01453409151831228)Node17:0.002436921831192641,BRO12:0.006987081661112447)Node16:0.005417113782285573)Node14:0)Node8:0,BRO8:0.002462026756884335)Node7:0)" + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/gard-out1.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-out1.nex Wed Jun 09 07:03:54 2021 +0000 |
| b |
| @@ -0,0 +1,37 @@ +#NEXUS + +BEGIN TAXA; + DIMENSIONS NTAX = 12; + TAXLABELS + 'BRO1_1' 'BRO2' 'BRO3_1' 'BRO4' 'BRO5' 'BRO6' 'BRO7_1' 'BRO9' 'BRO10' 'BRO11_1' 'BRO12' 'BRO8' ; +END; + +BEGIN CHARACTERS; + DIMENSIONS NCHAR = 428; + FORMAT + DATATYPE = DNA + GAP=- + MISSING=? + ; + +MATRIX + 'BRO1_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO2' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACCCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTGCATAAAGCCATTTACCGTACATAGCACATTATA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO3_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAGCTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO4' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCATACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO5' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO6' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAATACATAAAAACCC-AATTC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO7_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACACCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO9' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAATTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO10' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGCACATAAAGCCATTTATCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO11_1' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACTACCTGTAGTACATAAAAACCC-AACCC--ACATCAAAA----CCCTGCCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTGTCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGCACATAAAGTCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO12' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACAGTACCATAAA-TACTTGACTACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCTCCC-CATGCTTACAAGCAAGTACAGCAATCAACCTTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGGATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC + 'BRO8' ATTCTAATTTAAACTATTCT-CTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTAC-TGCCAGCCACCATGAATATTGTACGGTACCATAAA-TACTTGACCACCTGTAGTACATAAAAACCC-AATCC--ACATCAAAA----CCCCCCCCC-CATGCTTACAAGCAAGTACAGCAACCAACCCTCAA-CTATCACACATCAACTGCAACTCCAAAGCCAC-CCCTCACCCAC-TAGAATACCAACAAACCTACCCACCC-TTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-TCAGAT-AGGGGTCCCTTGACCACCATCC; +END; + +BEGIN ASSUMPTIONS; + CHARSET span_1 = 1-428; +END; +BEGIN TREES; + TREE tree_1 = (((BRO1_1:1e-10,BRO2:0.007446048662499141)Node2:1.699082282683926e-05,(((BRO5:0.002291051777868712,(BRO6:0.004965711012353363,BRO7_1:1e-10)Node9:0.0001955595843124865)Node7:0.002191267352110732,(BRO9:0.004469023573866088,((BRO10:0.002870586428367251,BRO11_1:0.01462820627459318)Node15:0.001454707803761366,BRO12:0.006027959855484483)Node14:0.005661145911839864)Node12:0.0003039715029625697)Node6:0.0002803682303139691,BRO8:0.002464847898104024)Node5:1.386828770154629e-05)Node1:3.347353150116037e-06,BRO3_1:0.002467834453766899,BRO4:0.002462875913900023); +END; |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/meme-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/meme-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/meme-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-out1.json Wed Jun 09 07:03:54 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, 0],\n+ [0, 0, 0, 4.065768798286446, 1, 0, 0.6666666666666666, 0, 0.1455427970670232],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [6.565759874687353, 0, 0.10495989356895, 0, 0.89504010643105, 0, 0.6666666666666666, 0, 0.1032447536564542],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [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+ [10.49514785248221, 0, 1.14531252379555e-10, 0, 0.9999999998854687, 0, 0.6666666666666666, 0, 0.1650332901748387],\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+ [13.09135310777685, 0, 5.726562618977749e-11, 0, 0.9999999999427344, 0, 0.6666666666666666, 0, 0.2058578980100819],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [12.37490343362032, 0, 0.05858880329925001, 0, 0.94141119670075, 0, 0.6666666666666666, 0, 0.1945919255213972],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [987.5019115722299, 0, 0.0004, 0, 0.9996, 0, 0.6666666666666666, 0, 15.52819377215],\n+ [14.55761344047962, 3.151090015539141, 0, 3.15098583171967, 1, 0, 0.6666666666666666, 0, 0.3417106414963155],\n+ [0, 0, 0, 5.632316287317649, 1, 0, 0.6666666666666666, 0, 0.2016206791610606],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [5.480073695171225, 0, 5.529684747073369e-10, 0, 0.9999999994470316, 0, 0.6666666666666666, 0, 0.08617263949271516],\n+ [0, 0, 0, 2.821925207775446, 1, 0, 0.6666666666666666, 0, 0.1010167838433599],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0],\n+ [7.490255319000378, 0, 2.281746655933769e-10, 0, 0.9999999997718253, 0, 0.6666666666666666, 0, 0.1177821881996506],\n+ [17.81018664392365, 0, 0'..b'.01220539771302355],\n+ [0.01297489997065711],\n+ [0.01419701929364967],\n+ [0.02306796533539959],\n+ [0.0138011088931582],\n+ [0.01467121445635504],\n+ [0.01605311140503505],\n+ [0.03067687144383888],\n+ [0.01835336741416609],\n+ [0.01951047494908151],\n+ [0.02134818687672324],\n+ [0.02126077850204813],\n+ [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 f304c108aa1f test-data/params.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/params.json Wed Jun 09 07:03:54 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 f304c108aa1f test-data/prime-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/prime-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/prime-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-out1.json Wed Jun 09 07:03:54 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 f304c108aa1f test-data/relax-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/relax-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/relax-in2.nex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nex Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b"@@ -0,0 +1,86 @@\n+#NEXUS\n+\n+[\n+Generated by HYPHY 0.9920070619beta(MP) for MacOS(Carbon) on Thu Jun 21 16:59:04 2007\n+\n+]\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 10;\n+\tTAXLABELS\n+\t\t'Human' 'Chimp' 'Baboon' 'RhMonkey' 'Cow' 'Pig' 'Horse' 'Cat' 'Mouse' 'Rat' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 561;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t;\n+\n+MATRIX\n+\t'Human' AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'Chimp' GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'Baboon' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'RhMonkey' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'Cow' ------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT\n+\t'Pig' ---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT\n+\t'Horse' ------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGA"..b'GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC\n+\t\'Mouse\' ---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC\n+\t\'Rat\' ---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC;\n+END;\n+\n+BEGIN TREES;\n+\tTREE tree = ((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey{PR}:0.002015,Baboon{PR}:0.003108){PR}:0.022733,(Human{PR}:0.004349,Chimp{PR}:0.000799){PR}:0.011873){PR}:0.101856){PR}:0.340802,Rat:0.050958,Mouse:0.097950);\n+END;\n+\n+BEGIN HYPHY;\n+\n+DATA_PANEL_SOURCE_PATH="";\n+DataSet CD2 = ReadDataFile (USE_NEXUS_FILE_DATA);\n+DataSetFilter CD2_part = CreateFilter (CD2,3,"0-560","(null)","TAA,TAG,TGA");\n+Tree CD2_tree=((((Pig,Cow)Node3,Horse,Cat)Node2,((RhMonkey,Baboon)Node9,(Human,Chimp)Node12)Node8)Node1,Rat,Mouse);\n+OpenDataPanel(CD2,"(null)","0,0,0,0,2,0,10","MG94xREV_3x4,6,0,14443523,CD2_tree",CD2_LF);\n+\n+global CD2_part_Shared_AC=0.5710714109234631;\n+global CD2_part_Shared_AT=0.2756961373814887;\n+global CD2_part_Shared_CG=0.4456308760366715;\n+global CD2_part_Shared_CT=0.9454291760502562;\n+global CD2_part_Shared_GT=0.3224080259059006;\n+CD2_tree.Node12.synRate=0.08168540352543764;\n+CD2_tree.Node8.nonSynRate=0.2938890030949185;\n+CD2_tree.Human.synRate=1e-30;\n+CD2_tree.Baboon.nonSynRate=0;\n+CD2_tree.Baboon.synRate=0.01716650886630832;\n+CD2_tree.Node12.nonSynRate=0.02962786133931161;\n+CD2_tree.Chimp.synRate=1e-30;\n+CD2_tree.Chimp.nonSynRate=0.005834136861061837;\n+CD2_tree.Node9.nonSynRate=0.0433794394076959;\n+CD2_tree.Human.nonSynRate=0;\n+CD2_tree.Node9.synRate=0.1139808847086709;\n+CD2_tree.Node8.synRate=0.1586154947684889;\n+CD2_tree.Rat.synRate=0.1533251749656354;\n+CD2_tree.Mouse.nonSynRate=0.2332402459120736;\n+CD2_tree.Mouse.synRate=0.4604267094040578;\n+CD2_tree.Rat.nonSynRate=0.1585006932449144;\n+CD2_tree.Node1.nonSynRate=0.5097883291072822;\n+CD2_tree.Node1.synRate=1.227004762734591;\n+CD2_tree.RhMonkey.synRate=0;\n+CD2_tree.Node3.synRate=0.1877287558837553;\n+CD2_tree.Pig.nonSynRate=0.4826366809736332;\n+CD2_tree.Horse.nonSynRate=0.518627673056701;\n+CD2_tree.Cow.nonSynRate=0.681831503936737;\n+CD2_tree.Cat.synRate=0.4672127128189641;\n+CD2_tree.Node3.nonSynRate=0.2648957141533021;\n+CD2_tree.Horse.synRate=0.430860769501357;\n+CD2_tree.Pig.synRate=0.3721230153643161;\n+CD2_tree.Node2.synRate=0.2137858662796737;\n+CD2_tree.RhMonkey.nonSynRate=0.01161863878954486;\n+CD2_tree.Cat.nonSynRate=0.7203773170684773;\n+CD2_tree.Node2.nonSynRate=0.1379570235930709;\n+CD2_tree.Cow.synRate=0.3646221318370894;\n+\n+END;\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/relax-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/relax-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out1.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| b'@@ -0,0 +1,492 @@\n+{\n+ "analysis":0,\n+ "branch attributes":{\n+ "0":{\n+ "Baboon":{\n+ "General descriptive":0.001858767762813579,\n+ "MG94xREV with separate rates for branch sets":0.001769472024099301,\n+ "Nucleotide GTR":0.001680040630127455,\n+ "RELAX alternative":0.001872256662230973,\n+ "RELAX null":0.001855569334462731,\n+ "RELAX partitioned descriptive":0.001898170574782418,\n+ "k (general descriptive)":0.09971581394819819,\n+ "original name":"Baboon"\n+ },\n+ "Cat":{\n+ "General descriptive":0.3644803308678196,\n+ "MG94xREV with separate rates for branch sets":0.2796030091674721,\n+ "Nucleotide GTR":0.2660909938917123,\n+ "RELAX alternative":0.3689219388980864,\n+ "RELAX null":0.3256077554105627,\n+ "RELAX partitioned descriptive":0.3717219559832593,\n+ "k (general descriptive)":2.314507643873676,\n+ "original name":"Cat"\n+ },\n+ "Chimp":{\n+ "General descriptive":0.001848680051431209,\n+ "MG94xREV with separate rates for branch sets":0.001825434296531533,\n+ "Nucleotide GTR":0.001818373670119325,\n+ "RELAX alternative":0.001831703934281931,\n+ "RELAX null":0.00183525802483954,\n+ "RELAX partitioned descriptive":0.001832717232153088,\n+ "k (general descriptive)":5.261186652622472,\n+ "original name":"Chimp"\n+ },\n+ "Cow":{\n+ "General descriptive":0.3733627618450006,\n+ "MG94xREV with separate rates for branch sets":0.2520490246808783,\n+ "Nucleotide GTR":0.2481025999892287,\n+ "RELAX alternative":0.342739998512865,\n+ "RELAX null":0.2948256709356563,\n+ "RELAX partitioned descriptive":0.3466331923230422,\n+ "k (general descriptive)":2.846155982935764,\n+ "original name":"Cow"\n+ },\n+ "Horse":{\n+ "General descriptive":0.2802176313870697,\n+ "MG94xREV with separate rates for branch sets":0.2158304510870495,\n+ "Nucleotide GTR":0.2090310577070883,\n+ "RELAX alternative":0.3058487498567987,\n+ "RELAX null":0.2559911331878715,\n+ "RELAX partitioned descriptive":0.3034694616209482,\n+ "k (general descriptive)":1.926646959057857,\n+ "original name":"Horse"\n+ },\n+ "Human":{\n+ "General descriptive":0,\n+ "MG94xREV with separate rates for branch sets":0,\n+ "Nucleotide GTR":0,\n+ "RELAX alternative":0,\n+ "RELAX null":0,\n+ "RELAX partitioned descriptive":0,\n+ "k (general descriptive)":1.462532487172471,\n+ "original name":"Human"\n+ },\n+ "Mouse":{\n+ "General descriptive":0.1307950021191255,\n+ "MG94xREV with separate rates for branch sets":0.1197727080219867,\n+ "Nucleotide GTR":0.1180171198334285,\n+ "RELAX alternative":0.1346501492117481,\n+ "RELAX null":0.1468861666244963,\n+ "RELAX partitioned descriptive":0.1475623398849678,\n+ "k (general descriptive)":0.4639609139295889,\n+ "original name":"Mouse"\n+ },\n+ "Node1":{\n+ "General descriptive":0.350050900813081,\n+ "MG94xREV with separate rates for branch sets":0.2857356440257563,\n+ "Nucleotide GTR":0.2767237570684924,\n+ "RELAX alternative":0.3856490868629754,\n+ "RELAX null":0.4521046025119397,\n+ "RELAX partitioned descriptive":0.4358952685746469,\n+ "k (general descriptive)":0.458870761901378\n+ },\n+ "Node12":{\n+ "General descriptive":0.01766384491594095,\n+ "MG94xREV with separate rates for branch sets":0.01800001211221997,\n+ "Nucleotide GTR":0.01784803874223016,\n+ "RELAX alternative":0.01835132674304535,\n+ "RELAX null":0.0182458522959868,\n+ "RELAX partitioned descriptive":0.01878351896299688,\n+ "k (general descriptive)":0.1241597340554799\n+ },\n+ "Node2":{\n+ "General descriptive":0.05771641706257456,\n+ "MG94xREV with separate rates for branch sets":0.06169547093990335,\n+ "Nucleotide GTR":0.06613162123865737,\n+ "REL'..b' "omega":2.19971015101232,\n+ "proportion":0.4620912608347691\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":1.054840660215593e-44,\n+ "proportion":0.4504132080156107\n+ },\n+ "1":{\n+ "omega":1.054840660215593e-44,\n+ "proportion":0.08749553114962015\n+ },\n+ "2":{\n+ "omega":6.350765030542244,\n+ "proportion":0.4620912608347691\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":36\n+ },\n+ "RELAX null":{\n+ "AIC-c":6946.046672507471,\n+ "Log Likelihood":-3437.336313352972,\n+ "Rate Distributions":{\n+ "Reference":{\n+ "0":{\n+ "omega":0.1150006822953211,\n+ "proportion":0.542405144031307\n+ },\n+ "1":{\n+ "omega":0.2401508033814633,\n+ "proportion":0.08223353569636478\n+ },\n+ "2":{\n+ "omega":3.69263720947284,\n+ "proportion":0.3753613202723282\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0.1150006822953211,\n+ "proportion":0.542405144031307\n+ },\n+ "1":{\n+ "omega":0.2401508033814633,\n+ "proportion":0.08223353569636478\n+ },\n+ "2":{\n+ "omega":3.69263720947284,\n+ "proportion":0.3753613202723282\n+ }\n+ }\n+ },\n+ "display order":3,\n+ "estimated parameters":35\n+ },\n+ "RELAX partitioned descriptive":{\n+ "AIC-c":6937.04707353565,\n+ "Log Likelihood":-3427.626871923648,\n+ "Rate Distributions":{\n+ "Reference":{\n+ "0":{\n+ "omega":0.1943306885168281,\n+ "proportion":0.3359458135547653\n+ },\n+ "1":{\n+ "omega":0.2607558478587815,\n+ "proportion":0.4332550437039296\n+ },\n+ "2":{\n+ "omega":4.134271224300374,\n+ "proportion":0.2307991427413052\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.4753488415962343\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.03858318603767072\n+ },\n+ "2":{\n+ "omega":6.017221959238516,\n+ "proportion":0.486067972366095\n+ }\n+ }\n+ },\n+ "display order":5,\n+ "estimated parameters":40\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/3/working/./input.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)Node3:0.08509899999999999,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":16.20300116404087,\n+ "p-value":5.690389451429301e-05,\n+ "relaxation or intensification parameter":2.344938789085876\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"Reference",\n+ "Cat":"Test",\n+ "Chimp":"Reference",\n+ "Cow":"Test",\n+ "Horse":"Test",\n+ "Human":"Reference",\n+ "Mouse":"Reference",\n+ "Node1":"Reference",\n+ "Node12":"Reference",\n+ "Node2":"Reference",\n+ "Node3":"Reference",\n+ "Node8":"Reference",\n+ "Node9":"Reference",\n+ "Pig":"Reference",\n+ "Rat":"Reference",\n+ "RhMonkey":"Reference"\n+ }\n+ },\n+ "timers":{\n+ "General descriptive model fitting":{\n+ "order":2,\n+ "timer":132\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":324\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":8\n+ },\n+ "RELAX alternative model fitting":{\n+ "order":3,\n+ "timer":65\n+ },\n+ "RELAX null model fitting":{\n+ "order":4,\n+ "timer":66\n+ },\n+ "RELAX partitioned descriptive":{\n+ "order":5,\n+ "timer":53\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/relax-out2-1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out2-1.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,525 @@\n+{\n+ "Synonymous site-posteriors": [\n+[0.2717348381268465, 0.5635158143073038, 0.5580958985234344, 0.4419267392327456, 0.1775513314393873, 0.01303903284026798, 0.00125071980641974, 0.2376006215377312, 0.8837687913991302, 0.697488732253998, 0.76440666757549, 0.1859131352278527, 0.4676839084660329, 0.5320161033357819, 0.4513687349306337, 0.8514990846254493, 0.9101555767748879, 0.9112112654445478, 0.9624478616388369, 0.9472735837633918, 0.8715894173292342, 0.9248557783401865, 0.3852870058193366, 0.7504386709677574, 0.7275694213063354, 0.1979029930878776, 0.2585255313006612, 0.426812371619399, 0.03564414482172501, 0.3292941826787388, 0.1427864928730872, 0.8324822227281018, 0.9311167984186458, 0.1209539167468769, 0.8726642109588801, 1.798577785061191e-05, 0.584102863529593, 0.5747348035616634, 0.5814406651776627, 0.02251840852563282, 0.1607002230623373, 0.499402751628698, 0.9327364905381349, 0.1164578922551683, 0.7414294602970922, 0.04004321943657974, 0.1252919499200681, 0.7016909689123084, 0.3099147090319344, 0.1594271385761372, 0.001721088532959928, 0.0002106542138058178, 0.7670245595319366, 0.01765606757145387, 0.08528617939935416, 0.01185048796937841, 0.008218049898468071, 0.294285815926654, 0.4088819101657737, 0.1819814701794264, 0.06741006997792491, 0.1648869485561294, 0.6641637464726119, 0.1696421815033135, 0.5337345685031449, 0.9785329157950278, 0.6089117121305408, 0.9214198863478258, 0.7040511824729966, 0.8748810706893103, 0.7603207301908244, 0.1587648197710778, 0.28009015626025, 0.9473769917649164, 0.03667497185975328, 0.6646432746680839, 0.005707942217110617, 0.4172795698582943, 0.002426641321239203, 0.9036479890682162, 0.8165937919459629, 0.5380686752231248, 0.8348947378138256, 0.8825623566861087, 0.003194607014896987, 0.1034323185116836, 0.1251183560640448, 0.6731739154042389, 0.02049494631105097, 0.7272701824195644, 0.9376578101739967, 0.03161216349993828, 0.08060038603464466, 0.05713766811791781, 0.7236799166647727, 0.03049686563145122, 0.4831167820690108, 0.3259152163804719, 0.9355990871535625, 0.2598255955335131, 0.649043721535527, 0.1395744847880144, 0.8655465087299661, 0.5535165112383126, 0.8759601400318501, 0.1331847979385494, 0.9385179832315519, 0.9590294197009215, 0.1177725177949566, 0.5310119897564728, 0.04436932195281112, 0.877273324169318, 0.07309972300058731, 0.8726642109588801, 0.0823189228969842, 0.674523501474146, 0.4093792912564727, 0.8837869026711356, 0.1208432028324516, 0.7875716367935024, 0.9342090047974666, 0.7281976470761374, 0.6335560301454017, 0.2642816632435872, 0.7601746562441594, 0.3971532429331721, 0.07967254820654134, 0.9205611063156326, 0.4126590346311199, 0.4718488374006657, 0.2324587146851173, 0.2530879180545083, 0.6735650752750825, 0.6778765556227805, 0.9393601651000962, 0.1757530496502532, 0.3931715696771638, 0.7913247469383754, 0.05849180455884406, 0.007027787474985664, 0.002980098295172601, 0.188566078048928, 0.02837364230845984, 0.008078062694748547, 0.4539148488391334, 0.2698860362225194, 0.03514662617223248, 0.8484422182215356, 0.5225500090930265, 0.8755046006217432, 0.01843684138990366, 0.6656855504934923, 0.7055653078864003, 0.236066638653311, 0.1567944657161159, 0.8781825877891227, 0.4362059051173987, 0.163327088806649, 0.004489982631214889, 0.03278376720971195, 0.03145887036879619, 0.6158371404365816, 0.8645373560796752, 0.6351698115277034, 0.04852978149651612, 0.2563374460202912, 0.07868312568368593, 0.9507071563814276, 0.007940480658871889, 0.9455733391892027, 0.4761025393051341, 0.06329409664274364, 0.486108446887078, 0.6554607928409875, 0.3294403859657761, 0.02718898835050054, 0.2632599441236705, 0.09462189267290307, 0.2747185708643275, 0.01971954733787938, 0.9591589529807978, 0.445066915720239, 0.7380186230528726, 0.3686112558749921, 0.9765948224615983, 0.9830372572797934, 0.3428744949444181],\n+ [0.6626894690463668, 0.4168101145890417, 0.4227716136375318, 0.5460469376257381, 0.7920802349484392, 0.9148946082433389, 0.6025519507878634, 0.757695330723024'..b'+ "proportion":0\n+ },\n+ "2":{\n+ "omega":1.00002621592498,\n+ "proportion":0.6185938027364208\n+ }\n+ }\n+ },\n+ "display order":2,\n+ "estimated parameters":41\n+ },\n+ "RELAX null":{\n+ "AIC-c":6910.777215627525,\n+ "Log Likelihood":-3414.491942969586,\n+ "Rate Distributions":{\n+ "Reference":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.04600287725570656\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.3432466763494891\n+ },\n+ "2":{\n+ "omega":1.896477292815783,\n+ "proportion":0.6107504463948045\n+ }\n+ },\n+ "Synonymous site-to-site rates":{\n+ "0":{\n+ "proportion":0.2641095265325168,\n+ "rate":0.2744837794048847\n+ },\n+ "1":{\n+ "proportion":0.6330324513232739,\n+ "rate":0.9729462345446451\n+ },\n+ "2":{\n+ "proportion":0.1028580221442092,\n+ "rate":3.029415427453047\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.04600287725570656\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.3432466763494891\n+ },\n+ "2":{\n+ "omega":1.896477292815783,\n+ "proportion":0.6107504463948045\n+ }\n+ }\n+ },\n+ "display order":3,\n+ "estimated parameters":40\n+ },\n+ "RELAX partitioned descriptive":{\n+ "AIC-c":6909.42794543134,\n+ "Log Likelihood":-3408.579104294618,\n+ "Rate Distributions":{\n+ "Reference":{\n+ "0":{\n+ "omega":0.05035684771569529,\n+ "proportion":0.3805224005150026\n+ },\n+ "1":{\n+ "omega":0.07013486723985318,\n+ "proportion":0.003462124163764896\n+ },\n+ "2":{\n+ "omega":2.344944921144001,\n+ "proportion":0.6160154753212325\n+ }\n+ },\n+ "Test":{\n+ "0":{\n+ "omega":0,\n+ "proportion":0.03160127773820932\n+ },\n+ "1":{\n+ "omega":0,\n+ "proportion":0.4079248249859382\n+ },\n+ "2":{\n+ "omega":1.11269394570475,\n+ "proportion":0.5604738972758525\n+ }\n+ }\n+ },\n+ "display order":5,\n+ "estimated parameters":45\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmpbauyxvdv/job_working_directory/000/5/working/./input.nex",\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":11.47546300090198,\n+ "p-value":0.0007052107640865835,\n+ "relaxation or intensification parameter":2.986519568748539e-05\n+ },\n+ "tested":{\n+ "0":{\n+ "BABOON":"Test",\n+ "CAT":"Reference",\n+ "CHIMP":"Test",\n+ "COW":"Reference",\n+ "HORSE":"Reference",\n+ "HUMAN":"Test",\n+ "MOUSE":"Reference",\n+ "Node1":"Test",\n+ "Node12":"Test",\n+ "Node2":"Reference",\n+ "Node3":"Reference",\n+ "Node8":"Test",\n+ "Node9":"Test",\n+ "PIG":"Reference",\n+ "RAT":"Reference",\n+ "RHMONKEY":"Test"\n+ }\n+ },\n+ "timers":{\n+ "General descriptive model fitting":{\n+ "order":2,\n+ "timer":127\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":645\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":8\n+ },\n+ "RELAX alternative model fitting":{\n+ "order":3,\n+ "timer":178\n+ },\n+ "RELAX null model fitting":{\n+ "order":4,\n+ "timer":115\n+ },\n+ "RELAX partitioned descriptive":{\n+ "order":5,\n+ "timer":216\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/relax-out2-2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out2-2.