| Previous changeset 35:841557158611 (2023-03-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92 |
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modified:
hyphy_absrel.xml macros.xml test-data/annotate-out1-full.nhx test-data/relax-in2.nex test-data/strike-ambigs-in1.fa test-data/strike-ambigs-in2.fa |
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added:
test-data/mss.tsv test-data/relax-in1-2.nhx test-data/relax-in2.nhx |
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removed:
scripts/annotator.bf test-data/annotate-in1.fa.gz test-data/annotate-out1-clade.nhx test-data/annotate-out1.json test-data/prime-out1.json test-data/relax-out1.json test-data/relax-out2-1.json test-data/sm19-out1.json test-data/sm19-out2.json 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 841557158611 -r 8db8d509d51b hyphy_absrel.xml --- a/hyphy_absrel.xml Thu Mar 02 15:09:44 2023 +0000 +++ b/hyphy_absrel.xml Tue Oct 07 20:51:45 2025 +0000 |
| [ |
| b'@@ -8,108 +8,139 @@\n <command detect_errors="exit_code"><![CDATA[\n @SYMLINK_FILES@\n ln -s \'$absrel_output\' ${input_file}.aBSREL.json &&\n- @HYPHYMPI@ absrel\n+ @HYPHYMP@ absrel\n --alignment ./$input_file\n @INPUT_TREE@\n --code \'$gencodeid\'\n @branch_options@\n --output \'$absrel_output\'\n --multiple-hits $multiple_hits\n- $srv\n+ @srv_options@\n+ --blb $blb\n+ --kill-zero-lengths $kill_zero_lengths > absrel_stdout.md\n @ERRORS@\n ]]></command>\n <inputs>\n <expand macro="inputs"/>\n <expand macro="gencode"/>\n- <param argument="--multiple-hits" type="select" label="Include support for multiple nucleotide substitutions">\n- <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>\n- <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>\n- <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>\n- </param>\n- <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" />\n <expand macro="branches"/>\n+ <section name="advanced_options" title="Advanced Options" expanded="false">\n+ <param argument="--multiple-hits" type="select" label="Include support for multiple nucleotide substitutions" help="Include support for multiple nucleotide substitutions.">\n+ <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>\n+ <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>\n+ <option value="None" selected="true">Use standard models which permit only single nucleotide changes to occur instantly</option>\n+ </param>\n+ <param argument="--blb" type="float" value="1.0" label="Bag of little bootstrap alignment resampling rate" help="[Advanced option] Bag of Little Bootstraps (BLB) alignment resampling rate (default: 1.0). This parameter controls the fraction of sites to resample for each bootstrap replicate. BLB uses down/upsampling approaches to speed up inference for very long alignments by analyzing subsets of the data."/>\n+ <conditional name="srv_conditional">\n+ <param name="srv_enabled" type="select" label="Include synonymous rate variation" help="Include synonymous rate variation.">\n+ <option value="true" selected="true">Yes</option>\n+ <option value="false">No</option>\n+ </param>\n+ <when value="true">\n+ <param argument="--syn-rates" type="integer" value="3" min="1" max="10" label="Synonymous rate classes" help="The number of alpha rate classes to include in the model [1-10, default 3]"/>\n+ </when>\n+ <when value="false">\n+ </when>\n+ </conditional>\n+ <expand macro="kill_zero_lengths_param"/>\n+ </section>\n </inputs>\n <outputs>\n+ <data name="absrel_md_report" format="markdown" from_work_dir="absrel_stdout.md" label="aBSREL Report (Markdown) for ${tool.name} on ${on_string}" />\n <data name="absrel_output" format="hyphy_results.json" />\n </outputs>\n <tests>\n- <test>\n+ <test expect_num_outputs="2">\n <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>\n <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>\n- <param name="multiple_hits" value="None" />\n <output name="absrel_output">\n <assert_contents>\n- <has_size value="10512" delta="100"/>\n- <has_text text="fits"/>\n- <ha'..b' p-values from these tests are then corrected for multiple testing to identify branches that show statistically significant evidence of positive selection.\n \n-Input\n------\n+**Input**\n \n 1. A *FASTA* sequence alignment.\n 2. A phylogenetic tree in the *Newick* format\n@@ -117,8 +148,7 @@\n Note: the names of sequences in the alignment must match the names of the sequences in the tree.\n \n \n-Output\n-------\n+**Output**\n \n A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).\n \n@@ -127,31 +157,48 @@\n \n A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)\n \n-Further reading\n----------------\n+**Further reading**\n \n http://hyphy.org/methods/selection-methods/#absrel\n \n \n-Tool options\n-------------\n+**Tool options**\n ::\n \n+ --alignment [required] An in-frame codon alignment in one of the formats supported by HyPhy\n \n- --code Which genetic code to use\n+ --tree [conditionally required] A phylogenetic tree (optionally annotated with {})\n+\n+ --code Which genetic code to use (see tool form for available options)\n \n --branches Which branches should be tested for selection?