| Previous changeset 25:1fb98a84e86d (2021-04-27) Next changeset 27:8c388fd08c09 (2021-06-09) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97" |
|
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 1fb98a84e86d -r 70de001b6768 scripts/hyphy_summary.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/hyphy_summary.py Wed Jun 09 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 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+ [2.416879473710861, 6.208129676636089, 0.9501251489404916, 1.0589504906291],\n+ [1.40787554952569, 5.591133776748825, 0.9468331097402819, 0.9899394492218799],\n+ [1.355846770273861, 5.587576320848404, 0.9468186115030925, 0.9896544191230306],\n+ [1.19730312499705, 5.591581681880384, 0.9467807517201781, 0.9889108417502884],\n+ [1.19730312499705, 5.591581681880385, 0.9467807517201781, 0.9889108417502884],\n+ [1.355846770273861, 5.587576320848404, 0.9468186115030925, 0.9896544191230306],\n+ [1.355846770273861, 5.587576320848403, 0.9468186115030925, 0.9896544191230306],\n+ [0.8995906688309244, 5.594143577985283, 0.9466094530503192, 0.9855596649645022],\n+ [6.422998071838682, 5.459270747984967, 0.9496205809102249, 1.047787992047515],\n+ [0.8263616796556618, 4.962381890578685, 0.9452991472766893, 0.9606199984313577],\n+ [1.044067957308116, 5.592799085749476, 0.946695528671986, 0.9872409006967778],\n+ [1.304863529952144, 5.591532374099517, 0.9468241668256043, 0.9897636163866641],\n+ [4.143729167971483, 3.371941711839532, 0.944477923048972, 0.9455893261012084],\n+ [1.202763782852373, 5.591329097426113, 0.9467791096500886, 0.9888786149436808],\n+ [1.355846770273861, 5.587576320848404, 0.9468186115030928, 0.989654419123035],\n+ [0.8429847890446958, 5.594846217874679, 0.9465529865450447, 0.9844596982291083],\n+ [1.006307760082907, 5.593130172470984, 0.9466828375359569, 0.9869926752594448],\n+ [1.19730312499705, 5.591581681880383, 0.9467807517201781, 0.9889108417502884],\n+ [1.087078938485238, 5.592683010775865, 0.9466830109285441, 0.9869960658421052],\n+ [0.7517238280995038, 5.596329463811911, 0.9463985197722358, 0.98146252874822],\n+ [1.355846770273861, 5.587576320848403, 0.9468186115030928, 0.989654419123035],\n+ [1.355846770273862, 5.587576320848407, 0.9468186115030929, 0.9896544191230371],\n+ [1.006307760082907, 5.593130172470983, 0.9466828375359569, 0.9869926752594448],\n+ [1.19730312499705, 5.591581681880383, 0.9467807517201781, 0.9889108417502884],\n+ [1.355846770273861, 5.587576320848402, 0.9468186115030925, 0.9896544191230306],\n+ [1.355846770273861, 5.587576320848405, 0.9468186115030925, 0.9896544191230306],\n+ [1.304863529952144, 5.591532374099516, 0.9468241668256044, 0.9897636163866662],\n+ [1.006307760082907, 5.593130172470983, 0.9466828375359569, 0.9869926752594448],\n+ [1.19730312499705, 5.591581681880383, 0.9467807517201781, 0.9889108417502884],\n+ [2.314286089218025, 5.572704246222457, 0.9498573647271824, 1.052998357204021],\n+ [1.304863529952143, 5.591532374099515, 0.9468241668256041, 0.9897636163866598],\n+ [1.202763782852373, 5.591329097426113, 0.9467791096500886, 0.9888786149436808],\n+ [1.19730312499705, 5.591581681880382, 0.9467807517201781, 0.9889108417502884],\n+ [0.8263616796556617'..b'de263":"background",\n+ "Node264":"background",\n+ "Node268":"background",\n+ "Node269":"background",\n+ "Node27":"background",\n+ "Node272":"background",\n+ "Node275":"background",\n+ "Node278":"background",\n+ "Node28":"background",\n+ "Node280":"background",\n+ "Node281":"background",\n+ "Node283":"background",\n+ "Node286":"background",\n+ "Node287":"background",\n+ "Node288":"background",\n+ "Node289":"background",\n+ "Node290":"background",\n+ "Node292":"background",\n+ "Node296":"background",\n+ "Node299":"background",\n+ "Node3":"background",\n+ "Node300":"background",\n+ "Node303":"background",\n+ "Node304":"background",\n+ "Node306":"background",\n+ "Node307":"background",\n+ "Node311":"background",\n+ "Node312":"background",\n+ "Node314":"background",\n+ "Node317":"background",\n+ "Node319":"background",\n+ "Node32":"background",\n+ "Node322":"background",\n+ "Node324":"background",\n+ "Node327":"background",\n+ "Node328":"background",\n+ "Node329":"background",\n+ "Node33":"background",\n+ "Node332":"background",\n+ "Node335":"background",\n+ "Node336":"background",\n+ "Node337":"background",\n+ "Node338":"background",\n+ "Node342":"background",\n+ "Node345":"background",\n+ "Node346":"background",\n+ "Node349":"background",\n+ "Node36":"background",\n+ "Node4":"background",\n+ "Node40":"background",\n+ "Node43":"background",\n+ "Node45":"background",\n+ "Node48":"background",\n+ "Node49":"background",\n+ "Node5":"background",\n+ "Node50":"background",\n+ "Node51":"background",\n+ "Node54":"background",\n+ "Node57":"background",\n+ "Node6":"background",\n+ "Node60":"background",\n+ "Node62":"background",\n+ "Node64":"background",\n+ "Node65":"background",\n+ "Node69":"background",\n+ "Node7":"background",\n+ "Node71":"background",\n+ "Node74":"background",\n+ "Node75":"background",\n+ "Node79":"background",\n+ "Node8":"background",\n+ "Node82":"background",\n+ "Node84":"background",\n+ "Node85":"background",\n+ "Node87":"background",\n+ "Node9":"background",\n+ "Node90":"background",\n+ "Node93":"background",\n+ "Node94":"background",\n+ "Node95":"background",\n+ "Node98":"background",\n+ "Node99":"background",\n+ "REFERENCE":"background"\n+ }\n+ },\n+ "timers":{\n+ "Baseline Fit":{\n+ "order":1,\n+ "timer":867\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":970\n+ },\n+ "Residue A analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue C analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue D analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue E analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue F analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue G analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue H analysis":{\n+ "order":21,\n+ "timer":6\n+ },\n+ "Residue I analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue K analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue L analysis":{\n+ "order":21,\n+ "timer":6\n+ },\n+ "Residue M analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue N analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue P analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue Q analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue R analysis":{\n+ "order":21,\n+ "timer":6\n+ },\n+ "Residue S analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue T analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue V analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue W analysis":{\n+ "order":21,\n+ "timer":5\n+ },\n+ "Residue Y analysis":{\n+ "order":21,\n+ "timer":5\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,2444 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[235.7472979068722, 0, 1, 0.9943760343206508, 0, 0, 0.6666666666666666, 0, 0, -31.93549672470295, -31.93549672470295],\n+ [3.125033384621221, 0, 1, 6.6249901946859, 0, 0, 0.6666666666666666, 0, 0, -43.49839666606186, -43.49831167050982],\n+ [1.901386439598346, 0, 1, 3.602316293041297, 0, 0, 0.6666666666666666, 0, 0, -17.09092958578331, -17.09092776449802],\n+ [1.622684212345616, 0, 1, 3.145879239633445, 0, 0, 0.6666666666666666, 0, 0, -61.02813244305516, -61.02813244305516],\n+ [0.8148105398437983, 0, 1, 1.499991884237639, 0, 0, 0.6666666666666666, 0, 0, -25.26062185068822, -25.26062185068822],\n+ [0.538978592942964, 0.01746277867903197, 1e-08, 9.230771679231886, 0.9999999899999999, 3.131671475355084, 0.09963705217536034, 1, 0, -30.93250048026707, -30.93322087121525],\n+ [1.853606022970019, 0, 1, 3.674707574937826, 0, 0, 0.6666666666666666, 0, 0, -28.34059025069893, -28.34050231902417],\n+ [0, 0, 0.01, 12.19527240220381, 0.99, 5.190712220882091, 0.03417278198780516, 1, 0, -32.1999009479721, -32.20034352402657],\n+ [0.805138687398488, 0, 1, 1.207708031097732, 0, 0, 0.6666666666666666, 0, 0, -19.49824980857283, -19.49824980857283],\n+ [0.7875298923722399, 0, 1, 1.18129483855836, 0, 0, 0.6666666666666666, 0, 0, -10.95089000994802, -10.95089000994802],\n+ [0, 0, 0.7902834145736399, 0, 0.2097165854263601, 0, 0.6666666666666666, 0, 0, -10.4967950075176, -10.49676470665957],\n+ [2.108936224301836, 0, 1, 4.25795369775854, 0, 0, 0.6666666666666666, 0, 0, -23.11396543022702, -23.11396543022702],\n+ [0, 0, 0.8, 0, 0.2, 0, 0.6666666666666666, 0, 0, -19.07061628099717, -19.07061628099717],\n+ [0, 0, 0.8, 0, 0.2, 0, 0.6666666666666666, 0, 0, -22.48983908138136, -22.48983908138136],\n+ [0.7292797817264002, 0, 1, 1.287619383037297, 0, 0, 0.6666666666666666, 0, 0, -17.62011150794451, -17.62000776683851],\n+ [0.4544007544431132, 0, 1, 0.8129996317234597, 0, 0, 0.6666666666666666, 0, 0, -10.67018378690468, -10.67007136928275],\n+ [3.126445023368568, 0, 1, 4.68966753505285, 0, 0, 0.6666666666666666, 0, 0, -28.6511695113687, -28.6511695113687],\n+ [0, 0, 0.7832306446577002, 0, 0.2167693553422998, 0, 0.6666666666666666, 0, 0, -10.32612700097242, -10.32610045104498],\n+ [0, 0, 0.8, 0, 0.2, 0, 0.6666666666666666, 0, 0, -17.66010584477118, -17.66010584477118],\n+ [1.582609657659543, 0.07748016346540233, 1e-08, 13.27219264690008, 0.9999999899999999, 3.752752164229889, 0.07196902171856812, 2, 0, -34.06058348245836, -34.06125069473573],\n+ [0.7933943793514222, 0, 1, 1.487274366455954, 0, 0, 0.6666666666666666, 0, 0, -24.42682387438615, -24.4266750820928],\n+ [1.924845547483019, 0, 1, 3.628962962048999, 0, 0, 0.6666666666666666, 0, 0, -9.22884735612317, -9.228785303980652],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1e-08, 10.15334067075988, 0.9999999899999999, 5.17018279350712, 0.03453604200412042, 1, 0, -15.66593469453643, -15.66609055380208],\n+ [1.642241264948948, 0, 1, 2.463361897423421, 0, 0, 0.6666666666666666, 0, 0, -34.78688795719844, -34.78688795719844],\n+ [0, 0, 0.8, 0, 0.2, 0, 0.6666666666666666, 0, 0, -16.61540439906428, -16.61540439906428],\n+ [30.1118279159421, 0, 1, 0.957598139734009, 0, 0, 0.6666666666666666, 0, 0, -34.52230675976102, -34.52230675976102],\n+ [1.9537851141012, 0, 1, 3.892151132092624, 0, 0, 0.6666666666666666, 0, 0, -16.46478282393715, -16.46478282393715],\n+ [0.804961518424102, 0, 1, 1.480059749183362, 0, 0, 0.6666666666666666, 0, 0, -21.43928875538542, -21.43920337247038],\n+ [1.953310497214501, 0, 1, 3.891048374461244, 0, 0, 0.6666666666666666, 0, 0, -23.1486449234974, -23.1486449234974],\n+ [1.077358264752097, 0, 1, 1.936877407404742, 0, 0, 0.6666666666666666, 0, 0, -30.49557060864319, -30.49551277592488],\n+ [0.4180911660685708, 0, 1, 0.7640377810705596, 0, 0, 0.6666666666666666, 0, 0, -28.21300164824159, -28.21297701245718'..b' "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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\n+ "gb_MW593179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_1171_2020_Segment_null_Host_Human":"background",\n+ "gb_MW593378_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_8518_2020_Segment_null_Host_Human":"background",\n+ "gb_MW593611_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_7938_2020_Segment_null_Host_Human":"background",\n+ "gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human":"background",\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":"background",\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":"background",\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":"background",\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":"background"\n+ }\n+ },\n+ "timers":{\n+ "MEME analysis":{\n+ "order":2,\n+ "timer":24\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":12\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":36\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 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+ [43.91674640638229, 130.5963018373365, 1, 0, 0.2516530818088152, 0.02277035713771986, 0, -0.02242166360482602, 1, 0.2516530818088152, 0.005686014239873573],\n+ [43.83435038616016, 130.6786978575586, 0, 0, 0.2511809336167382, 0, 0, 0, 1, 1, 1.164083856196478e-09],\n+ [43.91674640638229, 130.6786978575586, 1, 0, 0.2515343203342241, 0.02277035713771986, 0, -0.02242166360482602, 1, 0.2515343203342242, 0.005609037806678601],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [43.57129890616731, 131.0467497186165, 0, 1, 0.2495234556182251, 0, 0.007630864574262234, 0.007514009440575017, 0.7504765443817749, 1, 0.005614257503564472],\n+ [43.78522066638587, 130.8926196177772, 0, 1, 0.2506627091058418, 0, 0.007639850152897275, 0.007522857418682301, 0.7493372908941582, 1, 0.005611966246931293],\n+ [44.42698594704154, 130.2508543371215, 0, 1, 0.2543367027824963, 0, 0.00767749282789157, 0.007559923653120484, 0.7456632972175037, 1, 0.005582859181768383],\n+ [0, 0, 0, 0, null, null, null, null, 1, 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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+ "gb_MT326182_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CT_UW_1365_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT358638_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_DEU_FFM1_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT359866_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_ESP_VH198152683_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT451104_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC203_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT520188_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00184_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT520493_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_00316_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT601281_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_67_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT612186_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC1576_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT627613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S260_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT631787_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1651_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT641697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC595_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT683417_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_10131_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT706153_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_32_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT745697_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC2124_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT745746_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_SA01_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT750335_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1794_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MT772447_Organism_Seve'..b'nce",\n+ "gb_MW578233_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0795_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW578246_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0808_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW583187_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OK_CDC_STM_000003021_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW583265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000001669_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW585898_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_CDC_STM_000003612_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586184_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005891_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586256_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005477_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586385_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000005076_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586419_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IA_CDC_STM_000005050_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW586849_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_QDX_4292_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW592782_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2311_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_1171_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593378_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_8518_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593611_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_7938_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW593708_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4325_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW598427_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_nmimr_SARS_CoV_2_NTRA_15010_2020_Segment_null_Host_Human":"Reference",\n+ "gb_MW599514_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_Broad_CRSP_00376_2021_Segment_null_Host_Human":"Reference",\n+ "gb_MW599662_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_RI_Broad_RIDOH_00108_2020_Segment_null_Host_Human":"Reference"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,132 @@\n+{\n+ "nsp7": {\n+ "map": [],\n+ "tree": "((gb_MT470179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_France_40002VJ_2020_Segment_null_Host_Human,gb_MW460617_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_2810_2020_Segment_null_Host_Human)Node387,REFERENCE,gb_MW556183_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_CDC_9MR4_8909_2021_Segment_null_Host_Human,gb_MT834677_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_0519_2020_Segment_null_Host_Human,gb_MW406516_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AR_CDC_2_3693765_2020_Segment_null_Host_Human,gb_MW586766_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4270_2021_Segment_null_Host_Human,gb_MW276413_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_10909_2020_Segment_null_Host_Human,(gb_MT973055_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC6608_2020_Segment_null_Host_Human,gb_MW517337_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0048_2021_Segment_null_Host_Human)Node365,(gb_MW562693_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102046035_2020_Segment_null_Host_Human,((gb_MT628199_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1525_2020_Segment_null_Host_Human,gb_MW276545_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11572_2020_Segment_null_Host_Human)Node373,gb_MW276613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11950_2020_Segment_null_Host_Human)Node372)Node370,gb_MW585982_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_000003668_2021_Segment_null_Host_Human,gb_MW486275_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2499_2020_Segment_null_Host_Human,gb_MW586167_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000005966_2021_Segment_null_Host_Human,gb_MW571123_