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b"@@ -0,0 +1,3427 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 10;\n+\tTAXLABELS\n+\t\t'HUMAN' 'CHIMP' 'BABOON' 'RHMONKEY' 'COW' 'PIG' 'HORSE' 'CAT' 'MOUSE' 'RAT' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 561;\n+\tFORMAT\n+\t\tDATATYPE = DNA\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t;\n+\n+MATRIX\n+\t'HUMAN' AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'CHIMP' GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'BABOON' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'RHMONKEY' AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC\n+\t'COW' ------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT\n+\t'PIG' ---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT\n+\t'HORSE' ------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATAT"..b'023*t*relax._shared_srv.rv_gdd*relax.test.theta_CT*relax.test.omega3;\n+relax.test_Q_component_3[60][56]:=0.1659124550130927*t*relax._shared_srv.rv_gdd*relax.test.theta_GT*relax.test.omega3;\n+relax.test_Q_component_3[60][57]:=0.2714859010999351*t*relax._shared_srv.rv_gdd*relax.test.theta_AT*relax.test.omega3;\n+relax.test_Q_component_3[60][58]:=0.2217183243979596*t*relax._shared_srv.rv_gdd*relax.test.theta_CT;\n+relax.test_Q_component_3[60][59]:=0.2755785876068215*t*relax._shared_srv.rv_gdd*relax.test.theta_GT*relax.test.omega3;\n+\n+\n+relax.test_pi={\n+{0.04876086397632926} \n+{0.03982224127745371} \n+{0.0494959405650269} \n+{0.04152830682371345} \n+{0.01810345074594235} \n+{0.01478480742075003} \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+Model relax.test=(\'Exp(relax.test_Q_component_1)*1*relax.test.bsrel_mixture_aux_0+Exp(relax.test_Q_component_2)*1*(1-relax.test.bsrel_mixture_aux_0)*relax.test.bsrel_mixture_aux_1+Exp(relax.test_Q_component_3)*1*(1-relax.test.bsrel_mixture_aux_0)*(1-relax.test.bsrel_mixture_aux_1)\',relax.test_pi,EXPLICIT_FORM_MATRIX_EXPONENTIAL);\n+TRY_NUMERIC_SEQUENCE_MATCH=0;\n+ACCEPT_ROOTED_TREES=0;\n+Tree O_SJmzEX.tree_id_0=((((PIG{relax.reference},COW{relax.reference})Node3{relax.reference},HORSE{relax.reference},CAT{relax.reference})Node2{relax.reference},((RHMONKEY{relax.test},BABOON{relax.test})Node9{relax.test},(HUMAN{relax.test},CHIMP{relax.test})Node12{relax.test})Node8{relax.test})Node1{relax.test},RAT{relax.reference},MOUSE{relax.reference});\n+\n+O_SJmzEX.tree_id_0.PIG.t=0.4536172365685577;\n+O_SJmzEX.tree_id_0.COW.t=0.6103212983838633;\n+O_SJmzEX.tree_id_0.Node3.t=0.2484758643179366;\n+O_SJmzEX.tree_id_0.HORSE.t=0.4753747079725157;\n+O_SJmzEX.tree_id_0.CAT.t=0.6775352409130856;\n+O_SJmzEX.tree_id_0.Node2.t=0.1183276378467358;\n+O_SJmzEX.tree_id_0.RHMONKEY.t=0.01420592464486799;\n+O_SJmzEX.tree_id_0.BABOON.t=0.00485857082125907;\n+O_SJmzEX.tree_id_0.Node9.t=0.1015257435189256;\n+O_SJmzEX.tree_id_0.HUMAN.t=0;\n+O_SJmzEX.tree_id_0.CHIMP.t=0.006303088015069631;\n+O_SJmzEX.tree_id_0.Node12.t=0.05697754732758539;\n+O_SJmzEX.tree_id_0.Node8.t=0.4948729770972781;\n+O_SJmzEX.tree_id_0.Node1.t=1.445991686991002;\n+O_SJmzEX.tree_id_0.RAT.t=0.1315597576696033;\n+O_SJmzEX.tree_id_0.MOUSE.t=0.2736332745970835;SetParameter (DEFER_CONSTRAINT_APPLICATION, 1, 0);\n+SetParameter (DEFER_CONSTRAINT_APPLICATION, 0, 0);\n+\n+DataSet relax.codon_data = ReadDataFile(USE_NEXUS_FILE_DATA);\n+DataSetFilter relax.filter.default = CreateFilter(relax.codon_data,3,"0-560","5,4,6,7,3,2,0,1,9,8","TAA,TAG,TGA");\n+ASSUME_REVERSIBLE_MODELS=1;\n+USE_LAST_RESULTS=0;\n+LikelihoodFunction O_SJmzEX.likelihoodFunction = (relax.filter.default,O_SJmzEX.tree_id_0);\n+\n+END;\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/slac-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/slac-out1.json Wed Jun 09 07:03:54 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 f304c108aa1f test-data/sm19-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in1.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/sm19-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in2.nhx Wed Jun 09 07:03:54 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 f304c108aa1f test-data/sm19-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out1.json Wed Jun 09 07:03:54 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 f304c108aa1f test-data/sm19-out2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out2.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/strike-ambigs-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-in1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/strike-ambigs-in2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-in2.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/strike-ambigs-out1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-out1.fa Wed Jun 09 07:03:54 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 f304c108aa1f test-data/strike-ambigs-out2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-out2.fa Wed Jun 09 07:03:54 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' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/ORF6-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6-segment.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,7 @@\n+{\n+ "ORF6": {\n+ "map": [],\n+ "tree": "(REFERENCE,(gb_MW505295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3142_2021_Segment_null_Host_Human,gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human)Node184,epi_isl_1533799_hCoV_19_India_MH_NCCS_9947_2021,gb_MW155738_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11358_2020_Segment_null_Host_Human,gb_MW064840_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_QDX_825_2020_Segment_null_Host_Human,(gb_MW545306_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3723_2021_Segment_null_Host_Human,gb_MW547503_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC09I039_2020_Segment_null_Host_Human)Node194,(epi_isl_1543980_hCoV_19_Singapore_490_2021,gb_MW565832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0724_2021_Segment_null_Host_Human)Node198,(gb_MW093451_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_DSHS_0533_2020_Segment_null_Host_Human,gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human)Node201,(gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human,gb_MW156732_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10631_2020_Segment_null_Host_Human)Node206,epi_isl_1631286_hCoV_19_England_CAMC_14E7527_2021,gb_MW486406_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2638_2020_Segment_null_Host_Human,gb_MW035934_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_2214_2020_Segment_null_Host_Human,gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human,gb_MW154411_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC6964_2020_Segment_null_Host_Human,gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human,gb_MW134116_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_3258_2020_Segment_null_Host_Human,(gb_MW549937_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3900_2021_Segment_null_Host_Human,gb_MW549223_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3727_2020_Segment_null_Host_Human)Node226,((gb_MW545248_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3654_2021_Segment_null_Host_Human,gb_MW578246_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0808_2021_Segment_null_Host_Human)Node231,gb_MW549830_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2465_2020_Segment_null_Host_Human)Node230,gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human,epi_isl_1589923_hCoV_19_India_WB_1930300571091_2021,gb_MW539842_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00583_2020_Segment_null_Host_Human,(gb_MW208032_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_1590_2020_Segment_null_Host_Human,gb_MW056168_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_U'..b'piratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human,gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human,gb_MW406537_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_2_3693679_2020_Segment_null_Host_Human,gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human,(gb_MW156645_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11076_2020_Segment_null_Host_Human,gb_MW156971_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10203_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_MW420890_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2020316507_2020_Segment_null_Host_Human)Node62,epi_isl_1589926_hCoV_19_India_WB_1930300586246_2021,(gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human,gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human)Node71,gb_MW064863_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_QDX_779_2020_Segment_null_Host_Human,gb_MW155278_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12385_2020_Segment_null_Host_Human,epi_isl_1442952_hCoV_19_Singapore_321_2021,gb_MW193966_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_nimh_12171_2020_Segment_null_Host_Human,gb_MW462661_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2263_2020_Segment_null_Host_Human,epi_isl_1516887_hCoV_19_Australia_QLD1826_2021,gb_MW521810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3530_2020_Segment_null_Host_Human,gb_MW490888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2295_2020_Segment_null_Host_Human,gb_MW155642_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13394_2020_Segment_null_Host_Human,gb_MT847221_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_283_2020_Segment_null_Host_Human,gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human,gb_MW578233_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0795_2021_Segment_null_Host_Human,gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human,gb_MW543030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9A_6594_2020_Segment_null_Host_Human,gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human,gb_MT873189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_DPH_00301_2020_Segment_null_Host_Human,(gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human,gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human)Node100,gb_MT811511_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1079_SAN_2020_Segment_null_Host_Human)",\n+ "tree_tags": {}\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/ORF6-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6-site.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/ORF6.FADE.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.FADE.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,3142 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "A":{\n+ "0": [\n+[0.8995906688309242, 5.594143577985283, 0.946609453050319, 0.985559664964498],\n+ [1.044067957308116, 5.592799085749478, 0.9466955286719859, 0.9872409006967756],\n+ [1.036405878450414, 5.592977245431012, 0.9467064115746399, 0.9874538531239992],\n+ [1.19730312499705, 5.591581681880384, 0.9467807517201779, 0.9889108417502863],\n+ [0.834106476942848, 4.607368577968402, 0.9445445107901261, 0.9467914811705906],\n+ [1.594329564126259, 5.58405032798539, 0.9498733406998108, 1.053351676897583],\n+ [1.044067957308116, 5.592799085749476, 0.9466955286719857, 0.9872409006967714],\n+ [9.963744241830298, 5.54757896832387, 0.949796513525156, 1.051654650196095],\n+ [0.8341064769428478, 4.607368577968402, 0.9445445107901261, 0.9467914811705906],\n+ [0.8263616796556617, 4.962381890578685, 0.9452991472766892, 0.9606199984313556],\n+ [1.355846770273862, 5.587576320848405, 0.9468186115030929, 0.9896544191230371],\n+ 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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/ORF6.MEME-full.