| Previous changeset 26:8276bb2adea5 (2021-04-27) Next changeset 28:1dc833581081 (2021-06-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97" |
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added:
scripts/hyphy_summary.py 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 |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 scripts/hyphy_summary.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/hyphy_summary.py Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b"@@ -0,0 +1,668 @@\n+import argparse\n+import json\n+import re\n+from collections import defaultdict\n+\n+import BioExt\n+from Bio import SeqIO\n+from Bio.Seq import Seq\n+from Bio.SeqRecord import SeqRecord\n+from BioExt.uds import _align_par\n+\n+\n+class HyPhySummary(object):\n+\n+ def __init__(self, arguments, summary_json=None, annotation_json=None):\n+ self.arguments = arguments\n+ self.ref_map = ''\n+ self.summary_json = {}\n+ self.annotation_json = {}\n+ self.include_in_annotation = {}\n+ self.test_map = {}\n+ self.site_reports = {}\n+ self.labels = {}\n+ self.ref_seq_map = []\n+ self.cfel = {}\n+ self.relax = {}\n+ self.busted = {}\n+ self.slac = {}\n+ self.fel = {}\n+ self.meme = {}\n+ self.meme_full = {}\n+ self.prime = {}\n+ self.fade = {}\n+ self.bgm = {}\n+ self.ref_genes = [\n+ ['genome', 'ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGG"..b" return generate_error(char_index)\n+ current_node_annotation += current_char\n+ except Exception:\n+ return generate_error(char_index)\n+\n+ if (len(clade_stack) != 1):\n+ return generate_error(len(nwk_str) - 1)\n+\n+ if (len(current_node_name)):\n+ tree_json['name'] = current_node_name\n+\n+ return {\n+ 'json': tree_json,\n+ 'error': None\n+ }\n+\n+\n+if __name__ == '__main__':\n+ parser = argparse.ArgumentParser(description='Summarize selection analysis results.')\n+ parser.add_argument('--combined', help='Combined reference and query alignment from TN-93', required=False, type=str)\n+ parser.add_argument('--pvalue', help='p-value to use', required=False, type=float, default=0.05)\n+ parser.add_argument('--gene', help='Name of the gene or sequence being analyzed', required=False, type=str)\n+ parser.add_argument('--labels', help='JSON file with labels', required=False, type=str)\n+ parser.add_argument('--annotation-output', help='Write a JSON file with site annotations', required=True, type=str)\n+ parser.add_argument('--summary-output', help='Write a JSON file here segment annotations', required=True, type=str)\n+ parser.add_argument('--annotation-inputs', help='Comma-separated list of site annotation files to merge', required=False, type=str)\n+ parser.add_argument('--summary-inputs', help='Comma-separated list of segment annotation files to merge', required=False, type=str)\n+ parser.add_argument('--default-tag', help='Default name for sequences that have no explicit label', required=False, type=str, default='Reference')\n+ parser.add_argument('--name', help='The sequence ID to highlight', required=False, default='MN908947')\n+ parser.add_argument('--mode', help='Operation mode, generate a summary or merge multiple summaries', type=str, choices=['summary', 'merge'], default='summary')\n+ parser.add_argument('--relax', help='Path to RELAX.json file', required=False, type=str)\n+ parser.add_argument('--busted', help='Path to BUSTED.json file', required=False, type=str)\n+ parser.add_argument('--slac', help='Path to SLAC.json file', required=False, type=str)\n+ parser.add_argument('--fel', help='Path to FEL.json file', required=False, type=str)\n+ parser.add_argument('--cfel', help='Path to CFEL.json file', required=False, type=str)\n+ parser.add_argument('--meme', help='Path to MEME.json file', required=False, type=str)\n+ parser.add_argument('--meme-full', help='Path to MEME-full.json file', dest='meme_full', required=False, type=str)\n+ parser.add_argument('--prime', help='Path to PRIME.json file', required=False, type=str)\n+ parser.add_argument('--fade', help='Path to FADE.json file', required=False, type=str)\n+ parser.add_argument('--bgm', help='Path to BGM.json file', required=False, type=str)\n+ arguments = parser.parse_args()\n+ if arguments.mode == 'summary':\n+ analyzer = HyPhySummary(arguments)\n+ annotation_json, summary_json = analyzer.summary()\n+ if annotation_json is not None:\n+ with open(arguments.annotation_output, 'w') as fh:\n+ json.dump(annotation_json, fh, indent=1)\n+ if summary_json is not None:\n+ with open(arguments.summary_output, 'w') as fh:\n+ json.dump(summary_json, fh, indent=1)\n+ else:\n+ summary = {}\n+ annotation = {}\n+ for filename in arguments.annotation_inputs.split(','):\n+ with open(filename, 'r') as fh:\n+ annotation.update(json.load(fh))\n+ for filename in arguments.summary_inputs.split(','):\n+ with open(filename, 'r') as fh:\n+ summary.update(json.load(fh))\n+ with open(arguments.annotation_output, 'w') as fh:\n+ json.dump(annotation, fh, indent=1)\n+ with open(arguments.summary_output, 'w') as fh:\n+ json.dump(summary, fh, indent=1)\n+ exit(0)\n" |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/ORF6-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6-segment.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,7 @@\n+{\n+ "ORF6": {\n+ "map": [],\n+ "tree": "(REFERENCE,(gb_MW505295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3142_2021_Segment_null_Host_Human,gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human)Node184,epi_isl_1533799_hCoV_19_India_MH_NCCS_9947_2021,gb_MW155738_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11358_2020_Segment_null_Host_Human,gb_MW064840_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_QDX_825_2020_Segment_null_Host_Human,(gb_MW545306_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3723_2021_Segment_null_Host_Human,gb_MW547503_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC09I039_2020_Segment_null_Host_Human)Node194,(epi_isl_1543980_hCoV_19_Singapore_490_2021,gb_MW565832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0724_2021_Segment_null_Host_Human)Node198,(gb_MW093451_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_DSHS_0533_2020_Segment_null_Host_Human,gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human)Node201,(gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human,gb_MW156732_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10631_2020_Segment_null_Host_Human)Node206,epi_isl_1631286_hCoV_19_England_CAMC_14E7527_2021,gb_MW486406_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2638_2020_Segment_null_Host_Human,gb_MW035934_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_2214_2020_Segment_null_Host_Human,gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human,gb_MW154411_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC6964_2020_Segment_null_Host_Human,gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human,gb_MW134116_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_3258_2020_Segment_null_Host_Human,(gb_MW549937_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3900_2021_Segment_null_Host_Human,gb_MW549223_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3727_2020_Segment_null_Host_Human)Node226,((gb_MW545248_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3654_2021_Segment_null_Host_Human,gb_MW578246_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0808_2021_Segment_null_Host_Human)Node231,gb_MW549830_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2465_2020_Segment_null_Host_Human)Node230,gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human,epi_isl_1589923_hCoV_19_India_WB_1930300571091_2021,gb_MW539842_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_00583_2020_Segment_null_Host_Human,(gb_MW208032_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_1590_2020_Segment_null_Host_Human,gb_MW056168_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_U'..b'piratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human,gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