\n- All [default] : test all branches\n+ All [default]\n+ Internal\n+ Leaves\n+ Unlabeled branches\n+ Custom : Enter a branch label\n \n- Internal : test only internal branches (suitable for\n- intra-host pathogen evolution for example, where terminal branches\n- may contain polymorphism data)\n+ --multiple-hits Include support for multiple nucleotide substitutions\n+ Double : Include branch-specific rates for double nucleotide substitutions\n+ Double+Triple : Include branch-specific rates for double and triple nucleotide substitutions\n+ None [default] : Use standard models which permit only single nucleotide changes to occur instantly\n \n- Leaves: test only terminal (leaf) branches\n+ --srv Include synonymous rate variation (default: No)\n+ If Yes, then:\n+ --syn-rates The number alpha rate classes to include in the model [1-10, default 3]\n+\n+ --blb [Advanced option] Bag of Little Bootstraps (BLB) alignment resampling rate (default: 1.0). This parameter controls the fraction of sites to resample for each bootstrap replicate. BLB uses down/upsampling approaches to speed up inference for very long alignments by analyzing subsets of the data. For more details, see https://www.nature.com/articles/s43588-021-00129-5.\n+\n+ --output Write the resulting JSON to this file (default is to save to the same path as the alignment file + \'ABSREL.json\')\n \n- Unlabeled: if the Newick string is labeled using the {} notation,\n- test only branches without explicit labels\n- (see http://hyphy.org/tutorials/phylotree/)\n+\n+\n+ --kill-zero-lengths Automatically delete internal zero-length branches for computational efficiency\n+ Yes [default] : Automatically delete internal zero-length branches for computational efficiency (will not affect results otherwise)\n+ Constrain : Keep zero-length branches, but constrain their values to 0\n+ No : Keep all branches\n+\n+ --save-fit Save full adaptive aBSREL model fit to this file (default is not to save)\n \n \n \n@@ -159,4 +206,4 @@\n <expand macro="citations">\n <citation type="doi">10.1093/molbev/msv022</citation>\n </expand>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 841557158611 -r 8db8d509d51b macros.xml --- a/macros.xml Thu Mar 02 15:09:44 2023 +0000 +++ b/macros.xml Tue Oct 07 20:51:45 2025 +0000 |
| [ |
| b'@@ -1,12 +1,13 @@\n <?xml version="1.0"?>\n <macros>\n- <token name="@TOOL_VERSION@">2.5.47</token>\n+ <token name="@TOOL_VERSION@">2.5.83</token>\n <token name="@VERSION_SUFFIX@">0</token>\n- <token name="@PROFILE@">21.05</token>\n+ <token name="@PROFILE@">24.0</token>\n+ <token name="@SHELL_OPTIONS@">export TERM="vt100"; </token>\n \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+\t <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="An in-frame codon alignment in one of the formats supported by HyPhy" />\n+ <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file; this will override any trees included in the file" help="A phylogenetic tree (optionally annotated with {})"/>\n </xml>\n <xml name="bio_tools">\n <xrefs>\n@@ -15,17 +16,11 @@\n </xml>\n <xml name="substitution" tokens="argument">\n <param argument="@ARGUMENT@" 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+ <option value="JTT" selected="true">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@@ -37,12 +32,18 @@\n for invertebrate mitochondrial genomes</option>\n <option value="gcpREV">gcpREV - Specialist empirical\n model for green plant chloroplast genomes</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="GTR" selected="true">GTR - General time reversible\n+ model</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+ <param argument="--method" type="select" label="Posterior estimation method" help="The inference method to use for estimating the posterior distribution.">\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@@ -68,14 +69,14 @@\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" 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='..b' --branches \'$branch_cond.branch_label\'\n #else:\n --branches $branch_cond.branch_sel\n #end if\n- ]]>\n- </token>\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+ #end if\n+ ]]></token>\n+ <token name="@busted_advanced_options_command@"><![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.multiple_hits != \'None\':\n+ --multiple-hits $advanced.multiple_hits\n+ #end if\n+ #if $advanced.error_sink:\n+ --error-sink Yes\n+ #end if\n #if $advanced.save_alternative_model:\n --save-fit alternative_model.nhx\n #end if\n+ #if $advanced.mss.enabled == "true":\n+ --mss Yes\n+ --mss-type $advanced.mss.mss_type_cond.mss_type\n+ #if $advanced.mss.mss_type_cond.mss_type == "Random":\n+ --mss-classes $advanced.mss.mss_type_cond.mss_classes\n+ #elif $advanced.mss.mss_type_cond.mss_type == "Empirical":\n+ --mss-file $advanced.mss.mss_type_cond.mss_file\n+ #elif $advanced.mss.mss_type_cond.mss_type == "File":\n+ --mss-file $advanced.mss.mss_type_cond.mss_file\n+ --mss-neutral $advanced.mss.mss_type_cond.mss_neutral\n+ #elif $advanced.mss.mss_type_cond.mss_type == "Codon-file":\n+ --mss-file $advanced.mss.mss_type_cond.mss_file\n+ --mss-neutral $advanced.mss.mss_type_cond.mss_neutral\n+ #end if\n+ #end if\n #end if\n ]]></token>\n- <token name="@HYPHYMPI@">\\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\\${TMPDIR:-.