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.MEME-full.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,2444 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[235.7472979068722, 0, 1, 0.9943760343206508, 0, 0, 0.6666666666666666, 0, 0, -31.93549672470295, -31.93549672470295],\n+ [3.125033384621221, 0, 1, 6.6249901946859, 0, 0, 0.6666666666666666, 0, 0, -43.49839666606186, -43.49831167050982],\n+ [1.901386439598346, 0, 1, 3.602316293041297, 0, 0, 0.6666666666666666, 0, 0, -17.09092958578331, -17.09092776449802],\n+ [1.622684212345616, 0, 1, 3.145879239633445, 0, 0, 0.6666666666666666, 0, 0, -61.02813244305516, -61.02813244305516],\n+ [0.8148105398437983, 0, 1, 1.499991884237639, 0, 0, 0.6666666666666666, 0, 0, -25.26062185068822, -25.26062185068822],\n+ [0.538978592942964, 0.01746277867903197, 1e-08, 9.230771679231886, 0.9999999899999999, 3.131671475355084, 0.09963705217536034, 1, 0, -30.93250048026707, -30.93322087121525],\n+ [1.853606022970019, 0, 1, 3.674707574937826, 0, 0, 0.6666666666666666, 0, 0, -28.34059025069893, -28.34050231902417],\n+ [0, 0, 0.01, 12.19527240220381, 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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/ORF6.SLAC.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.SLAC.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,4781 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0":{\n+ "by-branch":{\n+ "AVERAGED": [\n+[0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [44.30740262828303, 130.37043765588, 1, 0, 0.2536521092555556, 0.02256959200225525, 0, -0.02222397288334375, 1, 0.2536521092555557, 0.005580025520913685],\n+ [44.15327252744373, 130.5245677567193, 0, 1, 0.2527697414601411, 0, 0.007661392925382973, 0.007544070296234822, 0.7472302585398589, 1, 0.00558460667963908],\n+ [44.08153844682656, 130.6786978575586, 1, 0, 0.252240094079802, 0.02268523366547771, 0, -0.02233784366963816, 1, 0.252240094079802, 0.005586229046527186],\n+ [43.99914242660442, 130.6786978575586, 0, 1, 0.2518873736647267, 0, 0.007652356630382193, 0.007535172378406127, 0.7481126263352733, 1, 0.005579404930925916],\n+ [44.21306418682298, 130.4647760973401, 0, 1, 0.2531120382236115, 0, 0.00766490412135378, 0.007547527723557193, 0.7468879617763885, 1, 0.005577806290397803],\n+ 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1, 0],\n+ [44.21306418682298, 130.4647760973401, 0, 1, 0.2531120382236115, 0, 0.00766490412135378, 0.007547527723557193, 0.7468879617763885, 1, 0.005582536378668013],\n+ [43.99914242660442, 130.6786978575586, 0, 1, 0.2518873736647267, 0, 0.007652356630382193, 0.007535172378406127, 0.7481126263352733, 1, 0.005610995690299318],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [43.99914242660442, 130.6786978575586, 1, 0, 0.2518873736647267, 0.02272771569737101, 0, -0.02237967515355384, 1, 0.2518873736647267, 0.005612056496775136],\n+ [44.367616686608, 130.3102235975551, 0, 1, 0.2539968241789083, 0, 0.007673994966721572, 0.007556479356396646, 0.7460031758210917, 1, 0.005611861400289367],\n+ [44.2948056817287, 130.5969563626529, 1, 0, 0.2532698233693144, 0.02257601054140064, 0, -0.02223029313228328, 1, 0.2532698233693145, 0.005581838321706729],\n+ [44.15327252744373, 130.5245677567193, 0, 1, 0.2527697414601412, 0, 0.007661392925382975, 0.007544070296234824, 0.7472302585398588, 1, 0.005581838321706729],\n+ [43.99914242660442, 130.6786978575586, 0, 1, 0.2518873736647267, 0, 0.007652356630382193, 0.007535172378406127, 0.7481126263352733, 1, 0.005612261737859944],\n+ [43.84501232576511, 130.832827958398, 0, 1, 0.2510050058693121, 0, 0.007643341626139722, 0.007526295425300025, 0.7489949941306879, 1, 0.005614125291650073],\n+ [43.78522066638586, 130.8926196177772, 0, 1, 0.2506627091058418, 0, 0.007639850152897275, 0.007522857418682301, 0.7493372908941582, 1, 0.005614188942122219],\n+ [44.01629825618177, 130.8717871833653, 0, 1, 0.2516826583443658, 0, 0.007641066279616809, 0.007524054922263002, 0.7483173416556342, 1, 0.005612328366098883],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [44.08219297214297, 130.508685322092, 0, 1, 0.252488522898'..b'acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0808_2021_Segment_null_Host_Human":"test",\n+ "gb_MW583187_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OK_CDC_STM_000003021_2021_Segment_null_Host_Human":"test",\n+ "gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586184_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005891_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005477_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586385_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000005076_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586419_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IA_CDC_STM_000005050_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_QDX_4292_2021_Segment_null_Host_Human":"test",\n+ "gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human":"test",\n+ "gb_MW592782_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2311_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_1171_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593378_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_8518_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593611_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_7938_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human":"test",\n+ "gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human":"test",\n+ "gb_MW598427_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_nmimr_SARS_CoV_2_NTRA_15010_2020_Segment_null_Host_Human":"test",\n+ "gb_MW599514_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00376_2021_Segment_null_Host_Human":"test",\n+ "gb_MW599662_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_Broad_RIDOH_00108_2020_Segment_null_Host_Human":"test"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "Primary SLAC analysis":{\n+ "order":2,\n+ "timer":1\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":4\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/ORF6.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.combined.fas Wed Jun 09 07:03:54 2021 +0000 |
| b |
| b'@@ -0,0 +1,531 @@\n+>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1284652/hCoV-19/Germany/SN-RKI-I-038291/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCACAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1442952/hCoV-19/Singapore/321/2021\n+ATGTTTCATCTCGTTGGCTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1512225/hCoV-19/USA/GA-CDC-STM-000041012/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGTACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1470937/hCoV-19/USA/NY-PRL-2021_03_29_01C17/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAC\n+\n+>epi_isl_1516887/hCoV-19/Australia/QLD1826/2021\n+ATGTTTCATCTCGTTGACTTTCATGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATCTGT\n+\n+>epi_isl_1533799/hCoV-19/India/MH-NCCS-9947/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATACTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1543980/hCoV-19/Singapore/490/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATTTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1589923/hCoV-19/India/WB-1930300571091/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAAGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1589926/hCoV-19/India/WB-1930300586246/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAATTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1631286/hCoV-19/England/CAMC-14E7527/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACTAATGGAGATTGAT\n+\n+\n+>REFERENCE\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human\n+AGATGTTATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MT860680_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_DRICM_isl_MH_09_2020_Segment_null_Host_Human\n+ATGCTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW571108_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS49_2021_Segment_null_Host_Human\n+ATGTATCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAAT'..b'AATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW521749_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NV_QDX_3543_2020_Segment_null_Host_Human\n+ATGTTTCATCTCGTTTACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTATATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human\n+ATGTTTCATCTCTTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATCCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW571185_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS69_2021_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTCTC\n+\n+>gb_MT745746_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_SA01_2020_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAC\n+\n+>gb_MW156732_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10631_2020_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTGTTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW435625_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_DSHS_1968_2020_Segment_null_Host_Human\n+ATGTTTCATTTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW420890_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2020316507_2020_Segment_null_Host_Human\n+ATGTTTCATTTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTTAT\n+\n+>gb_MW155387_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13741_2020_Segment_null_Host_Human\n+ATGTTTTATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW193966_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_nimh_12171_2020_Segment_null_Host_Human\n+ATTTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW560924_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00280_2021_Segment_null_Host_Human\n+CAGATGCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/ORF6.labels.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.labels.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| b'@@ -0,0 +1,179 @@\n+{\n+ "REFERENCE":"Reference",\n+ "epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021":"B-1-617",\n+ "epi_isl_1284652/hCoV-19/Germany/SN-RKI-I-038291/2021":"B-1-617",\n+ "epi_isl_1442952/hCoV-19/Singapore/321/2021":"B-1-617",\n+ "epi_isl_1470937/hCoV-19/USA/NY-PRL-2021_03_29_01C17/2021":"B-1-617",\n+ "epi_isl_1512225/hCoV-19/USA/GA-CDC-STM-000041012/2021":"B-1-617",\n+ "epi_isl_1516887/hCoV-19/Australia/QLD1826/2021":"B-1-617",\n+ "epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021":"B-1-617",\n+ "epi_isl_1533799/hCoV-19/India/MH-NCCS-9947/2021":"B-1-617",\n+ "epi_isl_1543980/hCoV-19/Singapore/490/2021":"B-1-617",\n+ "epi_isl_1589923/hCoV-19/India/WB-1930300571091/2021":"B-1-617",\n+ "epi_isl_1589926/hCoV-19/India/WB-1930300586246/2021":"B-1-617",\n+ "epi_isl_1631286/hCoV-19/England/CAMC-14E7527/2021":"B-1-617",\n+ "gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human":"Reference",\n+ 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"gb_MW586419_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IA_CDC_STM_000005050_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_QDX_4292_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW592782_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2311_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_1171_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593378_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_8518_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593611_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_7938_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW598427_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_nmimr_SARS_CoV_2_NTRA_15010_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW599514_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00376_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW599662_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_Broad_RIDOH_00108_2020_Segment_null_Host_Human":"Reference"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/merged-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/merged-segment.