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS68_2021_Segment_null_Host_Human,gb_MW525001_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000014_B04_2021_Segment_null_Host_Human,gb_MT810681_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1240_SAN_2020_Segment_null_Host_Human,gb_MW566853_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2890_2020_Segment_null_Host_Human,gb_MW579014_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101155076_2021_Segment_null_Host_Human,gb_MW518128_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_STM_291_2021_Segment_null_Host_Human,gb_MW570895_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00321_2021_Segment_null_Host_Human,gb_MW550719_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_2_3768763_2020_Segment_null_Host_Human,gb_MW420777_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012868464_2020_Segment_null_Host_Human,gb_MW586286_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005415_2021_Segment_null_Host_Human,gb_MW548941_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_S'..b'piratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14413_2020_Segment_null_Host_Human,gb_MT601276_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_52_2020_Segment_null_Host_Human,gb_MW406537_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IN_CDC_2_3693679_2020_Segment_null_Host_Human,gb_MW586700_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4173_2021_Segment_null_Host_Human,(gb_MW156645_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11076_2020_Segment_null_Host_Human,gb_MW156971_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10203_2020_Segment_null_Host_Human,epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021,gb_MW420890_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NMDOH_2020316507_2020_Segment_null_Host_Human)Node62,epi_isl_1589926_hCoV_19_India_WB_1930300586246_2021,(gb_MW509810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC11I035_2021_Segment_null_Host_Human,gb_MW596234_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_000008248_2021_Segment_null_Host_Human)Node71,gb_MW064863_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_QDX_779_2020_Segment_null_Host_Human,gb_MW155278_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12385_2020_Segment_null_Host_Human,epi_isl_1442952_hCoV_19_Singapore_321_2021,gb_MW193966_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_nimh_12171_2020_Segment_null_Host_Human,gb_MW462661_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2263_2020_Segment_null_Host_Human,epi_isl_1516887_hCoV_19_Australia_QLD1826_2021,gb_MW521810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3530_2020_Segment_null_Host_Human,gb_MW490888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2295_2020_Segment_null_Host_Human,gb_MW155642_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13394_2020_Segment_null_Host_Human,gb_MT847221_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_283_2020_Segment_null_Host_Human,gb_MW592637_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01774_2021_Segment_null_Host_Human,gb_MW578233_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0795_2021_Segment_null_Host_Human,gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human,gb_MW543030_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_IR9A_6594_2020_Segment_null_Host_Human,gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human,gb_MT873189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_DPH_00301_2020_Segment_null_Host_Human,(gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human,gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human)Node100,gb_MT811511_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1079_SAN_2020_Segment_null_Host_Human)",\n+ "tree_tags": {}\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,7 @@\n+{\n+ "nsp7": {\n+ "map": [],\n+ "tree": "((gb_MT470179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_France_40002VJ_2020_Segment_null_Host_Human,gb_MW460617_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_2810_2020_Segment_null_Host_Human)Node387,REFERENCE,gb_MW556183_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_CDC_9MR4_8909_2021_Segment_null_Host_Human,gb_MT834677_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_0519_2020_Segment_null_Host_Human,gb_MW406516_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AR_CDC_2_3693765_2020_Segment_null_Host_Human,gb_MW586766_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4270_2021_Segment_null_Host_Human,gb_MW276413_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_10909_2020_Segment_null_Host_Human,(gb_MT973055_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC6608_2020_Segment_null_Host_Human,gb_MW517337_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0048_2021_Segment_null_Host_Human)Node365,(gb_MW562693_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102046035_2020_Segment_null_Host_Human,((gb_MT628199_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1525_2020_Segment_null_Host_Human,gb_MW276545_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11572_2020_Segment_null_Host_Human)Node373,gb_MW276613_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_11950_2020_Segment_null_Host_Human)Node372)Node370,gb_MW585982_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_000003668_2021_Segment_null_Host_Human,gb_MW486275_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2499_2020_Segment_null_Host_Human,gb_MW586167_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NC_CDC_STM_000005966_2021_Segment_null_Host_Human,gb_MW571123_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_GHA_WACCBIP_nCoV_GS68_2021_Segment_null_Host_Human,gb_MW525001_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000014_B04_2021_Segment_null_Host_Human,gb_MT810681_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_1240_SAN_2020_Segment_null_Host_Human,gb_MW566853_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2890_2020_Segment_null_Host_Human,gb_MW579014_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101155076_2021_Segment_null_Host_Human,gb_MW518128_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AZ_CDC_STM_291_2021_Segment_null_Host_Human,gb_MW570895_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