human,gb_MW406537_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_2_3693679_2020_Segment_null_Host_Human,gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human,(gb_MW156645_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11076_2020_Segment_null_Host_Human,gb_MW156971_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10203_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_MW420890_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2020316507_2020_Segment_null_Host_Human)Node62,epi_isl_1589926_hCoV_19_India_WB_1930300586246_2021,(gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human,gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human)Node71,gb_MW064863_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_QDX_779_2020_Segment_null_Host_Human,gb_MW155278_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12385_2020_Segment_null_Host_Human,epi_isl_1442952_hCoV_19_Singapore_321_2021,gb_MW193966_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_nimh_12171_2020_Segment_null_Host_Human,gb_MW462661_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2263_2020_Segment_null_Host_Human,epi_isl_1516887_hCoV_19_Australia_QLD1826_2021,gb_MW521810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3530_2020_Segment_null_Host_Human,gb_MW490888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2295_2020_Segment_null_Host_Human,gb_MW155642_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13394_2020_Segment_null_Host_Human,gb_MT847221_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_283_2020_Segment_null_Host_Human,gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human,gb_MW578233_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0795_2021_Segment_null_Host_Human,gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human,gb_MW543030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9A_6594_2020_Segment_null_Host_Human,gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human,gb_MT873189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_DPH_00301_2020_Segment_null_Host_Human,(gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human,gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human)Node100,gb_MT811511_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1079_SAN_2020_Segment_null_Host_Human)",\n+ "tree_tags": {}\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/ORF6-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6-site.json Wed Jun 09 07:03:05 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/ORF6.FADE.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.FADE.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,3142 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "A":{\n+ "0": [\n+[0.8995906688309242, 5.594143577985283, 0.946609453050319, 0.985559664964498],\n+ [1.044067957308116, 5.592799085749478, 0.9466955286719859, 0.9872409006967756],\n+ [1.036405878450414, 5.592977245431012, 0.9467064115746399, 0.9874538531239992],\n+ [1.19730312499705, 5.591581681880384, 0.9467807517201779, 0.9889108417502863],\n+ [0.834106476942848, 4.607368577968402, 0.9445445107901261, 0.9467914811705906],\n+ [1.594329564126259, 5.58405032798539, 0.9498733406998108, 1.053351676897583],\n+ [1.044067957308116, 5.592799085749476, 0.9466955286719857, 0.9872409006967714],\n+ [9.963744241830298, 5.54757896832387, 0.949796513525156, 1.051654650196095],\n+ [0.8341064769428478, 4.607368577968402, 0.9445445107901261, 0.9467914811705906],\n+ [0.8263616796556617, 4.962381890578685, 0.9452991472766892, 0.9606199984313556],\n+ [1.355846770273862, 5.587576320848405, 0.9468186115030929, 0.9896544191230371],\n+ 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| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/ORF6.MEME-full.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.MEME-full.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
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| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/ORF6.SLAC.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.SLAC.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,4781 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0":{\n+ "by-branch":{\n+ "AVERAGED": [\n+[0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [44.30740262828303, 130.37043765588, 1, 0, 0.2536521092555556, 0.02256959200225525, 0, -0.02222397288334375, 1, 0.2536521092555557, 0.005580025520913685],\n+ [44.15327252744373, 130.5245677567193, 0, 1, 0.2527697414601411, 0, 0.007661392925382973, 0.007544070296234822, 0.7472302585398589, 1, 0.00558460667963908],\n+ [44.08153844682656, 130.6786978575586, 1, 0, 0.252240094079802, 0.02268523366547771, 0, -0.02233784366963816, 1, 0.252240094079802, 0.005586229046527186],\n+ [43.99914242660442, 130.6786978575586, 0, 1, 0.2518873736647267, 0, 0.007652356630382193, 0.007535172378406127, 0.7481126263352733, 1, 0.005579404930925916],\n+ [44.21306418682298, 130.4647760973401, 0, 1, 0.2531120382236115, 0, 0.00766490412135378, 0.007547527723557193, 0.7468879617763885, 1, 0.005577806290397803],\n+ 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1, 0],\n+ [44.21306418682298, 130.4647760973401, 0, 1, 0.2531120382236115, 0, 0.00766490412135378, 0.007547527723557193, 0.7468879617763885, 1, 0.005582536378668013],\n+ [43.99914242660442, 130.6786978575586, 0, 1, 0.2518873736647267, 0, 0.007652356630382193, 0.007535172378406127, 0.7481126263352733, 1, 0.005610995690299318],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [43.99914242660442, 130.6786978575586, 1, 0, 0.2518873736647267, 0.02272771569737101, 0, -0.02237967515355384, 1, 0.2518873736647267, 0.005612056496775136],\n+ [44.367616686608, 130.3102235975551, 0, 1, 0.2539968241789083, 0, 0.007673994966721572, 0.007556479356396646, 0.7460031758210917, 1, 0.005611861400289367],\n+ [44.2948056817287, 130.5969563626529, 1, 0, 0.2532698233693144, 0.02257601054140064, 0, -0.02223029313228328, 1, 0.2532698233693145, 0.005581838321706729],\n+ [44.15327252744373, 130.5245677567193, 0, 1, 0.2527697414601412, 0, 0.007661392925382975, 0.007544070296234824, 0.7472302585398588, 1, 0.005581838321706729],\n+ [43.99914242660442, 130.6786978575586, 0, 1, 0.2518873736647267, 0, 0.007652356630382193, 0.007535172378406127, 0.7481126263352733, 1, 0.005612261737859944],\n+ [43.84501232576511, 130.832827958398, 0, 1, 0.2510050058693121, 0, 0.007643341626139722, 0.007526295425300025, 0.7489949941306879, 1, 0.005614125291650073],\n+ [43.78522066638586, 130.8926196177772, 0, 1, 0.2506627091058418, 0, 0.007639850152897275, 0.007522857418682301, 0.7493372908941582, 1, 0.005614188942122219],\n+ [44.01629825618177, 130.8717871833653, 0, 1, 0.2516826583443658, 0, 0.007641066279616809, 0.007524054922263002, 0.7483173416556342, 1, 0.005612328366098883],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [44.08219297214297, 130.508685322092, 0, 1, 0.252488522898'..b'acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0808_2021_Segment_null_Host_Human":"test",\n+ "gb_MW583187_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OK_CDC_STM_000003021_2021_Segment_null_Host_Human":"test",\n+ "gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586184_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005891_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005477_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586385_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000005076_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586419_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IA_CDC_STM_000005050_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_QDX_4292_2021_Segment_null_Host_Human":"test",\n+ "gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human":"test",\n+ "gb_MW592782_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2311_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_1171_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593378_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_8518_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593611_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_7938_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human":"test",\n+ "gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human":"test",\n+ "gb_MW598427_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_nmimr_SARS_CoV_2_NTRA_15010_2020_Segment_null_Host_Human":"test",\n+ "gb_MW599514_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00376_2021_Segment_null_Host_Human":"test",\n+ "gb_MW599662_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_Broad_RIDOH_00108_2020_Segment_null_Host_Human":"test"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "Primary SLAC analysis":{\n+ "order":2,\n+ "timer":1\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":4\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/ORF6.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.combined.fas Wed Jun 09 07:03:05 2021 +0000 |