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,132 @@\n+{\n+ "nsp7": {\n+ "map": [],\n+ "tree": "((gb_MT470179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_France_40002VJ_2020_Segment_null_Host_Human,gb_MW460617_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_2810_2020_Segment_null_Host_Human)Node387,REFERENCE,gb_MW556183_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_CDC_9MR4_8909_2021_Segment_null_Host_Human,gb_MT834677_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_0519_2020_Segment_null_Host_Human,gb_MW406516_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AR_CDC_2_3693765_2020_Segment_null_Host_Human,gb_MW586766_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4270_2021_Segment_null_Host_Human,gb_MW276413_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_10909_2020_Segment_null_Host_Human,(gb_MT973055_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC6608_2020_Segment_null_Host_Human,gb_MW517337_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0048_2021_Segment_null_Host_Human)Node365,(gb_MW562693_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102046035_2020_Segment_null_Host_Human,((gb_MT628199_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1525_2020_Segment_null_Host_Human,gb_MW276545_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11572_2020_Segment_null_Host_Human)Node373,gb_MW276613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11950_2020_Segment_null_Host_Human)Node372)Node370,gb_MW585982_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_000003668_2021_Segment_null_Host_Human,gb_MW486275_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2499_2020_Segment_null_Host_Human,gb_MW586167_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000005966_2021_Segment_null_Host_Human,gb_MW571123_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS68_2021_Segment_null_Host_Human,gb_MW525001_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000014_B04_2021_Segment_null_Host_Human,gb_MT810681_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1240_SAN_2020_Segment_null_Host_Human,gb_MW566853_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2890_2020_Segment_null_Host_Human,gb_MW579014_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101155076_2021_Segment_null_Host_Human,gb_MW518128_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_STM_291_2021_Segment_null_Host_Human,gb_MW570895_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00321_2021_Segment_null_Host_Human,gb_MW550719_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_2_3768763_2020_Segment_null_Host_Human,gb_MW420777_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012868464_2020_Segment_null_Host_Human,gb_MW586286_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005415_2021_Segment_null_Host_Human,gb_MW548941_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_S'..b'piratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human,gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human,gb_MW406537_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_2_3693679_2020_Segment_null_Host_Human,gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human,(gb_MW156645_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11076_2020_Segment_null_Host_Human,gb_MW156971_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10203_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_MW420890_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2020316507_2020_Segment_null_Host_Human)Node62,epi_isl_1589926_hCoV_19_India_WB_1930300586246_2021,(gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human,gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human)Node71,gb_MW064863_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_QDX_779_2020_Segment_null_Host_Human,gb_MW155278_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12385_2020_Segment_null_Host_Human,epi_isl_1442952_hCoV_19_Singapore_321_2021,gb_MW193966_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_nimh_12171_2020_Segment_null_Host_Human,gb_MW462661_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2263_2020_Segment_null_Host_Human,epi_isl_1516887_hCoV_19_Australia_QLD1826_2021,gb_MW521810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3530_2020_Segment_null_Host_Human,gb_MW490888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2295_2020_Segment_null_Host_Human,gb_MW155642_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13394_2020_Segment_null_Host_Human,gb_MT847221_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_283_2020_Segment_null_Host_Human,gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human,gb_MW578233_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0795_2021_Segment_null_Host_Human,gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human,gb_MW543030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9A_6594_2020_Segment_null_Host_Human,gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human,gb_MT873189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_DPH_00301_2020_Segment_null_Host_Human,(gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human,gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human)Node100,gb_MT811511_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1079_SAN_2020_Segment_null_Host_Human)",\n+ "tree_tags": {}\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/merged-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/merged-site.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp7-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7-segment.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,7 @@\n+{\n+ "nsp7": {\n+ "map": [],\n+ "tree": 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"tree_tags": {}\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp7-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7-site.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp7.FADE.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.FADE.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,3775 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "A":{\n+ "0": [\n+[2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129],\n+ [2.693374054144683, 5.447411670296412, 0.9467570683845876, 0.9955252951947779],\n+ [1.688653150925858, 5.451721466912741, 0.9466016845428151, 0.9924655022317769],\n+ [2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129],\n+ [1.895030664619211, 4.52086406954309, 0.9445058895733424, 0.9528696179522672],\n+ [1.758305195386422, 3.944714326314311, 0.9429120087101439, 0.9247026627110535],\n+ [2.693374054144683, 5.447411670296409, 0.9467570683845873, 0.9955252951947714],\n+ [3.496602106477276, 5.440799403189085, 0.9468488043583334, 0.9973401437079507],\n+ [1.543475628257214, 3.863513868034641, 0.9427148781074345, 0.9213279007167833],\n+ [2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129],\n+ [1.758305195386422, 3.944714326314311, 0.9429120087101438, 0.9247026627110516],\n+ [1.758305195386422, 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Fit":{\n+ "order":1,\n+ "timer":525\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":680\n+ },\n+ "Residue A analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue C analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue D analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue E analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue F analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue G analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue H analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue I analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue K analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue L analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue M analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue N analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue P analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue Q analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue R analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue S analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue T analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue V analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue W analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue Y analysis":{\n+ "order":21,\n+ "timer":8\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp7.MEME-full.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.MEME-full.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp7.SLAC.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.SLAC.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
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"gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585982_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_000003668_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585995_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WV_CDC_STM_000003152_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586140_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005978_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586167_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000005966_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586286_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005415_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586766_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4270_2021_Segment_null_Host_Human":"test",\n+ "gb_MW589574_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4494168_2021_Segment_null_Host_Human":"test",\n+ "gb_MW589620_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4464910_2020_Segment_null_Host_Human":"test",\n+ "gb_MW590718_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC434_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593416_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_880_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593460_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4649_2020_Segment_null_Host_Human":"test",\n+ "gb_MW596017_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000007226_2021_Segment_null_Host_Human":"test",\n+ "gb_MW596107_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000008078_2021_Segment_null_Host_Human":"test",\n+ "gb_MW596147_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000008176_2021_Segment_null_Host_Human":"test",\n+ "gb_MW599561_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00424_2021_Segment_null_Host_Human":"test"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "Primary SLAC analysis":{\n+ "order":2,\n+ "timer":2\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":7\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp7.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.combined.fas Wed Jun 09 07:03:54 2021 +0000 |
| b |