}" -np \\${GALAXY_SLOTS:-1}} HYPHYMPI</token>\n+ <token name="@srv_options@"><![CDATA[\n+ #if $srv_conditional.srv_enabled == \'true\':\n+ --srv Yes\n+ #if $srv_conditional.syn_rates:\n+ --syn-rates $srv_conditional.syn_rates\n+ #end if\n+ #end if\n+ ]]></token>\n+ <token name="@HYPHYMPI@">\\${GALAXY_MPIRUN:-mpirun --allow-run-as-root --oversubscribe -mca orte_tmpdir_base "\\${TMPDIR:-.}" -np \\${GALAXY_SLOTS:-1}} HYPHYMPI </token>\n+ <token name="@HYPHYMP@">hyphy CPU=\\${GALAXY_SLOTS:-4} </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+ <token name="@HYPHY_ENVIRONMENT@">\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@">\n @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\\$HYPHY_LIB\n- ]]></token>\n+ </token>\n <token name="@SYMLINK_FILES@"><![CDATA[\n #if $input_nhx is not None:\n ln -s \'$input_nhx\' input.nhx &&\n@@ -213,4 +359,7 @@\n ln -s \'$input_file\' input.$input_file.extension &&\n #set $input_file = \'input.%s\' % $input_file.extension\n ]]></token>\n+ <token name="@SYMLINK_FILES_NO_TREE@"><![CDATA[\n+ ln -s \'$input_file\' input.$input_file.extension &&\n+ ]]></token>\n </macros>\n' |
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| diff -r 841557158611 -r 8db8d509d51b scripts/annotator.bf --- a/scripts/annotator.bf Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,102 +0,0 @@ -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 841557158611 -r 8db8d509d51b 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 841557158611 -r 8db8d509d51b test-data/annotate-out1-clade.nhx --- a/test-data/annotate-out1-clade.nhx Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -(((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 |
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| diff -r 841557158611 -r 8db8d509d51b test-data/annotate-out1-full.nhx --- a/test-data/annotate-out1-full.nhx Thu Mar 02 15:09:44 2023 +0000 +++ b/test-data/annotate-out1-full.nhx Tue Oct 07 20:51:45 2025 +0000 |
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| @@ -1,1 +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 +((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1:0.000523,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated}:1e-06)Node1:1e-06,REFERENCE:0.000262,(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated}:0.001835,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3:1e-06,(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}:0.000786,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated}:0.000785,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated}:0.823959)Node11{Annotated}:1e-06)Node9{Annotated}:1e-06)Node7:0.000262)Node5:1e-06)Node5 \ No newline at end of file |
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| diff -r 841557158611 -r 8db8d509d51b test-data/annotate-out1.json --- a/test-data/annotate-out1.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -{ - "REFERENCE":"Annotated", - "epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021":"Annotated", - "epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021":"Annotated", - "gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3":"Annotated", - "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", - "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", - "gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4":"Annotated" -} \ No newline at end of file |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/mss.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mss.tsv Tue Oct 07 20:51:45 2025 +0000 |
| b |
| @@ -0,0 +1,68 @@ +codon1 codon2 class +AAA AAG SELECTED +AAC AAT SELECTED +ACA ACC SELECTED +ACA ACG SELECTED +ACA ACT NEUTRAL +ACC ACG SELECTED +ACC ACT SELECTED +ACG ACT SELECTED +AGA AGG NEUTRAL +AGA CGA SELECTED +AGC AGT SELECTED +AGG CGG SELECTED +ATA ATC SELECTED +ATA ATT NEUTRAL +ATC ATT SELECTED +CAA CAG SELECTED +CAC CAT SELECTED +CCA CCC SELECTED +CCA CCG SELECTED +CCA CCT SELECTED +CCC CCG SELECTED +CCC CCT SELECTED +CCG CCT SELECTED +CGA CGC SELECTED +CGA CGG SELECTED +CGA CGT NEUTRAL +CGC CGG SELECTED +CGC CGT SELECTED +CGG CGT SELECTED +CTA CTC SELECTED +CTA CTG SELECTED +CTA CTT NEUTRAL +CTA TTA NEUTRAL +CTC CTG SELECTED +CTC CTT NEUTRAL +CTG CTT SELECTED +CTG TTG SELECTED +GAA GAG SELECTED +GAC GAT SELECTED +GCA GCC SELECTED +GCA GCG SELECTED +GCA GCT NEUTRAL +GCC GCG SELECTED +GCC GCT SELECTED +GCG GCT SELECTED +GGA GGC SELECTED +GGA GGG SELECTED +GGA GGT NEUTRAL +GGC GGG SELECTED +GGC GGT SELECTED +GGG GGT SELECTED +GTA GTC SELECTED +GTA GTG SELECTED +GTA GTT SELECTED +GTC GTG SELECTED +GTC GTT SELECTED +GTG GTT SELECTED +TAC TAT SELECTED +TCA TCC SELECTED +TCA TCG SELECTED +TCA TCT SELECTED +TCC TCG SELECTED +TCC TCT SELECTED +TCG TCT SELECTED +TGC TGT SELECTED +TTA TTG SELECTED +TTC TTT NEUTRAL |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/prime-out1.json --- a/test-data/prime-out1.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,391 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/relax-in1-2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1-2.nhx Tue Oct 07 20:51:45 2025 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Baboon{TEST2}:0.011873):0.340802,Rat{TEST3}:0.050958); |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/relax-in2.nex --- a/test-data/relax-in2.nex Thu Mar 02 15:09:44 2023 +0000 +++ b/test-data/relax-in2.nex Tue Oct 07 20:51:45 2025 +0000 |