| b |
| b'@@ -0,0 +1,531 @@\n+>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1284652/hCoV-19/Germany/SN-RKI-I-038291/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCACAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1442952/hCoV-19/Singapore/321/2021\n+ATGTTTCATCTCGTTGGCTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1512225/hCoV-19/USA/GA-CDC-STM-000041012/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGTACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1470937/hCoV-19/USA/NY-PRL-2021_03_29_01C17/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAC\n+\n+>epi_isl_1516887/hCoV-19/Australia/QLD1826/2021\n+ATGTTTCATCTCGTTGACTTTCATGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATCTGT\n+\n+>epi_isl_1533799/hCoV-19/India/MH-NCCS-9947/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATACTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1543980/hCoV-19/Singapore/490/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATTTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1589923/hCoV-19/India/WB-1930300571091/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAAGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1589926/hCoV-19/India/WB-1930300586246/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAATTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>epi_isl_1631286/hCoV-19/England/CAMC-14E7527/2021\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACTAATGGAGATTGAT\n+\n+\n+>REFERENCE\n+ATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human\n+AGATGTTATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MT860680_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_DRICM_isl_MH_09_2020_Segment_null_Host_Human\n+ATGCTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW571108_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS49_2021_Segment_null_Host_Human\n+ATGTATCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAAT'..b'AATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW521749_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NV_QDX_3543_2020_Segment_null_Host_Human\n+ATGTTTCATCTCGTTTACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTATATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human\n+ATGTTTCATCTCTTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATCCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW571185_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS69_2021_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTCTC\n+\n+>gb_MT745746_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_SA01_2020_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAC\n+\n+>gb_MW156732_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10631_2020_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human\n+ATGTTTCATCTTGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTGTTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW435625_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_DSHS_1968_2020_Segment_null_Host_Human\n+ATGTTTCATTTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW420890_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2020316507_2020_Segment_null_Host_Human\n+ATGTTTCATTTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTTAT\n+\n+>gb_MW155387_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13741_2020_Segment_null_Host_Human\n+ATGTTTTATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW193966_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_nimh_12171_2020_Segment_null_Host_Human\n+ATTTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n+\n+>gb_MW560924_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00280_2021_Segment_null_Host_Human\n+CAGATGCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGAT\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/ORF6.labels.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/ORF6.labels.json Wed Jun 09 07:03:05 2021 +0000 |
| b |
| b'@@ -0,0 +1,179 @@\n+{\n+ "REFERENCE":"Reference",\n+ "epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021":"B-1-617",\n+ "epi_isl_1284652/hCoV-19/Germany/SN-RKI-I-038291/2021":"B-1-617",\n+ "epi_isl_1442952/hCoV-19/Singapore/321/2021":"B-1-617",\n+ "epi_isl_1470937/hCoV-19/USA/NY-PRL-2021_03_29_01C17/2021":"B-1-617",\n+ "epi_isl_1512225/hCoV-19/USA/GA-CDC-STM-000041012/2021":"B-1-617",\n+ "epi_isl_1516887/hCoV-19/Australia/QLD1826/2021":"B-1-617",\n+ "epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021":"B-1-617",\n+ "epi_isl_1533799/hCoV-19/India/MH-NCCS-9947/2021":"B-1-617",\n+ "epi_isl_1543980/hCoV-19/Singapore/490/2021":"B-1-617",\n+ "epi_isl_1589923/hCoV-19/India/WB-1930300571091/2021":"B-1-617",\n+ "epi_isl_1589926/hCoV-19/India/WB-1930300586246/2021":"B-1-617",\n+ "epi_isl_1631286/hCoV-19/England/CAMC-14E7527/2021":"B-1-617",\n+ "gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human":"Reference",\n+ 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"gb_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 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/merged-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/merged-segment.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,132 @@\n+{\n+ "nsp7": {\n+ "map": [],\n+ "tree": 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oV_19_India_WB_1930300586246_2021,(gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human,gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human)Node71,gb_MW064863_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_QDX_779_2020_Segment_null_Host_Human,gb_MW155278_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12385_2020_Segment_null_Host_Human,epi_isl_1442952_hCoV_19_Singapore_321_2021,gb_MW193966_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_nimh_12171_2020_Segment_null_Host_Human,gb_MW462661_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2263_2020_Segment_null_Host_Human,epi_isl_1516887_hCoV_19_Australia_QLD1826_2021,gb_MW521810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3530_2020_Segment_null_Host_Human,gb_MW490888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2295_2020_Segment_null_Host_Human,gb_MW155642_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13394_2020_Segment_null_Host_Human,gb_MT847221_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_283_2020_Segment_null_Host_Human,gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human,gb_MW578233_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0795_2021_Segment_null_Host_Human,gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human,gb_MW543030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9A_6594_2020_Segment_null_Host_Human,gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human,gb_MT873189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_DPH_00301_2020_Segment_null_Host_Human,(gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human,gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human)Node100,gb_MT811511_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1079_SAN_2020_Segment_null_Host_Human)",\n+ "tree_tags": {}\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/merged-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/merged-site.json Wed Jun 09 07:03:05 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp7-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7-segment.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,7 @@\n+{\n+ "nsp7": {\n+ "map": [],\n+ "tree": 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"tree_tags": {}\n+ }\n+}\n\\ No newline at end of file\n' |