| b'@@ -0,0 +1,588 @@\n+>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1409773/hCoV-19/England/CAMC-141DB08/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATTCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1415264/hCoV-19/India/MH-NCCS-128864/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGTTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1415273/hCoV-19/India/MH-NCCS-87216/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAATAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1564187/hCoV-19/England/CAMC-14D5BFD/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCTATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1583966/hCoV-19/England/CAMC-14D1B4C/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATTTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1641831/hCoV-19/Germany/BY-RKI-I-076082/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGACATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1648157/hCoV-19/USA/CA-CDC-QDX23571833/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTTTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAATCTTACAA\n+\n+>epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGATATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1635400/hCoV-19/Scotland/CAMC-14DEDB2/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGCGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1652109/hCoV-19/Singapore/565/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAGTGCTGGACAACAGGGCAACCTTACAA\n+\n+\n+>REFERENCE\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW579030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101421353_2021_Segment_null_Host_Human\n+TCAAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAA'..b'_MW550719_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_2_3768763_2020_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAAGTGCATATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MT827207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0041_2020_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAAGTGTACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACCGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW524933_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_0000014_D07_2021_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAAGTGTACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW449300_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012152791_2020_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAAGTGTACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATTCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW153116_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7846_2020_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAGGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW406612_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OK_CDC_2_3693466_2020_Segment_null_Host_Human\n+TCTAAAATGTCGGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW012269_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_SRB_NP01_2020_Segment_null_Host_Human\n+TCTAAAATTTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW525004_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NM_CDC_STM_0000014_B01_2021_Segment_null_Host_Human\n+TCTAAAGTGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MT937322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0133_2020_Segment_null_Host_Human\n+TCTAGAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCTATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MT831570_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S2629_2020_Segment_null_Host_Human\n+TCTGAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp7.labels.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.labels.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| b'@@ -0,0 +1,198 @@\n+{\n+ "REFERENCE":"Reference",\n+ "epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021":"B-1-617",\n+ "epi_isl_1409773/hCoV-19/England/CAMC-141DB08/2021":"B-1-617",\n+ "epi_isl_1415264/hCoV-19/India/MH-NCCS-128864/2021":"B-1-617",\n+ "epi_isl_1415273/hCoV-19/India/MH-NCCS-87216/2021":"B-1-617",\n+ "epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021":"B-1-617",\n+ "epi_isl_1564187/hCoV-19/England/CAMC-14D5BFD/2021":"B-1-617",\n+ "epi_isl_1583966/hCoV-19/England/CAMC-14D1B4C/2021":"B-1-617",\n+ "epi_isl_1635400/hCoV-19/Scotland/CAMC-14DEDB2/2021":"B-1-617",\n+ "epi_isl_1641831/hCoV-19/Germany/BY-RKI-I-076082/2021":"B-1-617",\n+ "epi_isl_1648157/hCoV-19/USA/CA-CDC-QDX23571833/2021":"B-1-617",\n+ "epi_isl_1652109/hCoV-19/Singapore/565/2021":"B-1-617",\n+ "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT291831_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_Beijing_IME_BJ01_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT380729_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_1999_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT412283_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_5772_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT446348_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_BIE_080_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT451046_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC142_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT451174_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC278_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT451724_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1057_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT460125_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1105_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT470179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_France_40002VJ_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT499218_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_TUN_COV1663_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT512423_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_3688_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT609578_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_0348_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT609579_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_0349_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT612207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1606_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT628119_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1404_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT628199_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1525_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT642069_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S1116_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT704128_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0028_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT731735_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_137_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT755838_Organism_Severe_acute_respiratory_syndrome_coro'..b',\n+ "gb_MW577113_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00314_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW577730_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101009422_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW577930_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101239410_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW578033_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101679988_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW578122_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101329819_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW578256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_2_3714171_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW579014_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101155076_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW579030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101421353_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW585982_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_000003668_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW585995_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WV_CDC_STM_000003152_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586140_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005978_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586167_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000005966_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586286_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005415_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586766_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4270_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW589574_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4494168_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW589620_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4464910_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW590718_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC434_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593416_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_880_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593460_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4649_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW596017_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000007226_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW596107_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000008078_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW596147_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000008176_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW599561_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00424_2021_Segment_null_Host_Human":"Reference"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8-segment.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| @@ -0,0 +1,122 @@ +{ + "nsp8": { + "map": [], + "rates": { + "mean-omega": { + "B-1-617": 21.18256593595067, + "Reference": 0, + "background": 0.5156677174296214 + }, + "T": { + "B-1-617": 0.003269500911862614, + "Reference": 0.001919664151147453, + "background": 0.10664581418249912 + }, + "relax": { + "B-1-617": [ + { + "omega": 0, + "proportion": 0.3229316344832856 + }, + { + "omega": 0, + "proportion": 0.6561871399951409 + }, + { + "omega": 887.8019782663979, + "proportion": 0.02088122552157349 + } + ], + "Reference": [ + { + "omega": 0, + "proportion": 0.3229316344832856 + }, + { + "omega": 0, + "proportion": 0.6561871399951409 + }, + { + "omega": 887.8019782663979, + "proportion": 0.02088122552157349 + } + ], + "background": [ + { + "omega": 0, + "proportion": 0.3229316344832856 + }, + { + "omega": 0, + "proportion": 0.6561871399951409 + }, + { + "omega": 2.618905128891877, + "proportion": 0.02088122552157349 + } + ] + }, + "busted": { + "Background": { + "0": { + "omega": 0, + "proportion": 0.02741862862724963 + }, + "1": { + "omega": 0.1719979491289183, + "proportion": 0.8111826871363725 + }, + "2": { + "omega": 2.232058479326601, + "proportion": 0.1613986842363778 + } + }, + "Synonymous site-to-site rates": { + "0": { + "proportion": 0, + "rate": 0.9502886367487763 + }, + "1": { + "proportion": 1, + "rate": 1 + }, + "2": { + "proportion": 0, + "rate": 1.059678592887729 + } + }, + "Test": { + "0": { + "omega": 0.9993684330797956, + "proportion": 0 + }, + "1": { + "omega": 0.999368433118802, + "proportion": 0 + }, + "2": { + "omega": 25.32658549655282, + "proportion": 1 + } + } + } + }, + "relax": { + "p": 0.07260318641568564, + "K": 7.051367447513434 + }, + "busted": { + "p": 0.3056667368082906 + }, + "tree": "(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)", + "tree_tags": {}, + "prime-properties": [ + "Factor I bipolar", + "Factor II secondary structure", + "Factor III volume", + "Factor IV composition", + "Factor V charge" + ], + "bgm": [] + } +} \ No newline at end of file |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8-site.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.BUSTED.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.BUSTED.