| b |
| @@ -27,9 +27,7 @@ 'Rat' ---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC; END; -BEGIN TREES; - TREE tree = (((Pig:0.147969,Cow:0.213430):0.085099,Baboon{PR}:0.003108){PR}:0.340802,Rat:0.050958); -END; + BEGIN HYPHY; |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/relax-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nhx Tue Oct 07 20:51:45 2025 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(((Pig:0.147969,Cow:0.213430):0.085099,Baboon{TEST}:0.003108){TEST}:0.340802,Rat:0.050958) \ No newline at end of file |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/relax-out1.json --- a/test-data/relax-out1.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,493 +0,0 @@\n-{\n- "analysis":0,\n- "branch attributes":{\n- "0":{\n- "Baboon":{\n- "General descriptive":0.001859058366368826,\n- "MG94xREV with separate rates for branch sets":0.001769294089885709,\n- "Nucleotide GTR":0.001685167654714891,\n- "RELAX alternative":0.001873708670384941,\n- "RELAX null":0.001859167714920677,\n- "RELAX partitioned descriptive":0.001898817195216417,\n- "k (general descriptive)":0.09969742933359635,\n- "original name":"Baboon"\n- },\n- "Cat":{\n- "General descriptive":0.3650161006190072,\n- "MG94xREV with separate rates for branch sets":0.2796018473093496,\n- "Nucleotide GTR":0.2660536011315811,\n- "RELAX alternative":0.3685874431614762,\n- "RELAX null":0.3167334440346762,\n- "RELAX partitioned descriptive":0.3719472357609613,\n- "k (general descriptive)":2.319877215422834,\n- "original name":"Cat"\n- },\n- "Chimp":{\n- "General descriptive":0.001895983937468787,\n- "MG94xREV with separate rates for branch sets":0.001826027667597702,\n- "Nucleotide GTR":0.001820258053351119,\n- "RELAX alternative":0.001831530791728368,\n- "RELAX null":0.001834052740714585,\n- "RELAX partitioned descriptive":0.001832682515795942,\n- "k (general descriptive)":5.158328270628251,\n- "original name":"Chimp"\n- },\n- "Cow":{\n- "General descriptive":0.3737128696500712,\n- "MG94xREV with separate rates for branch sets":0.2521304147607955,\n- "Nucleotide GTR":0.2480198736772598,\n- "RELAX alternative":0.3426997068768813,\n- "RELAX null":0.2931467439343907,\n- "RELAX partitioned descriptive":0.3469082289876269,\n- "k (general descriptive)":2.852150041266453,\n- "original name":"Cow"\n- },\n- "Horse":{\n- "General descriptive":0.2804279827409984,\n- "MG94xREV with separate rates for branch sets":0.2158535884657318,\n- "Nucleotide GTR":0.2090998951755368,\n- "RELAX alternative":0.3058441352816696,\n- "RELAX null":0.2546949756245578,\n- "RELAX partitioned descriptive":0.3035514182923183,\n- "k (general descriptive)":1.929916608813313,\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)":1.485684693044203,\n- "original name":"Human"\n- },\n- "Mouse":{\n- "General descriptive":0.1308809509233143,\n- "MG94xREV with separate rates for branch sets":0.1197584101055861,\n- "Nucleotide GTR":0.1181058300538561,\n- "RELAX alternative":0.1346294129227689,\n- "RELAX null":0.1438267359449897,\n- "RELAX partitioned descriptive":0.148454172127534,\n- "k (general descriptive)":0.4625550584398252,\n- "original name":"Mouse"\n- },\n- "Node1":{\n- "General descriptive":0.3500691487967139,\n- "MG94xREV with separate rates for branch sets":0.2856782993656827,\n- "Nucleotide GTR":0.2767105173979571,\n- "RELAX alternative":0.385503346940632,\n- "RELAX null":0.4352096867868785,\n- "RELAX partitioned descriptive":0.4379872513902164,\n- "k 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Likelihood":-3437.63727539638,\n- "Rate Distributions":{\n- "Reference":{\n- "0":{\n- "omega":1.408928936991542e-20,\n- "proportion":0.265244047162938\n- },\n- "1":{\n- "omega":1.410337865928411e-20,\n- "proportion":0.28512630848952\n- },\n- "2":{\n- "omega":3.213510017765925,\n- "proportion":0.4496296443475419\n- }\n- },\n- "Test":{\n- "0":{\n- "omega":1.408928936991542e-20,\n- "proportion":0.265244047162938\n- },\n- "1":{\n- "omega":1.410337865928411e-20,\n- "proportion":0.28512630848952\n- },\n- "2":{\n- "omega":3.213510017765925,\n- "proportion":0.4496296443475419\n- }\n- }\n- },\n- "display order":3,\n- "estimated parameters":35\n- },\n- "RELAX partitioned descriptive":{\n- "AIC-c":6937.049237937651,\n- "Log Likelihood":-3427.627954124649,\n- "Rate Distributions":{\n- "Reference":{\n- "0":{\n- "omega":0.1847557016619168,\n- "proportion":0.4766160247339328\n- },\n- "1":{\n- "omega":0.3367540359539261,\n- "proportion":0.3005513276312735\n- },\n- "2":{\n- "omega":4.272816072857538,\n- "proportion":0.2228326476347937\n- }\n- },\n- "Test":{\n- "0":{\n- "omega":1.127143149593234e-21,\n- "proportion":0.2367540589657237\n- },\n- "1":{\n- "omega":1.128270292740756e-21,\n- "proportion":0.2771164325302933\n- },\n- "2":{\n- "omega":6.023626417874829,\n- "proportion":0.4861295085039831\n- }\n- }\n- },\n- "display order":5,\n- "estimated parameters":40\n- }\n- },\n- "input":{\n- "file name":"/tmp/tmpkgsdjj1d/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- "runtime":"2.5.32",\n- "test results":{\n- "LRT":16.80113246476958,\n- "p-value":4.150852429507523e-05,\n- "relaxation or intensification parameter":2.334214628944839\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":127\n- },\n- "Overall":{\n- "order":0,\n- "timer":396\n- },\n- "Preliminary model fitting":{\n- "order":1,\n- "timer":8\n- },\n- "RELAX alternative model fitting":{\n- "order":3,\n- "timer":103\n- },\n- "RELAX null model fitting":{\n- "order":4,\n- "timer":41\n- },\n- "RELAX partitioned descriptive":{\n- "order":5,\n- "timer":116\n- }\n- }\n-}\n\\ No newline at end of file\n' |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/relax-out2-1.json --- a/test-data/relax-out2-1.