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| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp7-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7-site.json Wed Jun 09 07:03:05 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp7.FADE.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.FADE.json Wed Jun 09 07:03:05 2021 +0000 |
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"Residue S analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue T analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue V analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue W analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue Y analysis":{\n+ "order":21,\n+ "timer":8\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp7.MEME-full.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.MEME-full.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
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"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":"background",\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":"background",\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":"background",\n+ "gb_MW589574_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4494168_2021_Segment_null_Host_Human":"background",\n+ "gb_MW589620_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4464910_2020_Segment_null_Host_Human":"background",\n+ "gb_MW590718_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC434_2020_Segment_null_Host_Human":"background",\n+ 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| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp7.SLAC.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.SLAC.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
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"gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585982_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_000003668_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585995_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WV_CDC_STM_000003152_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586140_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005978_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586167_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000005966_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586286_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005415_2021_Segment_null_Host_Human":"test",\n+ "gb_MW586766_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4270_2021_Segment_null_Host_Human":"test",\n+ "gb_MW589574_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4494168_2021_Segment_null_Host_Human":"test",\n+ "gb_MW589620_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4464910_2020_Segment_null_Host_Human":"test",\n+ "gb_MW590718_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC434_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593416_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_880_2020_Segment_null_Host_Human":"test",\n+ "gb_MW593460_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4649_2020_Segment_null_Host_Human":"test",\n+ "gb_MW596017_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000007226_2021_Segment_null_Host_Human":"test",\n+ "gb_MW596107_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000008078_2021_Segment_null_Host_Human":"test",\n+ "gb_MW596147_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000008176_2021_Segment_null_Host_Human":"test",\n+ "gb_MW599561_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00424_2021_Segment_null_Host_Human":"test"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "Primary SLAC analysis":{\n+ "order":2,\n+ "timer":2\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":7\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp7.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.combined.fas Wed Jun 09 07:03:05 2021 +0000 |
| b |
| b'@@ -0,0 +1,588 @@\n+>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1409773/hCoV-19/England/CAMC-141DB08/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATTCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1415264/hCoV-19/India/MH-NCCS-128864/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGTTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1415273/hCoV-19/India/MH-NCCS-87216/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAATAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1564187/hCoV-19/England/CAMC-14D5BFD/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCTATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1583966/hCoV-19/England/CAMC-14D1B4C/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATTTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1641831/hCoV-19/Germany/BY-RKI-I-076082/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGACATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1648157/hCoV-19/USA/CA-CDC-QDX23571833/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTTTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAATCTTACAA\n+\n+>epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGATATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1635400/hCoV-19/Scotland/CAMC-14DEDB2/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGCGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>epi_isl_1652109/hCoV-19/Singapore/565/2021\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAGTGCTGGACAACAGGGCAACCTTACAA\n+\n+\n+>REFERENCE\n+TCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW579030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101421353_2021_Segment_null_Host_Human\n+TCAAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAA'..b'_MW550719_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_2_3768763_2020_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAAGTGCATATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MT827207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0041_2020_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAAGTGTACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACCGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW524933_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_0000014_D07_2021_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAAGTGTACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW449300_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012152791_2020_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAAGTGTACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATTCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW153116_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7846_2020_Segment_null_Host_Human\n+TCTAAAATGTCAGATGTAAGGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW406612_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OK_CDC_2_3693466_2020_Segment_null_Host_Human\n+TCTAAAATGTCGGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW012269_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_SRB_NP01_2020_Segment_null_Host_Human\n+TCTAAAATTTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MW525004_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NM_CDC_STM_0000014_B01_2021_Segment_null_Host_Human\n+TCTAAAGTGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MT937322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0133_2020_Segment_null_Host_Human\n+TCTAGAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCTATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n+\n+>gb_MT831570_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S2629_2020_Segment_null_Host_Human\n+TCTGAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTAGACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAA\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp7.labels.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.labels.json Wed Jun 09 07:03:05 2021 +0000 |