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,580 @@\n+{\n+ "Evidence Ratios":{\n+ "constrained": [\n+[0.9898739518379264, 0.991027168169301, 0.9898739518379268, 0.9897812891397899, 0.9906204835370439, 0.9853516617064797, 0.9880798288003553, 0.9889781190332573, 0.988350548699827, 0.989374526624819, 0.9897812891397899, 0.9927999621758878, 0.9898739523607402, 0.9898739518379268, 0.9853516617064797, 0.9898739518379268, 0.9930617996638492, 0.9898739518379268, 0.9956363652357774, 0.9953242584232271, 0.9898739518379268, 0.9927999621758878, 0.9906204835370439, 0.9909311149283309, 0.9898739518379268, 0.9888494594022271, 0.9898739518379268, 0.9942729604246417, 0.9875096976732132, 0.9910812249043462, 0.9889781181731668, 0.9953242584232271, 0.9888494594022271, 0.9888494594022271, 0.9883505486998261, 0.9965511193500521, 25.13531965114348, 0.9852148186803413, 0.9918415472526246, 0.9918415472526246, 0.9889781181731668, 0.9852148186803413, 0.9942729604246417, 0.9888494579313646, 0.9898739518379264, 0.9965511193500521, 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"gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",\n+ "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",\n+ "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",\n+ "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"\n+ }\n+ },\n+ "timers":{\n+ "Constrained BUSTED model fitting":{\n+ "order":3,\n+ "timer":3\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":76\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":6\n+ },\n+ "Unconstrained BUSTED model fitting":{\n+ "order":2,\n+ "timer":66\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.CFEL.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.CFEL.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,589 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [3.206171473304911, 0, 0.03175555207671071, 5.433962997865532e-05, 0, 0, 0.9766417072604165, 1, -1, 0.1428350861439815],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 2.691597641547223, 0.6095939176926283, 0, 0, 0, 1, 1, -1, 0.334509864610243],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [3.229642435228862, 0, 2.162021710309243, 0.004452160407161729, 0, 0, 0.8693548005974709, 1, -1, 0.1442288861347906],\n+ [0, 2.170494633509469, 0.2961869984298745, 0, 0, 0, 0.9875062279782896, 1, -1, 0.2697178710749373],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [6.636646908481298, 0, 1.139449512908137, 6.624437421595782e-05, 0, 0, 0.906603671841744, 1, -1, 0.2958257534388632],\n+ [0, 3.585093121716918, 0.4689445336386987, 0, 0, 0, 1, 1, -1, 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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.FADE.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.FADE.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,4714 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "A":{\n+ "0": [\n+[2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [1.117825271287792, 5.297486980684134, 0.94604302164483, 0.9890764026148687],\n+ [2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [18.9004123856017, 5.317669856443896, 0.9492912500886677, 1.056046759725475],\n+ [1.278267402694179, 5.298403086637607, 0.9461144831242656, 0.9904628995183727],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [19.19497341524307, 5.317540422140158, 0.9492955761547635, 1.056141673876794],\n+ [2.522173999598023, 5.296053746322004, 0.9463762215641978, 0.9955727079586607],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [1.495447087063753, 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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.FEL.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.FEL.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.MEME-full.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.MEME-full.json Wed Jun 09 07:03:54 2021 +0000 |
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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.MEME.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.MEME.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,916 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [3.180864197338322, 2.543979863949704, 1, 4.771296296007484, 0, 0, 0.6666666666666666, 0, 0, -9.280586212023099, -9.280586212023099],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0.0002152055713864022, 5.380139284660055e-05, 1, 0.5537159057721711, 0, 0, 0.6666666666666666, 0, 0, -9.653547986238197, -9.653323462942367],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [3.192432742671397, 2.614421539287398, 1, 4.788649114007091, 0, 0, 0.6666666666666666, 0, 0, -9.282601941350496, -9.282601941350496],\n+ [0, 0, 1, 1.464518485321612, 0, 0, 0.6666666666666666, 0, 0, -10.62393719963694, -10.62320682078165],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [6.613018745603487, 0.9469109242998108, 1, 9.919528118405228, 0, 0, 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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.PRIME.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.PRIME.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,596 @@\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+ [3.250710398632764, 2.543979863949704, 0.000260278000831112, -9.279879778998792, -9.280586210458985, 1, -0.03083220306091588, 1, -9.279441534952744, 0.246012012715961, 1, -9.279441534952742, 0.3671614662852546, 1, -9.279441534952742, -0.1712639841078613, 1, -9.279441534952737, 0.2624930750589453, 1, -9.279441534952737],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0.5537159057721711, 1.458738094193731e-05, -9.653318580984834, -9.653547984340634, 1, 0.5104924519363182, 1, -9.653308651005229, -0.1367278481442925, 1, -9.653308651005229, 0.5919809397222774, 1, -9.653308651005229, -0.1178049485056483, 1, -9.653308651005229, 0.6168893659032167, 1, -9.653308651005229],\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, 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| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.RELAX.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.RELAX.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,557 @@\n+{\n+ "Synonymous site-posteriors": [\n+[1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1],\n+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] \n+ ],\n+ "analysis":0,\n+ "branch attributes":{\n+ "0":{\n+ "Node20":{\n+ "MG94xREV with separate rates for branch sets":0.001634892352012191,\n+ "Nucleotide GTR":0.001684521619549293,\n+ "RELAX alternative":0.001888715982590274,\n+ "RELAX null":0.001729201145341893\n+ },\n+ "Node38":{\n+ "MG94xREV with separate rates for branch sets":0.001919664136946674,\n+ "Nucleotide GTR":0.00168484920326581,\n+ "RELAX alternative":0.001886373803275281,\n+ "RELAX null":0.001757668602191916\n+ },\n+ "Node4":{\n+ "MG94xREV with separate rates for branch sets":0.001634608725455373,\n+ "Nucleotide GTR":0.001683801387489096,\n+ "RELAX alternative":0.001736927843216757,\n+ "RELAX null":0.001719649158870973\n+ },\n+ "REFERENCE":{\n+ "MG94xREV with separate rates for branch sets":0,\n+ "Nucleotide GTR":0,\n+ "RELAX alternative":0,\n+ "RELAX null":0,\n+ "original name":"REFERENCE"\n+ },\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{\n+ "MG94xREV with separate rates for branch sets":0,\n+ "Nucleotide GTR":0,\n+ "RELAX alternative":0,\n+ "RELAX null":0,\n+ "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"\n+ },\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{\n+ "MG94xREV with separate rates for branch sets":0.001728428276944542,\n+ "Nucleotide GTR":0.001682745450340891,\n+ "RELAX alternative":0.001737560358174388,\n+ "RELAX null":0.001737701430364698,\n+ "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"\n+ },\n+ "epi_'..b'Unclassified",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"Unclassified",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"Unclassified",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"Unclassified",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"Unclassified",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"Unclassified",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"Unclassified",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"Unclassified",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"Unclassified",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"Unclassified",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"Unclassified",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"Unclassified",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"Unclassified",\n+ "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"Unclassified",\n+ "epi_isl_1652105_hCoV_19_Singapore_561_2021":"Unclassified",\n+ "epi_isl_1652118_hCoV_19_Singapore_575_2021":"Unclassified",\n+ "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Unclassified",\n+ "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"Unclassified"\n+ }\n+ },\n+ "timers":{\n+ "Overall":{\n+ "order":0,\n+ "timer":67\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "RELAX alternative model fitting":{\n+ "order":3,\n+ "timer":50\n+ },\n+ "RELAX null model fitting":{\n+ "order":4,\n+ "timer":12\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.SLAC.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.SLAC.json Wed Jun 09 07:03:54 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1350 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0":{\n+ "by-branch":{\n+ "AVERAGED": [\n+[0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [147.0112938906491, 421.9561434851458, 2, 13, 0.2583826142471318, 0.01360439696209771, 0.03080888902961936, 0.1540517400002438, 0.2141909453461294, 0.9297070045663574, 0.02664074934348415],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [145.5893054241774, 422.7504844557024, 0, 1, 0.2561659556775853, 0, 0.002365461511623139, 0.02118071607920737, 0.7438340443224147, 1, 0.001731141176898499],\n+ [145.8316085824376, 422.1143927092281, 2, 1, 0.256770200425351, 0.01371444791318621, 0.00236902606798543, -0.1015886995925552, 0.9830709003936052, 0.1639346082666348, 0.005234957209780722],\n+ [145.1406999043445, 423.0445443145819, 0, 1, 0.2554460915363381, 0, 0.002363817270401638, 0.0211659932835469, 0.7445539084636619, 1, 0.001731048067785009],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [145.8529411821772, 422.1089052052787, 1, 1, 0.2568005969236854, 0.006856221012032613, 0.00236905686581922, -0.04017877666355647, 0.9340534534196389, 0.4476546472670097, 0.003467134004764108],\n+ [145.4861542433911, 422.5873910598001, 0, 1, 0.2561044347976854, 0, 0.002366374437940792, 0.02118889056568302, 0.7438955652023147, 1, 0.001730401012235807],\n+ [145.1406999043445, 423.0445443145819, 0, 1, 0.2554460915363381, 0, 0.002363817270401638, 0.0211659932835469, 0.7445539084636619, 1, 0.001731056498022235],\n+ [145.1406999043445, 422.9908819061909, 0, 2, 0.2554702194900108, 0, 0.004728234308472756, 0.04233735698155978, 0.5543245940662527, 1, 0.003467572164636923],\n+ [145.4122726402566, 422.7729715786698, 2, 1, 0.2559240566694972, 0.01375399726368289, 0.002365335693684286, -0.1019758749195625, 0.9832377106374066, 0.1629667896213286, 0.005208678680963088],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [145.6740026904847, 422.5112415284417, 2, 0, 0.2563846987803072, 0.01372928568626911, 0, -0.1229341930368812, 1, 0.06573311376866875, 0.003469467349330688],\n+ [144.5765205593867, 423.0765753966273, 0, 2, 0.2546916798117659, 0, 0.004727276612100382, 0.04232878161694121, 0.5554844921418073, 1, 0.003467824865270607],\n+ [144.9219748984333, 422.7847834659717, 0, 1, 0.2552761135272754, 0, 0.00236526961023063, 0.02117899776382157, 0.7447238864727246, 1, 0.00173293384624849],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [145.2040645709122, 422.7419367207535, 1, 0, 0.2556652643749197, 0.006886859558339965, 0, -0.06166602849626656, 