00321_2021_Segment_null_Host_Human,gb_MW550719_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_PA_CDC_2_3768763_2020_Segment_null_Host_Human,gb_MW420777_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012868464_2020_Segment_null_Host_Human,gb_MW586286_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000005415_2021_Segment_null_Host_Human,gb_MW548941_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Str'..b'_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC278_2020_Segment_null_Host_Human,epi_isl_1583966_hCoV_19_England_CAMC_14D1B4C_2021,(gb_MW420606_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2012663262_2020_Segment_null_Host_Human,gb_MW156759_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13581_2020_Segment_null_Host_Human,gb_MW486330_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2532_2020_Segment_null_Host_Human)Node76,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,gb_MT940476_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC336_2020_Segment_null_Host_Human,epi_isl_1415273_hCoV_19_India_MH_NCCS_87216_2021,gb_MW559163_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101251032_2020_Segment_null_Host_Human,gb_MT380729_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_VI_CDC_1999_2020_Segment_null_Host_Human,gb_MW321295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC17192_2020_Segment_null_Host_Human,(gb_MW454728_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MGH_03452_2020_Segment_null_Host_Human,epi_isl_1415264_hCoV_19_India_MH_NCCS_128864_2021,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,gb_MW517346_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SC_COVID21_0036_2021_Segment_null_Host_Human)Node17,(gb_MW523879_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_IL_CDC_STM_A100264_2021_Segment_null_Host_Human,gb_MW240753_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0289_2020_Segment_null_Host_Human)Node13,gb_MW156992_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10174_2020_Segment_null_Host_Human,gb_MW562737_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102453487_2020_Segment_null_Host_Human,(gb_MT451046_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC142_2020_Segment_null_Host_Human,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)Node26,epi_isl_1641831_hCoV_19_Germany_BY_RKI_I_076082_2021,gb_MT291831_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_Beijing_IME_BJ01_2020_Segment_null_Host_Human,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,gb_MW590718_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC434_2020_Segment_null_Host_Human,gb_MW521457_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_1516xF10_2020_Segment_null_Host_Human,gb_MT731735_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_137_2020_Segment_null_Host_Human,gb_MW521689_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_QDX_3455_2020_Segment_null_Host_Human,gb_MT825091_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IRN_COVID19_IRVSH1_2020_Segment_null_Host_Human,gb_MW030253_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_PER_covper022_2020_Segment_null_Host_Human)",\n+ "tree_tags": {}\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,3775 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "A":{\n+ "0": [\n+[2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129],\n+ [2.693374054144683, 5.447411670296412, 0.9467570683845876, 0.9955252951947779],\n+ [1.688653150925858, 5.451721466912741, 0.9466016845428151, 0.9924655022317769],\n+ [2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129],\n+ [1.895030664619211, 4.52086406954309, 0.9445058895733424, 0.9528696179522672],\n+ [1.758305195386422, 3.944714326314311, 0.9429120087101439, 0.9247026627110535],\n+ [2.693374054144683, 5.447411670296409, 0.9467570683845873, 0.9955252951947714],\n+ [3.496602106477276, 5.440799403189085, 0.9468488043583334, 0.9973401437079507],\n+ [1.543475628257214, 3.863513868034641, 0.9427148781074345, 0.9213279007167833],\n+ [2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129],\n+ [1.758305195386422, 3.944714326314311, 0.9429120087101438, 0.9247026627110516],\n+ [1.758305195386422, 3.944714326314311, 0.9429120087101438, 0.9247026627110516],\n+ [2.888738053131405, 5.442048000971297, 0.9467761145568184, 0.9959015784347245],\n+ [2.888738053131407, 5.442048000971297, 0.9467761145568186, 0.9959015784347287],\n+ [2.135355976597445, 4.427368796461389, 0.9442611618171567, 0.9484401238711249],\n+ [1.758305195386422, 3.944714326314311, 0.9429120087101439, 0.9247026627110535],\n+ [2.888738053131406, 5.442048000971297, 0.9467761145568186, 0.9959015784347287],\n+ [3.83477558833969, 5.441686558585306, 0.9468869782913305, 0.998097200677287],\n+ [3.83477558833969, 5.441686558585306, 0.9468869782913305, 0.998097200677287],\n+ [2.888738053131406, 5.442048000971297, 0.9467761145568186, 0.9959015784347287],\n+ [1.369335396501189, 5.455049142067401, 0.9465154080004033, 0.9907742351666092],\n+ [1.758305195386422, 3.944714326314311, 0.9429120087101439, 0.9247026627110535],\n+ [2.797626563980584, 5.443095023696286, 0.9467728178118203, 0.9958364274464081],\n+ [2.135355976597445, 4.42736879646139, 0.9442611618171569, 0.948440123871129],\n+ [2.135355976597445, 4.427368796461389, 0.9442611618171568, 0.948440123871127],\n+ [16.90687074975244, 2.155399144164864, 0.9391452000191042, 0.8639997310649982],\n+ [2.693374054144683, 5.44741167029641, 0.9467570683845874, 0.9955252951947736],\n+ [2.888738053131406, 5.442048000971298, 0.9467761145568186, 0.9959015784347287],\n+ [4.866933492896364, 5.43775322191688, 0.9469826836016578, 0.9999999999999846],\n+ [2.506966928736593, 6.070890801375212, 0.9499653379157128, 1.062949156257778],\n+ [3.834775588339692, 5.441686558585308, 0.9468869782913308, 0.9980972006772938],\n+ [3.496602106477275, 5.440799403189085, 0.9468488043583333, 0.9973401437079484],\n+ [1.758305195386423, 3.944714326314311, 0.9429120087101438, 0.9247026627110516],\n+ [3.834775588339691, 5.441686558585306, 0.9468869782913305, 0.998097200677287],\n+ [2.888738053131406, 5.442048000971297, 0.9467761145568186, 0.9959015784347287],\n+ [1.68988272928716, 5.454272551359437, 0.9466143314318377, 0.9927138768247789],\n+ [2.117065489713, 5.445211592005363, 0.9466756419384051, 0.9939196351965929],\n+ [1.89503066461921, 4.520864069543092, 0.9445058895733421, 0.9528696179522632],\n+ [0.9509652292400816, 5.46385854024827, 0.9463373931761325, 0.9873018217934487],\n+ [2.888738053131406, 5.442048000971297, 0.9467761145568184, 0.9959015784347245],\n+ [2.888738053131406, 5.442048000971297, 0.9467761145568186, 0.9959015784347287],\n+ [2.506966928736592, 6.070890801375207, 0.9499653379157128, 1.062949156257778],\n+ [2.693374054144683, 5.44741167029641, 0.9467570683845874, 0.9955252951947736],\n+ [1.89503066461921, 4.520864069543092, 0.9445058895733424, 0.9528696179522672],\n+ [1.543475628257214, 3.8635'..b' "Node311":"background",\n+ "Node314":"background",\n+ "Node315":"background",\n+ "Node317":"background",\n+ "Node320":"background",\n+ "Node323":"background",\n+ "Node324":"background",\n+ "Node325":"background",\n+ "Node327":"background",\n+ "Node330":"background",\n+ "Node333":"background",\n+ "Node335":"background",\n+ "Node338":"background",\n+ "Node339":"background",\n+ "Node34":"background",\n+ "Node340":"background",\n+ "Node342":"background",\n+ "Node345":"background",\n+ "Node348":"background",\n+ "Node349":"background",\n+ "Node35":"background",\n+ "Node352":"background",\n+ "Node356":"background",\n+ "Node357":"background",\n+ "Node358":"background",\n+ "Node359":"background",\n+ "Node36":"background",\n+ "Node363":"background",\n+ "Node365":"background",\n+ "Node368":"background",\n+ "Node369":"background",\n+ "Node37":"background",\n+ "Node370":"background",\n+ "Node372":"background",\n+ "Node373":"background",\n+ "Node378":"background",\n+ "Node379":"background",\n+ "Node38":"background",\n+ "Node380":"background",\n+ "Node384":"background",\n+ "Node387":"background",\n+ "Node39":"background",\n+ "Node4":"background",\n+ "Node40":"background",\n+ "Node41":"background",\n+ "Node42":"background",\n+ "Node43":"background",\n+ "Node44":"background",\n+ "Node45":"background",\n+ "Node46":"background",\n+ "Node47":"background",\n+ "Node48":"background",\n+ "Node49":"background",\n+ "Node5":"background",\n+ "Node50":"background",\n+ "Node52":"background",\n+ "Node53":"background",\n+ "Node54":"background",\n+ "Node55":"background",\n+ "Node6":"background",\n+ "Node61":"background",\n+ "Node64":"background",\n+ "Node65":"background",\n+ "Node69":"background",\n+ "Node7":"background",\n+ "Node70":"background",\n+ "Node71":"background",\n+ "Node72":"background",\n+ "Node75":"background",\n+ "Node76":"background",\n+ "Node77":"background",\n+ "Node8":"background",\n+ "Node82":"background",\n+ "Node83":"background",\n+ "Node84":"background",\n+ "Node87":"background",\n+ "Node9":"background",\n+ "Node91":"background",\n+ "Node92":"background",\n+ "Node93":"background",\n+ "Node96":"background",\n+ "Node99":"background",\n+ "REFERENCE":"background"\n+ }\n+ },\n+ "timers":{\n+ "Baseline Fit":{\n+ "order":1,\n+ "timer":525\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":680\n+ },\n+ "Residue A analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue C analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue D analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue E analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue F analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue G analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue H analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue I analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue K analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue L analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue M analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue N analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue P analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue Q analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue R analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue S analysis":{\n+ "order":21,\n+ "timer":7\n+ },\n+ "Residue T analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue V analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue W analysis":{\n+ "order":21,\n+ "timer":8\n+ },\n+ "Residue Y analysis":{\n+ "order":21,\n+ "timer":8\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,2780 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[1.533233887808136, 0, 1, 2.299850831712206, 0, 0, 0.6666666666666666, 0, 0, -16.56566149074754, -16.56566149074754],\n+ [0, 0, 0.75, 0, 0.25, 0, 0.6666666666666666, 0, 0, -16.88964547105427, -16.88964547105427],\n+ [0, 0, 0.75, 0, 0.25, 0, 0.6666666666666666, 0, 0, -24.47211853487119, -24.47211853487119],\n+ [1.295715290722678, 0, 1, 2.295630142033382, 0, 0, 0.6666666666666666, 0, 0, -10.04860590985424, -10.04856678334092],\n+ [1.06359724532521, 0, 1, 2.039940283043322, 0, 0, 0.6666666666666666, 0, 0, -9.909026090220614, -9.908993243173951],\n+ [0, 0, 0.7832306446577002, 0, 0.2167693553422998, 0, 0.6666666666666666, 0, 0, -10.69541935397552, -10.6953779153434],\n+ [0, 0, 0.75, 0, 0.25, 0, 0.6666666666666666, 0, 0, -12.38315488324839, -12.38315488324839],\n+ [2.175519777386203, 0, 1, 4.120954733511092, 0, 0, 0.6666666666666666, 0, 0, -20.75823363081466, -20.75810516213063],\n+ [1.284730273091628, 0, 1, 2.428936645367013, 0, 0, 0.6666666666666666, 0, 0, -17.19802156473746, -17.19802156473746],\n+ [1.295715290722678, 0, 1, 2.295630142033382, 0, 0, 0.6666666666666666, 0, 0, -10.04856707385707, -10.04852794942069],\n+ [0, 0, 0.7832299949177, 0, 0.2167700050823, 0, 0.6666666666666666, 0, 0, -10.28150240199277, -10.28145555927408],\n+ [1.607298970237319, 0, 1, 3.112288693752653, 0, 0, 0.6666666666666666, 0, 0, -29.24029873712604, -29.24029873712604],\n+ [0.658147989764945, 0, 1, 1.217776126473278, 0, 0, 0.6666666666666666, 0, 0, -23.38985336540182, -23.38975051605309],\n+ [2.143051227544403, 0, 1, 4.339833844109792, 0, 0, 0.6666666666666666, 0, 0, -33.28267795814402, -33.28267795814402],\n+ [2.602377158701931, 0, 1, 3.903565738052897, 0, 0, 0.6666666666666666, 0, 0, -23.21434083792724, -23.21434083792724],\n+ [1.539104687059178, 0, 1, 2.884102842134074, 0, 0, 0.6666666666666666, 0, 0, -16.43961163715615, -16.43957985748816],\n+ [1.29894919452411, 0, 1, 2.531200969263668, 0, 0, 0.6666666666666666, 0, 0, -28.82368247604683, -28.82360517845598],\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+ [0.5390223852715083, 0, 1, 0.8085335779072623, 0, 0, 0.6666666666666666, 0, 0, -23.54105531906072, -23.54105531906072],\n+ [1.324589033354356, 0, 1, 1.986883550031534, 0, 0, 0.6666666666666666, 0, 0, -18.6439645958698, -18.6439645958698],\n+ [0, 0, 0.7832306446577002, 0, 0.2167693553422998, 0, 0.6666666666666666, 0, 0, -10.81484080015047, -10.8147964435159],\n+ [3.445052929084436, 0, 1, 5.167579393626656, 0, 0, 0.6666666666666666, 0, 0, -14.26808822734033, -14.26808822734033],\n+ [1.295715290722678, 0, 1, 2.295630142033382, 0, 0, 0.6666666666666666, 0, 0, -10.04275437602897, -10.04271556337925],\n+ [1.245246374032009, 0, 1, 2.447604827828623, 0, 0, 0.6666666666666666, 0, 0, -32.4833701844678, -32.48335137337359],\n+ [0, 0, 0.01, 8.728513932042947, 0.99, 4.990124005422622, 0.037894537959832, 1, 0, -26.13349547396117, -26.13405909098374],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0.4302031050413119, 0, 1, 0.6453046575619679, 0, 0, 0.6666666666666666, 0, 0, -18.32738445208919, -18.32738445208919],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 0.7890816332122995, 0, 0.2109183667877005, 0, 0.6666666666666666, 0, 0, -24.12967211555828, -24.12966252199628],\n+ [0, 0, 0.8, 0, 0.2, 0, 0.6666666666666666, 0, 0, -20.52097029563734, -20.52097029563734],\n+ [1.088026693043902, 0, 1, 2.048118506312161, 0, 0, 0.6666666666666666, 0, 0, -18.53776428660746, -18.53738288695755],\n+ [1.089879890358478, 0, 1, 1.634819835537717, 0, 0, 0.6666666666666666, 0, 0, -41.25068707292752, -41.25068707292752],\n+ [0.7209482995925045, 0, 1, 1.326490859193524, 0, 0, 0.6666666666666666, 0, 0, -17.97336820755874, -17.9733619737836],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [2.176642434954817, 0, 1, 4.420977185211881, 0, 0, 0.6666666666666666, 0, '..b'und",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"background",\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":"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+ "gb_MW593416_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_880_2020_Segment_null_Host_Human":"background",\n+ "gb_MW593460_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FHCRC_4649_2020_Segment_null_Host_Human":"background",\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":"background",\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":"background",\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":"background",\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":"background"\n+ }\n+ },\n+ "timers":{\n+ "MEME analysis":{\n+ "order":2,\n+ "timer":59\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":24\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":84\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,5244 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0":{\n+ "by-branch":{\n+ "AVERAGED": [\n+[75.21726851651356, 163.6940894156486, 0, 1, 0.3148333723751685, 0, 0.006108956062920642, 0.007567306802312253, 0.6851666276248315, 1, 0.004137678108204586],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [75.2497273928074, 163.6616305393547, 1, 0, 0.3149692339623897, 0.0132890846870441, 0, -0.01646150011769675, 1, 0.3149692339623897, 0.00413937051268764],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [75.28831762809149, 163.6291716630609, 0, 1, 0.3151226720633364, 0, 0.006111379712042806, 0.00757030903318438, 0.6848773279366636, 1, 0.004130319073497585],\n+ [74.98180835674931, 163.9394365862927, 0, 1, 0.3138348302790098, 0, 0.006099813570321934, 0.007555981782829428, 0.6861651697209902, 1, 0.004133581103629891],\n+ [75.20828178574392, 163.7092075054085, 1, 0, 0.3147876784109879, 0.01329640800528905, 0, -0.01647057168334556, 1, 0.314787678410988, 0.004133715723948402],\n+ [75.20828178574392, 163.7092075054085, 1, 0, 0.3147876784109879, 0.01329640800528905, 0, -0.01647057168334556, 1, 0.314787678410988, 0.004130916500797859],\n+ [75.3228538832219, 163.6007667669208, 0, 1, 0.3152591346065261, 0, 0.006112440789624678, 0.00757162341481037, 0.6847408653934739, 1, 0.004131349621335782],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [74.98552677079654, 163.9319625203558, 1, 0, 0.3138553271812463, 0.01333590684848606, 0, -0.0165194998245418, 1, 0.3138553271812463, 0.004144782059060885],\n+ [75.09690427827023, 163.8205850128821, 0, 1, 0.3143215027961171, 0, 0.006104238975348332, 0.007561463635573879, 0.685678497203883, 1, 0.004137476508736943],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [74.53871127179761, 164.2359193164465, 0, 1, 0.3121718211359573, 0, 0.006088802036497388, 0.007542341538251447, 0.6878281788640428, 1, 0.00413387672462659],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [74.64395742028103, 164.2810431746506, 0, 1, 0.3124158511433084, 0, 0.006087129596181583, 0.007540269847303289, 0.6875841488566916, 1, 0.004134217944972438],\n+ [0, 0, 0, 0, null, null, null, null, 1, 1, 0],\n+ [75.17529908540716, 163.7497015095244, 1, 0, 0.3146397358929289, 0.01330224172256226, 0, -0.01647779804541949, 1, 0.3146397358929289, 0.00413019971082432],\n+ [75.40177251440174, 163.5194724286402, 1, 0, 0.3155925816993682, 0.01326228769766652, 0, -0.01642830606000345, 1, 0.3155925816993682, 0.004130971091991785],\n+ [75.16683617868044, 163.7567844714622, 1, 0, 0.3146061321778967, 0.01330373939941921, 0, -0.01647965325278233, 1, 0.3146061321778968, 0.004130382801605758],\n+ [75.16683617868044, 163.7506531124719, 1, 0, 0.3146142059406952, 0.01330373939941921, 0, -0.01647965325278233, 1, 0.3146142059406951, 0.004129499344078667],\n+ [75.20828178574392, 163.7092075054085, 1, 0, 0.3147876784109879, 0.01329640800528905, 0, -0.01647057168334556, 1, 0.314787678410988, 0.004133715716434751],\n+ [75.20828178574392, 163.7092075054085, 1, 0, 0.3147876784109879, 0.01329640800528905, 0, -0.01647057168334556, 1, 0.314787678410988, 0.004130916556115025],\n+ [75.70828178574392, 163.2092075054085, 0, 1, 0.316880451114583, 0, 0.00612710529806881, 0.007589788684515843, 0.6831195488854169, 1, 0.004129948146002587],\n+ [75.23962345087004, 163.6778658402823, 1, 0, 0.3149188603735102, 0.0132908692805059, 0, -0.01646371073537082, 1, 0.3149188603735102, 0.004129948146002587],\n+ [75.20828178574392, 163.7092075054085, 0, 1, 0.3147876784109879, 0, 0.006108391917827609, 0.007566607982586585, 0.685212321589012, 1, 