| b |
| b'@@ -0,0 +1,198 @@\n+{\n+ "REFERENCE":"Reference",\n+ "epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021":"B-1-617",\n+ "epi_isl_1409773/hCoV-19/England/CAMC-141DB08/2021":"B-1-617",\n+ "epi_isl_1415264/hCoV-19/India/MH-NCCS-128864/2021":"B-1-617",\n+ "epi_isl_1415273/hCoV-19/India/MH-NCCS-87216/2021":"B-1-617",\n+ "epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021":"B-1-617",\n+ "epi_isl_1564187/hCoV-19/England/CAMC-14D5BFD/2021":"B-1-617",\n+ "epi_isl_1583966/hCoV-19/England/CAMC-14D1B4C/2021":"B-1-617",\n+ "epi_isl_1635400/hCoV-19/Scotland/CAMC-14DEDB2/2021":"B-1-617",\n+ "epi_isl_1641831/hCoV-19/Germany/BY-RKI-I-076082/2021":"B-1-617",\n+ "epi_isl_1648157/hCoV-19/USA/CA-CDC-QDX23571833/2021":"B-1-617",\n+ "epi_isl_1652109/hCoV-19/Singapore/565/2021":"B-1-617",\n+ "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT291831_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_Beijing_IME_BJ01_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT380729_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_1999_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT412283_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_5772_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT446348_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_BIE_080_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT451046_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC142_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT451174_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC278_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT451724_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1057_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT460125_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1105_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT470179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_France_40002VJ_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT499218_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_TUN_COV1663_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT512423_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_3688_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT609578_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_0348_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT609579_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VA_DCLS_0349_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT612207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1606_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT628119_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1404_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT628199_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1525_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT642069_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S1116_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT704128_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0028_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT731735_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_137_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT755838_Organism_Severe_acute_respiratory_syndrome_coro'..b',\n+ "gb_MW577113_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00314_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW577730_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101009422_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW577930_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101239410_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW578033_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101679988_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW578122_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101329819_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW578256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_2_3714171_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW579014_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101155076_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW579030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101421353_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW585982_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_000003668_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW585995_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WV_CDC_STM_000003152_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586140_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005978_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586167_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000005966_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586286_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005415_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586766_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4270_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW589574_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4494168_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW589620_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_4464910_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW590718_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC434_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593416_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_880_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593460_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4649_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW596017_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000007226_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW596107_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000008078_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW596147_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000008176_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW599561_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00424_2021_Segment_null_Host_Human":"Reference"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8-segment.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8-segment.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| @@ -0,0 +1,122 @@ +{ + "nsp8": { + "map": [], + "rates": { + "mean-omega": { + "B-1-617": 21.18256593595067, + "Reference": 0, + "background": 0.5156677174296214 + }, + "T": { + "B-1-617": 0.003269500911862614, + "Reference": 0.001919664151147453, + "background": 0.10664581418249912 + }, + "relax": { + "B-1-617": [ + { + "omega": 0, + "proportion": 0.3229316344832856 + }, + { + "omega": 0, + "proportion": 0.6561871399951409 + }, + { + "omega": 887.8019782663979, + "proportion": 0.02088122552157349 + } + ], + "Reference": [ + { + "omega": 0, + "proportion": 0.3229316344832856 + }, + { + "omega": 0, + "proportion": 0.6561871399951409 + }, + { + "omega": 887.8019782663979, + "proportion": 0.02088122552157349 + } + ], + "background": [ + { + "omega": 0, + "proportion": 0.3229316344832856 + }, + { + "omega": 0, + "proportion": 0.6561871399951409 + }, + { + "omega": 2.618905128891877, + "proportion": 0.02088122552157349 + } + ] + }, + "busted": { + "Background": { + "0": { + "omega": 0, + "proportion": 0.02741862862724963 + }, + "1": { + "omega": 0.1719979491289183, + "proportion": 0.8111826871363725 + }, + "2": { + "omega": 2.232058479326601, + "proportion": 0.1613986842363778 + } + }, + "Synonymous site-to-site rates": { + "0": { + "proportion": 0, + "rate": 0.9502886367487763 + }, + "1": { + "proportion": 1, + "rate": 1 + }, + "2": { + "proportion": 0, + "rate": 1.059678592887729 + } + }, + "Test": { + "0": { + "omega": 0.9993684330797956, + "proportion": 0 + }, + "1": { + "omega": 0.999368433118802, + "proportion": 0 + }, + "2": { + "omega": 25.32658549655282, + "proportion": 1 + } + } + } + }, + "relax": { + "p": 0.07260318641568564, + "K": 7.051367447513434 + }, + "busted": { + "p": 0.3056667368082906 + }, + "tree": "(REFERENCE,(gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021,(epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021,gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021,gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node38,epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human,epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021,epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021,gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human,epi_isl_1652118_hCoV_19_Singapore_575_2021,epi_isl_1652105_hCoV_19_Singapore_561_2021,gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)", + "tree_tags": {}, + "prime-properties": [ + "Factor I bipolar", + "Factor II secondary structure", + "Factor III volume", + "Factor IV composition", + "Factor V charge" + ], + "bgm": [] + } +} \ No newline at end of file |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8-site.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8-site.json Wed Jun 09 07:03:05 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.BUSTED.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.BUSTED.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,580 @@\n+{\n+ "Evidence Ratios":{\n+ "constrained": [\n+[0.9898739518379264, 0.991027168169301, 0.9898739518379268, 0.9897812891397899, 0.9906204835370439, 0.9853516617064797, 0.9880798288003553, 0.9889781190332573, 0.988350548699827, 0.989374526624819, 0.9897812891397899, 0.9927999621758878, 0.9898739523607402, 0.9898739518379268, 0.9853516617064797, 0.9898739518379268, 0.9930617996638492, 0.9898739518379268, 0.9956363652357774, 0.9953242584232271, 0.9898739518379268, 0.9927999621758878, 0.9906204835370439, 0.9909311149283309, 0.9898739518379268, 0.9888494594022271, 0.9898739518379268, 0.9942729604246417, 0.9875096976732132, 0.9910812249043462, 0.9889781181731668, 0.9953242584232271, 0.9888494594022271, 0.9888494594022271, 0.9883505486998261, 0.9965511193500521, 25.13531965114348, 0.9852148186803413, 0.9918415472526246, 0.9918415472526246, 0.9889781181731668, 0.9852148186803413, 0.9942729604246417, 0.9888494579313646, 0.9898739518379264, 0.9965511193500521, 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"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+ "Constrained BUSTED model fitting":{\n+ "order":3,\n+ "timer":3\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":76\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":6\n+ },\n+ "Unconstrained BUSTED model fitting":{\n+ "order":2,\n+ "timer":66\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.CFEL.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.CFEL.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,589 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [3.206171473304911, 0, 0.03175555207671071, 5.433962997865532e-05, 0, 0, 0.9766417072604165, 1, -1, 0.1428350861439815],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 2.691597641547223, 0.6095939176926283, 0, 0, 0, 1, 1, -1, 0.334509864610243],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [3.229642435228862, 0, 2.162021710309243, 0.004452160407161729, 0, 0, 0.8693548005974709, 1, -1, 0.1442288861347906],\n+ [0, 2.170494633509469, 0.2961869984298745, 0, 0, 0, 0.9875062279782896, 1, -1, 0.2697178710749373],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [6.636646908481298, 0, 1.139449512908137, 6.624437421595782e-05, 0, 0, 0.906603671841744, 1, -1, 0.2958257534388632],\n+ [0, 3.585093121716918, 0.4689445336386987, 0, 0, 0, 1, 1, -1, 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| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.FADE.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.FADE.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,4714 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "A":{\n+ "0": [\n+[2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [1.117825271287792, 5.297486980684134, 0.94604302164483, 0.9890764026148687],\n+ [2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [18.9004123856017, 5.317669856443896, 0.9492912500886677, 1.056046759725475],\n+ [1.278267402694179, 5.298403086637607, 0.9461144831242656, 0.9904628995183727],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [19.19497341524307, 5.317540422140158, 0.9492955761547635, 1.056141673876794],\n+ [2.522173999598023, 5.296053746322004, 0.9463762215641978, 0.9955727079586607],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [1.495447087063753, 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"timer":2\n+ },\n+ "Residue L analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue M analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue N analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue P analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue Q analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue R analysis":{\n+ "order":21,\n+ "timer":3\n+ },\n+ "Residue S analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue T analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue V analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue W analysis":{\n+ "order":21,\n+ "timer":3\n+ },\n+ "Residue Y analysis":{\n+ "order":21,\n+ "timer":2\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.FEL.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.FEL.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
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| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.MEME-full.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.MEME-full.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
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| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.MEME.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.MEME.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,916 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [3.180864197338322, 2.543979863949704, 1, 4.771296296007484, 0, 0, 0.6666666666666666, 0, 0, -9.280586212023099, -9.280586212023099],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0.0002152055713864022, 5.380139284660055e-05, 1, 0.5537159057721711, 0, 0, 0.6666666666666666, 0, 0, -9.653547986238197, -9.653323462942367],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [3.192432742671397, 2.614421539287398, 1, 4.788649114007091, 0, 0, 0.6666666666666666, 0, 0, -9.282601941350496, -9.282601941350496],\n+ [0, 0, 1, 1.464518485321612, 0, 0, 0.6666666666666666, 0, 0, -10.62393719963694, -10.62320682078165],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [6.613018745603487, 0.9469109242998108, 1, 9.919528118405228, 0, 0, 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| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.PRIME.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.PRIME.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