1, 0.2556652643749198, 0.001731477826576347],\n+ [145.4861542433911, 422.6990899755353, 1, 0, 0.2560540875069506, 0.006873506315432944, 0, -0.06154646144968366, 1, 0.2560540875069506, 0.001729315851762792],\n+ [144.9551193854748, 423.2301248334516, 0, 3, 0.2551194717925874, 0, 0.007088342308290441, 0.06347013687029401, 0.4132947274045454, 1, 0.005199356347141997],\n+ [145.6136982549165, 422.5715459640099, 1, 0, 0.2562785636136836, 0.006867485765311479, 0, -0.06149255249274786, 1, 0.2562785636136836, 0.001730674922882492],\n+ [145.0565770101724, 422.9633058846278, 0, 6, 0.2553723582190828, 0, 0.01418562772827539, 0.1270203517755656, 0.1704648824625068, 1, 0.01048699203960315],\n+ [145.9861542433911, 422.1990899755353, 0, 1, 0.2569340822007363, 0, 0.002368550818188514, 0.02120837821825352, 0.7430659177992637, 1, 0.00172931598734411],\n+ [145.5893054241774, 422.8397764862196, 0, 1, 0.2561257156915259, 0, 0.002364961991773709, 0.02117624329955963, 0.7438742843084741, 1, 0.001731607586790447],\n+ [145.4861542433911, 422.6990899755353, 1, 0, 0.2560540875069506, 0.006873506315432944, 0, -0.06154646144968366, 1, 0.2560540875069506, 0.001731056555105113],\n+ [145.6406999043445, 422.5445443145819, 0, 2, 0.2563260862301238, 0, 0.004733228784776385, 0.04238207'..b'oV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Node20":"test",\n+ "Node38":"test",\n+ "Node4":"test",\n+ "REFERENCE":"test",\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"test",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"test",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"test",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"test",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"test",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"test",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"test",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"test",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"test",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"test",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"test",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"test",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"test",\n+ "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"test",\n+ "epi_isl_1652105_hCoV_19_Singapore_561_2021":"test",\n+ "epi_isl_1652118_hCoV_19_Singapore_575_2021":"test",\n+ "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"test",\n+ "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"test",\n+ "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"test",\n+ "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"test",\n+ "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"test",\n+ "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"test",\n+ "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"test",\n+ "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"test",\n+ "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"test",\n+ "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"test",\n+ "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"test",\n+ "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"test",\n+ "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"test"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":0\n+ },\n+ "Primary SLAC analysis":{\n+ "order":2,\n+ "timer":1\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":1\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.combined.fas Wed Jun 09 07:03:54 2021 +0000 |
| b |
| b'@@ -0,0 +1,96 @@\n+>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACGGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAATTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTGTGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAATTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTATAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021\n+GCTATAGCCTCAGAGTTTAGT'..b'TGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAGTACGTGTGATGGTATAACATTTATTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGATAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAATTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTTGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGTCTAGATGTGAGGACAAGAGGTCAAAACTTACTATGGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGTTTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGACGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATATCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAGTTCTCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCTTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATTCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human\n+GCTATAGCTTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCGCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.combined.fas.BGM.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.combined.fas.BGM.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| b'@@ -0,0 +1,253 @@\n+{\n+ "analysis":{\n+ "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",\n+ "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",\n+ "contact":"apoon42@uwo.ca",\n+ "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.",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree",\n+ "version":"1.2"\n+ },\n+ "branch attributes":{\n+ "0":{\n+ "Node10":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node12":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node13":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node16":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node19":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node2":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node20":{\n+ "models.codon.MG_REV.ModelDescription":0.001732564301319626\n+ },\n+ "Node23":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node24":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node27":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node28":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node29":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node3":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node30":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node33":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node34":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node35":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node36":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node38":{\n+ "models.codon.MG_REV.ModelDescription":0.001730721769143463\n+ },\n+ "Node4":{\n+ "models.codon.MG_REV.ModelDescription":0.001731994998894883\n+ },\n+ "Node40":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node43":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node44":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node47":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node50":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node54":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node57":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node58":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node8":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "REFERENCE":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{\n+ "models.codon.MG_REV.ModelDescription":0.001729346788706704\n+ },\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{\n+ "models.codon.MG_REV.ModelDescription":0.001726770081665013\n+ },\n+ "epi_isl_1416968_hCoV_19_Guadelo'..b'"AIC-c":2565.76651309329,\n+ "Log Likelihood":-1205.948282908683,\n+ "Rate Distributions":null,\n+ "display order":0,\n+ "estimated parameters":76\n+ }\n+ },\n+ "input":{\n+ "datatype":"codon",\n+ "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",\n+ "number of sequences":32,\n+ "number of sites":198,\n+ "trees":{\n+ "0":"((((epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021)Node3,(epi_isl_1652118_hCoV_19_Singapore_575_2021,(epi_isl_1652105_hCoV_19_Singapore_561_2021,((gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human)Node13,(epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)Node16)Node12)Node10)Node8)Node2,((gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,((gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021)Node24,((((gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human)Node30,((((gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,(gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node40)Node38)Node36,((epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human)Node44,(epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human)Node47)Node43)Node35,(epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021)Node50)Node34,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021)Node33)Node29,(epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human)Node54)Node28,((gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human)Node58,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021)Node57)Node27)Node23)Node19,REFERENCE)"\n+ }\n+ },\n+ "settings":{\n+ "burn-in":10000,\n+ "data-type":"codon",\n+ "max-parents":1,\n+ "min-subs":1,\n+ "samples":100,\n+ "steps":100000,\n+ "threshold":0.5\n+ },\n+ "tested":0,\n+ "timers":{\n+ "Baseline fit":{\n+ "order":1,\n+ "timer":4\n+ },\n+ "Network inference":{\n+ "order":2,\n+ "timer":0\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":4\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r f304c108aa1f test-data/summary/nsp8.labels.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.labels.json Wed Jun 09 07:03:54 2021 +0000 |
| b |
| @@ -0,0 +1,34 @@ +{ + "REFERENCE":"Reference", + "epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021":"B-1-617", + "epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021":"B-1-617", + "epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021":"B-1-617", + "epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021":"B-1-617", + "epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021":"B-1-617", + "epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021":"B-1-617", + "epi_isl_1543980/hCoV-19/Singapore/490/2021":"B-1-617", + "epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021":"B-1-617", + "epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021":"B-1-617", + "epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021":"B-1-617", + "epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021":"B-1-617", + "epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021":"B-1-617", + "epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021":"B-1-617", + "epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021":"B-1-617", + "epi_isl_1652105/hCoV-19/Singapore/561/2021":"B-1-617", + "epi_isl_1652118/hCoV-19/Singapore/575/2021":"B-1-617", + "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Reference", + "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Reference", + "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"Reference", + "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"Reference", + "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Reference", + "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"Reference", + "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"Reference", + "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"Reference", + "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"Reference", + "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"Reference", + "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"Reference", + "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"Reference", + "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"Reference", + "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"Reference", + "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"Reference" +} \ No newline at end of file |