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,493 +0,0 @@\n-{\n- "analysis":0,\n- "branch attributes":{\n- "0":{\n- "BABOON":{\n- "General descriptive":0.001858528201768933,\n- "MG94xREV with separate rates for branch sets":0.001729040005725717,\n- "Nucleotide GTR":0.001685167654714891,\n- "RELAX alternative":0.001823573976182991,\n- "RELAX null":0.001855504238020734,\n- "RELAX partitioned descriptive":0.001856473113608415,\n- "k (general descriptive)":0.09974837182960776,\n- "original name":"BABOON"\n- },\n- "CAT":{\n- "General descriptive":0.3649687317465272,\n- "MG94xREV with separate rates for branch sets":0.2761191158060541,\n- "Nucleotide GTR":0.2660536011315811,\n- "RELAX alternative":0.3317928646169214,\n- "RELAX null":0.3252639231399129,\n- "RELAX partitioned descriptive":0.3330192884009499,\n- "k (general descriptive)":2.321295373553348,\n- "original name":"CAT"\n- },\n- "CHIMP":{\n- "General descriptive":0.00184909269599246,\n- "MG94xREV with separate rates for branch sets":0.001822551054713939,\n- "Nucleotide 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"AIC-c":6946.046147526199,\n- "Log Likelihood":-3437.336050862336,\n- "Rate Distributions":{\n- "Reference":{\n- "0":{\n- "omega":0.07516343499603452,\n- "proportion":0.2524283429126023\n- },\n- "1":{\n- "omega":0.1730729265669467,\n- "proportion":0.3734402861071174\n- },\n- "2":{\n- "omega":3.70326279512502,\n- "proportion":0.3741313709802804\n- }\n- },\n- "Test":{\n- "0":{\n- "omega":0.07516343499603452,\n- "proportion":0.2524283429126023\n- },\n- "1":{\n- "omega":0.1730729265669467,\n- "proportion":0.3734402861071174\n- },\n- "2":{\n- "omega":3.70326279512502,\n- "proportion":0.3741313709802804\n- }\n- }\n- },\n- "display order":3,\n- "estimated parameters":35\n- },\n- "RELAX partitioned descriptive":{\n- "AIC-c":6944.507313452719,\n- "Log Likelihood":-3431.356991882183,\n- "Rate Distributions":{\n- "Reference":{\n- "0":{\n- "omega":0,\n- "proportion":0.3694476627871225\n- },\n- "1":{\n- "omega":0.03660893085044142,\n- "proportion":0.1726741298596992\n- },\n- "2":{\n- "omega":3.988980749944551,\n- "proportion":0.4578782073531784\n- }\n- },\n- "Test":{\n- "0":{\n- "omega":0.224878249826745,\n- "proportion":0.2953732524277409\n- },\n- "1":{\n- "omega":0.231175241198686,\n- "proportion":0.5325206774143161\n- },\n- "2":{\n- "omega":4.178788461910403,\n- "proportion":0.172106070157943\n- }\n- }\n- },\n- "display order":5,\n- "estimated parameters":40\n- }\n- },\n- "input":{\n- "file name":"/tmp/tmps1cqwvdh/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- "runtime":"2.5.36",\n- "test results":{\n- "LRT":9.706171521456781,\n- "p-value":0.001836502097725456,\n- "relaxation or intensification parameter":0.3695692925647034\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":159\n- },\n- "Overall":{\n- "order":0,\n- "timer":428\n- },\n- "Preliminary model fitting":{\n- "order":1,\n- "timer":13\n- },\n- "RELAX alternative model fitting":{\n- "order":3,\n- "timer":61\n- },\n- "RELAX null model fitting":{\n- "order":4,\n- "timer":53\n- },\n- "RELAX partitioned descriptive":{\n- "order":5,\n- "timer":141\n- }\n- }\n-}\n\\ No newline at end of file\n' |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/sm19-out1.json --- a/test-data/sm19-out1.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2606 +0,0 @@\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- 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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/sm19-out2.json --- a/test-data/sm19-out2.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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No newline at end of file\n' |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/strike-ambigs-in1.fa --- a/test-data/strike-ambigs-in1.fa Thu Mar 02 15:09:44 2023 +0000 +++ b/test-data/strike-ambigs-in1.fa Tue Oct 07 20:51:45 2025 +0000 |
| b |