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| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.RELAX.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.RELAX.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,557 @@\n+{\n+ "Synonymous site-posteriors": [\n+[1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1],\n+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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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 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.SLAC.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.SLAC.json Wed Jun 09 07:03:05 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1350 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0":{\n+ "by-branch":{\n+ "AVERAGED": [\n+[0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [147.0112938906491, 421.9561434851458, 2, 13, 0.2583826142471318, 0.01360439696209771, 0.03080888902961936, 0.1540517400002438, 0.2141909453461294, 0.9297070045663574, 0.02664074934348415],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [145.5893054241774, 422.7504844557024, 0, 1, 0.2561659556775853, 0, 0.002365461511623139, 0.02118071607920737, 0.7438340443224147, 1, 0.001731141176898499],\n+ [145.8316085824376, 422.1143927092281, 2, 1, 0.256770200425351, 0.01371444791318621, 0.00236902606798543, -0.1015886995925552, 0.9830709003936052, 0.1639346082666348, 0.005234957209780722],\n+ [145.1406999043445, 423.0445443145819, 0, 1, 0.2554460915363381, 0, 0.002363817270401638, 0.0211659932835469, 0.7445539084636619, 1, 0.001731048067785009],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [145.8529411821772, 422.1089052052787, 1, 1, 0.2568005969236854, 0.006856221012032613, 0.00236905686581922, -0.04017877666355647, 0.9340534534196389, 0.4476546472670097, 0.003467134004764108],\n+ [145.4861542433911, 422.5873910598001, 0, 1, 0.2561044347976854, 0, 0.002366374437940792, 0.02118889056568302, 0.7438955652023147, 1, 0.001730401012235807],\n+ [145.1406999043445, 423.0445443145819, 0, 1, 0.2554460915363381, 0, 0.002363817270401638, 0.0211659932835469, 0.7445539084636619, 1, 0.001731056498022235],\n+ [145.1406999043445, 422.9908819061909, 0, 2, 0.2554702194900108, 0, 0.004728234308472756, 0.04233735698155978, 0.5543245940662527, 1, 0.003467572164636923],\n+ [145.4122726402566, 422.7729715786698, 2, 1, 0.2559240566694972, 0.01375399726368289, 0.002365335693684286, -0.1019758749195625, 0.9832377106374066, 0.1629667896213286, 0.005208678680963088],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [145.6740026904847, 422.5112415284417, 2, 0, 0.2563846987803072, 0.01372928568626911, 0, -0.1229341930368812, 1, 0.06573311376866875, 0.003469467349330688],\n+ [144.5765205593867, 423.0765753966273, 0, 2, 0.2546916798117659, 0, 0.004727276612100382, 0.04232878161694121, 0.5554844921418073, 1, 0.003467824865270607],\n+ [144.9219748984333, 422.7847834659717, 0, 1, 0.2552761135272754, 0, 0.00236526961023063, 0.02117899776382157, 0.7447238864727246, 1, 0.00173293384624849],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [145.2040645709122, 422.7419367207535, 1, 0, 0.2556652643749197, 0.006886859558339965, 0, -0.06166602849626656, 1, 0.2556652643749198, 0.001731477826576347],\n+ [145.4861542433911, 422.6990899755353, 1, 0, 0.2560540875069506, 0.006873506315432944, 0, -0.06154646144968366, 1, 0.2560540875069506, 0.001729315851762792],\n+ [144.9551193854748, 423.2301248334516, 0, 3, 0.2551194717925874, 0, 0.007088342308290441, 0.06347013687029401, 0.4132947274045454, 1, 0.005199356347141997],\n+ [145.6136982549165, 422.5715459640099, 1, 0, 0.2562785636136836, 0.006867485765311479, 0, -0.06149255249274786, 1, 0.2562785636136836, 0.001730674922882492],\n+ [145.0565770101724, 422.9633058846278, 0, 6, 0.2553723582190828, 0, 0.01418562772827539, 0.1270203517755656, 0.1704648824625068, 1, 0.01048699203960315],\n+ [145.9861542433911, 422.1990899755353, 0, 1, 0.2569340822007363, 0, 0.002368550818188514, 0.02120837821825352, 0.7430659177992637, 1, 0.00172931598734411],\n+ [145.5893054241774, 422.8397764862196, 0, 1, 0.2561257156915259, 0, 0.002364961991773709, 0.02117624329955963, 0.7438742843084741, 1, 0.001731607586790447],\n+ [145.4861542433911, 422.6990899755353, 1, 0, 0.2560540875069506, 0.006873506315432944, 0, -0.06154646144968366, 1, 0.2560540875069506, 0.001731056555105113],\n+ [145.6406999043445, 422.5445443145819, 0, 2, 0.2563260862301238, 0, 0.004733228784776385, 0.04238207'..b'oV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human,epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Node20":"test",\n+ "Node38":"test",\n+ "Node4":"test",\n+ "REFERENCE":"test",\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"test",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"test",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"test",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"test",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"test",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"test",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"test",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"test",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"test",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"test",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"test",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"test",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"test",\n+ "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"test",\n+ "epi_isl_1652105_hCoV_19_Singapore_561_2021":"test",\n+ "epi_isl_1652118_hCoV_19_Singapore_575_2021":"test",\n+ "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"test",\n+ "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"test",\n+ "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"test",\n+ "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"test",\n+ "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"test",\n+ "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"test",\n+ "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"test",\n+ "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"test",\n+ "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"test",\n+ "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"test",\n+ "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"test",\n+ "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"test",\n+ "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"test",\n+ "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"test"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":0\n+ },\n+ "Primary SLAC analysis":{\n+ "order":2,\n+ "timer":1\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":1\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.combined.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.combined.fas Wed Jun 09 07:03:05 2021 +0000 |
| b |
| b'@@ -0,0 +1,96 @@\n+>epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACGGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAATTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTGTGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAATTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTATAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021\n+GCTATAGCCTCAGAGTTTAGT'..b'TGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAGTACGTGTGATGGTATAACATTTATTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGATAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAATTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTTGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGTCTAGATGTGAGGACAAGAGGTCAAAACTTACTATGGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGTTTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGACGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATATCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAGTTCTCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCTTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATTCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+\n+>gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human\n+GCTATAGCTTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCGCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.combined.fas.BGM.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.combined.fas.BGM.json Wed Jun 09 07:03:05 2021 +0000 |
| b |
| b'@@ -0,0 +1,253 @@\n+{\n+ "analysis":{\n+ "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond",\n+ "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950",\n+ "contact":"apoon42@uwo.ca",\n+ "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\\nmap substitution (non-synonymous only for coding data) events to branches in the\\nphylogeny and then analyzes the joint distribution of the\\nsubstitution map using a Bayesian graphical model (network).\\nNext, a Markov chain Monte Carlo analysis is used to generate\\na random sample of network structures from the posterior\\ndistribution given the data. Each node in the network\\nrepresents a codon site in the alignment, and links (edges)\\nbetween nodes indicate high posterior support for correlated\\nsubstitutions at the two sites over time, which implies coevolution.",\n+ "requirements":"in-frame codon alignment and a phylogenetic tree",\n+ "version":"1.2"\n+ },\n+ "branch attributes":{\n+ "0":{\n+ "Node10":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node12":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node13":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node16":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node19":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node2":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node20":{\n+ "models.codon.MG_REV.ModelDescription":0.001732564301319626\n+ },\n+ "Node23":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node24":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node27":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node28":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node29":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node3":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node30":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node33":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node34":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node35":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node36":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node38":{\n+ "models.codon.MG_REV.ModelDescription":0.001730721769143463\n+ },\n+ "Node4":{\n+ "models.codon.MG_REV.ModelDescription":0.001731994998894883\n+ },\n+ "Node40":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node43":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node44":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node47":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node50":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node54":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node57":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node58":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "Node8":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "REFERENCE":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{\n+ "models.codon.MG_REV.ModelDescription":0.001729346788706704\n+ },\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{\n+ "models.codon.MG_REV.ModelDescription":0\n+ },\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{\n+ "models.codon.MG_REV.ModelDescription":0.001726770081665013\n+ },\n+ "epi_isl_1416968_hCoV_19_Guadelo'..b'"AIC-c":2565.76651309329,\n+ "Log Likelihood":-1205.948282908683,\n+ "Rate Distributions":null,\n+ "display order":0,\n+ "estimated parameters":76\n+ }\n+ },\n+ "input":{\n+ "datatype":"codon",\n+ "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas",\n+ "number of sequences":32,\n+ "number of sites":198,\n+ "trees":{\n+ "0":"((((epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021,gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human)Node4,epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021)Node3,(epi_isl_1652118_hCoV_19_Singapore_575_2021,(epi_isl_1652105_hCoV_19_Singapore_561_2021,((gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human,gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human)Node13,(epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)Node16)Node12)Node10)Node8)Node2,((gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human,epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021)Node20,((gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human,epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021)Node24,((((gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human,gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human)Node30,((((gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human,(gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human,(gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human,epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021)Node40)Node38)Node36,((epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021,gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human)Node44,(epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human)Node47)Node43)Node35,(epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021,epi_isl_1543980_hCoV_19_Singapore_490_2021)Node50)Node34,epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021)Node33)Node29,(epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021,gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human)Node54)Node28,((gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human,gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human)Node58,epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021)Node57)Node27)Node23)Node19,REFERENCE)"\n+ }\n+ },\n+ "settings":{\n+ "burn-in":10000,\n+ "data-type":"codon",\n+ "max-parents":1,\n+ "min-subs":1,\n+ "samples":100,\n+ "steps":100000,\n+ "threshold":0.5\n+ },\n+ "tested":0,\n+ "timers":{\n+ "Baseline fit":{\n+ "order":1,\n+ "timer":4\n+ },\n+ "Network inference":{\n+ "order":2,\n+ "timer":0\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":4\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 8276bb2adea5 -r 4b8d7aec27f0 test-data/summary/nsp8.labels.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.labels.json Wed Jun 09 07:03:05 2021 +0000 |
| b |
| @@ -0,0 +1,34 @@ +{ + "REFERENCE":"Reference", + "epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021":"B-1-617", + "epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021":"B-1-617", + "epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021":"B-1-617", + "epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021":"B-1-617", + "epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021":"B-1-617", + "epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021":"B-1-617", + "epi_isl_1543980/hCoV-19/Singapore/490/2021":"B-1-617", + "epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021":"B-1-617", + "epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021":"B-1-617", + "epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021":"B-1-617", + "epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021":"B-1-617", + "epi_isl_1592421/hCoV-19/USA/MA-CDC-STM-000044850/2021":"B-1-617", + "epi_isl_1615709/hCoV-19/England/CAMC-14E792B/2021":"B-1-617", + "epi_isl_1632256/hCoV-19/England/RAND-14E1D70/2021":"B-1-617", + "epi_isl_1652105/hCoV-19/Singapore/561/2021":"B-1-617", + "epi_isl_1652118/hCoV-19/Singapore/575/2021":"B-1-617", + "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Reference", + "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Reference", + "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"Reference", + "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"Reference", + "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Reference", + "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"Reference", + "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"Reference", + "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"Reference", + "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"Reference", + "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"Reference", + "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"Reference", + "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"Reference", + "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"Reference", + "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"Reference", + "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"Reference" +} \ No newline at end of file |