| b'@@ -1,260 +1,20 @@\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->epi_i'..b'NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGTACAGAAATGGAAAAGGAAGGGAAGATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAAAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACAYCCCGCAGGGTTAAAAAAGAARAAATCAGTAACAGTACTAGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAYRAAGAMTTCAGGAAGTATACTGCATTTACCATACCTAGTACAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAARCARAATCCAGACATGGTTATCTATCAATACATGGATGATTTGTATGTAGGCTCTGACTTAGAAATAGGGCAACATAGAACAAAAATAGAGGAACTGAGACAACATCTGTTGMAGTGGGGRTTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTYTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+>N15619990\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATATAATACTCCAGTATTTGCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCTTTAGATAAAGAGTTCAGGAAGTACACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGGTATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCARRRTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAACCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAGATAGGGCAACATAGAACAAAAATAGAGGAACTGAGACAACATCTGTTGAAATGGGGGTTTACCACACCAGACAAGAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+>N3199901\n+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTTAGAGAACTTAATAAGAGGACTCAAGACTTTTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCMTTACATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGGTTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGAAATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGMAATAGGGCAGCATAGAAYAAAAATAGATGAACTGAGACARCATCTGTTGAKGTGGGGATTTACCACACCAGACAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+>N14519991\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGTACAGAAATGGAAAAGGAAGGRAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCYATAAAGAAAAAAGACAGTACTAARTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAATACCACATCCCGCRGGGTTRAARAAGAAAAAATCARTAACAGTACTGGATGTGGGTGATGCATATTTYTCAGTTCCCTTAGATGAAAATTTYAGAAAATATACTGCATTTACTATACCTAGTATAAACAATGAGACACCAGGGRTTAGRTATCAGTACAATGTGCTKCCACAGGGATGGAAAGGATCACCAGCAATATTCCAGAGTAGCATGACAAAAATYTTAGAGCCTTTTAGAAAACAAAATCCAGACATGGTCATCTATCAATACATGGATGAYYTGTATGTAGGATCTGACTTAGAAATAGGRCAGCAYAGAGCAAAAATAGAGGAACTGAGACAACATCTGTTGARGTGGGGRTTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTYCTTTGGATGGGKTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n' |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/strike-ambigs-in2.fa --- a/test-data/strike-ambigs-in2.fa Thu Mar 02 15:09:44 2023 +0000 +++ b/test-data/strike-ambigs-in2.fa Tue Oct 07 20:51:45 2025 +0000 |
| b |
| b'@@ -1,455 +1,20 @@\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_MW'..b'AGCAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAATTGGAAAAGGAAGGAAAGATTTCAAAAATTGGGCCTGAAAATCCATATAACACTCCAGTATTTGCCATAAAGAAAAAAGACGGYGCTAAATGGAGAAAATTAATGGATTTCAGAGAGCTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTACAAAAGAAAAAATCARTAACAGTACTAGATGTGGGWGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTACACTGCATTTACCATACCTAGTACAAACAATGAGACACCAGGGGTTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTGTCAATACATGGATGAYTTGTATGTAGCATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAACATCTGTGGAGGTGGGGGTTTTACACACCAGACAAAAAACATCAGAAAGAACCTCCCTTCAARTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTGCAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAATTATGTAAACTCCTTAGGGGAACCAAAGCACTAACAGAAGTAATACCACTAACAAAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTAATAGCAGAAATACAGAAGCAGGGGNNNNNN\n+>N19419981\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAACCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAACAAGAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCARTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATARAGAMTTCAGGAAGTACACAGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTRCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGAAATAGTTATTTATCAATACATGGATGATCTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAACTAAGACAACATCTGTTGARGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAATGCTGCCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+>T90200101\n+CCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAGAAAATAAAAGCATTAATGGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGRCRGTACTAACTGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAGGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGARACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCGATATTCCAAAGTAGTATGACAAAAATCTTAGAACCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACGTGGATGATTTGTATGTAAGCTCTGACTTAGAAATAGGGCAGCATAGAACAAAGATAGAGGAACTGAGACAGCATCTGTTGAAGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCGTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGAGCTGCCAGAAAAAGATAGCTGGACTGTCAATGACATACAGAAGCTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGAGCCAAAGCACTGACAGAAGTAATAACATTAACAAGAGAAGCAGAGCTAGAACTGGCAGAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+>N69199906\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTGTACAGAAATGGAAAAAGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAAAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGATTAAAAAAGAAAAAGTCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCTTTAGATAAAGAATTCAGGAAGTATACTGCATTTACCATACCTAGTACAAACAATGAGACACCAGGAATTAGATATCAGTACAATGTGCTTCCACARGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATATATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAGCATCTGTTRAAGTGGGGGTTTACCACACCAGACAAAAAACATCAGAAAGAACCCCCRTTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n' |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/strike-ambigs-out1.fa --- a/test-data/strike-ambigs-out1.fa Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,8 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/strike-ambigs-out2.fa --- a/test-data/strike-ambigs-out2.fa Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,14 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/summary/ORF6-segment.json --- a/test-data/summary/ORF6-segment.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1135 +0,0 @@\n-{\n- "ORF6": {\n- "map": [\n- 27201,\n- 27204,\n- 27207,\n- 27210,\n- 27213,\n- 27216,\n- 27219,\n- 27222,\n- 27225,\n- 27228,\n- 27231,\n- 27234,\n- 27237,\n- 27240,\n- 27243,\n- 27246,\n- 27249,\n- 27252,\n- 27255,\n- 27258,\n- 27261,\n- 27264,\n- 27267,\n- 27270,\n- 27273,\n- 27276,\n- 27279,\n- 27282,\n- 27285,\n- 27288,\n- 27291,\n- 27294,\n- 27297,\n- 27300,\n- 27303,\n- 27306,\n- 27309,\n- 27312,\n- 27315,\n- 27318,\n- 27321,\n- 27324,\n- 27327,\n- 27330,\n- 27333,\n- 27336,\n- 27339,\n- 27342,\n- 27345,\n- 27348,\n- 27351,\n- 27354,\n- 27357,\n- 27360,\n- 27363,\n- 27366,\n- 27369,\n- 27372,\n- 27375,\n- 27378,\n- 27381\n- ],\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_'..b' "gb_MW064863_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_QDX_779_2020_Segment_null_Host_Human": [\n- "Reference",\n- false,\n- 0.005652737786801275\n- ],\n- "gb_MW155278_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12385_2020_Segment_null_Host_Human": [\n- "Reference",\n- false,\n- 0.00557872293700733\n- ],\n- "epi_isl_1442952_hCoV_19_Singapore_321_2021": [\n- "Reference",\n- false,\n- 0.00557872293700733\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- "Reference",\n- false,\n- 0.005612858460151898\n- ],\n- "gb_MW462661_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2263_2020_Segment_null_Host_Human": [\n- "Reference",\n- false,\n- 0.005587511279835753\n- ],\n- "epi_isl_1516887_hCoV_19_Australia_QLD1826_2021": [\n- "Reference",\n- 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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/ORF6.SLAC.json --- a/test-data/summary/ORF6.SLAC.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/ORF6.combined.fas --- a/test-data/summary/ORF6.combined.fas Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,531 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/summary/ORF6.labels.json --- a/test-data/summary/ORF6.labels.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,179 +0,0 @@\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- "gb_MT326182_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_1365_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT358638_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_DEU_FFM1_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT359866_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_ESP_VH198152683_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT451104_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC203_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT520188_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00184_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT520493_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00316_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT601281_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_67_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT612186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1576_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT627613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S260_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT631787_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1651_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT641697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC595_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT683417_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_10131_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT706153_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_32_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT745697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC2124_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT745746_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_SA01_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT750335_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1794_2020_Segment_null_Host_Human":"Reference",\n- "gb_MT772447_Organism_Seve'..b'nce",\n- "gb_MW578233_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0795_2021_Segment_null_Host_Human":"Reference",\n- "gb_MW578246_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0808_2021_Segment_null_Host_Human":"Reference",\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":"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_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human":"Reference",\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":"Reference",\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":"Reference",\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":"Reference",\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":"Reference",\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":"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 841557158611 -r 8db8d509d51b test-data/summary/merged-segment.json --- a/test-data/summary/merged-segment.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 841557158611 -r 8db8d509d51b test-data/summary/merged-site.json --- a/test-data/summary/merged-site.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp7-segment.json --- a/test-data/summary/nsp7-segment.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp7.SLAC.json --- a/test-data/summary/nsp7.SLAC.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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"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- 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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp7.combined.fas --- a/test-data/summary/nsp7.combined.fas Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,588 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/summary/nsp7.labels.json --- a/test-data/summary/nsp7.labels.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,198 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/summary/nsp8-segment.json --- a/test-data/summary/nsp8-segment.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1183 +0,0 @@\n-{\n- "nsp8": {\n- "map": [\n- 12091,\n- 12094,\n- 12097,\n- 12100,\n- 12103,\n- 12106,\n- 12109,\n- 12112,\n- 12115,\n- 12118,\n- 12121,\n- 12124,\n- 12127,\n- 12130,\n- 12133,\n- 12136,\n- 12139,\n- 12142,\n- 12145,\n- 12148,\n- 12151,\n- 12154,\n- 12157,\n- 12160,\n- 12163,\n- 12166,\n- 12169,\n- 12172,\n- 12175,\n- 12178,\n- 12181,\n- 12184,\n- 12187,\n- 12190,\n- 12193,\n- 12196,\n- 12199,\n- 12202,\n- 12205,\n- 12208,\n- 12211,\n- 12214,\n- 12217,\n- 12220,\n- 12223,\n- 12226,\n- 12229,\n- 12232,\n- 12235,\n- 12238,\n- 12241,\n- 12244,\n- 12247,\n- 12250,\n- 12253,\n- 12256,\n- 12259,\n- 12262,\n- 12265,\n- 12268,\n- 12271,\n- 12274,\n- 12277,\n- 12280,\n- 12283,\n- 12286,\n- 12289,\n- 12292,\n- 12295,\n- 12298,\n- 12301,\n- 12304,\n- 12307,\n- 12310,\n- 12313,\n- 12316,\n- 12319,\n- 12322,\n- 12325,\n- 12328,\n- 12331,\n- 12334,\n- 12337,\n- 12340,\n- 12343,\n- 12346,\n- 12349,\n- 12352,\n- 12355,\n- 12358,\n- 12361,\n- 12364,\n- 12367,\n- 12370,\n- 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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8-site.json --- a/test-data/summary/nsp8-site.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8.BUSTED.json --- a/test-data/summary/nsp8.BUSTED.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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|
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8.CFEL.json --- a/test-data/summary/nsp8.CFEL.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8.FADE.json --- a/test-data/summary/nsp8.FADE.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8.FEL.json --- a/test-data/summary/nsp8.FEL.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8.MEME-full.json --- a/test-data/summary/nsp8.MEME-full.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8.MEME.json --- a/test-data/summary/nsp8.MEME.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8.PRIME.json --- a/test-data/summary/nsp8.PRIME.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,596 +0,0 @@\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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"epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",\n- "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",\n- "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",\n- "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",\n- "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",\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":"background",\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":"background",\n- "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"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- "Model fitting":{\n- "order":1,\n- "timer":5\n- },\n- "PRIME analysis":{\n- "order":2,\n- "timer":19\n- },\n- "Total time":{\n- "order":0,\n- "timer":25\n- }\n- }\n-}\n\\ No newline at end of file\n' |
| b |
| diff -r 841557158611 -r 8db8d509d51b test-data/summary/nsp8.RELAX.json --- a/test-data/summary/nsp8.RELAX.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,557 +0,0 @@\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, 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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 841557158611 -r 8db8d509d51b test-data/summary/nsp8.SLAC.json --- a/test-data/summary/nsp8.SLAC.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1350 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/summary/nsp8.combined.fas --- a/test-data/summary/nsp8.combined.fas Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,96 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/summary/nsp8.combined.fas.BGM.json --- a/test-data/summary/nsp8.combined.fas.BGM.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,253 +0,0 @@\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 841557158611 -r 8db8d509d51b test-data/summary/nsp8.labels.json --- a/test-data/summary/nsp8.labels.json Thu Mar 02 15:09:44 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,34 +0,0 @@ -{ - "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 |