0.004129457773123913],\n+ [75.20828178574392, 163.7092075054085, 0, 1, 0.3147876784109879, 0, 0.006108391917827609, 0.007566607982586585, 0.685212321589012, 1, 0.004132077063322063],\n+ [75.628245943396'..b'e_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2101009422_2021_Segment_null_Host_Human":"test",\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":"test",\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":"test",\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":"test",\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":"test",\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":"test",\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":"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_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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +{} \ No newline at end of file |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 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, 0.9889781181731668, 0.9953242584232271, 0.9853516617064797, 0.992154409566355, 0.9870114629546288, 0.9910812249043471, 0.9898739523607402, 0.9898739518379259, 0.9850252204427772, 0.9956363652357774, 0.9870114629546279, 0.9918415472526255, 0.9852148186803413, 0.9953242584232271, 0.9918415472526255, 0.9850252204427772, 0.9898739518379268, 0.9910812249043471, 0.9956363652357774, 0.9898739518379264, 0.9850252204427763, 0.9930618001690927, 0.9956363652357774, 0.9850252204427763, 0.9927999621758878, 0.9965511193500521, 0.9909311149283309, 0.9898739518379251, 0.9903437970819426, 0.9889781181731668, 0.9906204835370439, 0.992154409566355, 0.9918415472526255, 0.985295756376881, 0.9898739523607393, 0.9965511193500521, 0.988849459402228, 0.9930617996638492, 0.9880798288003553, 0.9898739518379264, 0.9850252204427772, 0.9909311149283309, 0.9930618006884053, 0.9850252204427772, 0.9883505486998261, 0.9864186408890355, 0.9930617996638492, 0.9850252204427772, 0.9883505486998261, 0.9903437970819426, 0.9918415472526255, 0.9852148186803413, 0.9910812249043462, 0.9942729604246417, 0.9910812249043462, 0.9898739523607402, 0.9883505490263698, 0.9953496025065315, 0.9953496025065315, 0.989949703415869, 0.9904917523355582, 0.9953496025065315, 0.9942729604246417, 0.9898739523607402, 0.9903437970819426, 0.9910812249043471, 0.9875096976732132, 0.9845430842971005, 0.9888494594022271, 0.9893745237101182, 0.9852148186803413, 0.9953496025065315, 0.991027168169301, 0.991027168169301, 0.9893745237101174, 0.9883505486998261, 0.9930618006884053, 0.9930618006884058, 0.9898739523607393, 0.9898739518379268, 0.9965511193500521, 0.991493380871755, 0.9850252204427772, 0.9888494594022271, 0.9888494599031924, 0.991027168169301, 25.07231821165741, 0.9921544095663559, 0.9927999621758878, 0.9953496025065315, 0.9930618006884058, 0.9927999621758878, 0.9965511193500521, 0.9942729604246413, 0.9930617956571987, 0.9845430842971005, 0.9910812249043471, 0.9875096976732132, 0.9930618006884071, 0.9930618006884053, 0.9853516617064797, 0.9930617996638501, 0.9927999621758878, 0.9898739523607402, 0.9897812891397899, 0.9898739523607402, 0.9852148186803413, 0.9831688610767204, 0.9953242584232271, 0.9904917523355591, 0.9956363652357774, 0.9909311149283309, 0.9888494594022271, 0.9888494614381848, 0.9910812249043471, 0.9898739523607402, 0.991081224904348, 0.9880798288003553, 0.9965511193500521, 0.989949703415869, 0.9888494594022271, 0.9956363652357774, 0.9883505486998261, 0.9880798288003553, 0.9953242584232271, 0.989949703415869, 0.9880798288003553, 0.9850252204427772, 0.992154409566355, 0.9942729604246413, 0.9897812891397899, 0.9893745237101174, 0.9942729604246413, 0.990980695768284, 0.9898739523607402, 0.9831688610767204, 0.9893745237101174, 0.9883505486998261, 0.989949703415869, 0.9888494614381844, 0.9930618006884071, 0.9898739518379264, 0.990980695768284, 0.985295756376881, 0.9898739518379259, 0.9942729604246417, 0.9889781181731668, 0.9898739518379264, 0.9888494599031924, 0.9965511193500521, 0.990980695768284, 0.99093111492'..b'epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",\n+ "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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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, 0.4455007553375522],\n+ [6.636646908481298, 0, 1.139449512908137, 6.624437421595782e-05, 0, 0, 0.906603671841744, 1, -1, 0.2958257534388632],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [6.1753737985279, 0, 0.6747812225964546, 0.0008286376705392658, 0, 0, 0.9318895682175306, 1, -1, 0.275210444662231],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 2.525862203077411, 0, 0, 0, 0, 0.9967237889019069, 1, -1, 0.3138254899904328],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 2.732340409070313, 0, 0, 0, 0, 0.9864042469335919, 1, -1, 0.339479353486676],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [6.138037520514744, 0, 0.002569672061179798, 0, 0, 0, 0.966625447399751, 1, -1, 0.2734404264031591],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 2.524146157767697, 0.7467703676904078, 0, 0, 0, 1, 1, -1, 0.3137257081336548],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [20.45569800257852, 2.869360506651708, 0, 0, 0, 0, 0.8631784781924842, 1, -1, 1.267772969506594],\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+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [11.83304129427042, 0, 3030.146710177266, 0, 1, 0, 0.00724053140174763, 1, 0.25, 0.987396913560512],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 3.197005952555818, 0, 0, 0, 0, 0.984992303013053, 1, -1, 0.3972116762113058],\n+ [15.5072203666105, 0, 0.06830082577521719, 0, 0, 0, 0.9698119015081345, 1, -1, 0.6908329511612732],\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+ [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+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 1.96219769621343, 1.575465255150986, 0, 0, 0, 1, 1, -1, 0.2440323508941374],\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+ [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+ [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+ [6.142239259843736, 0, 0, 0, 0, 0, 0.9658107256738867, 1, -1, 0.2736272170517046],\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, 1.692063018416472, 0.4337954874831223, 0, 0, 0, 0.9397342242479334, 1, -1, 0.2102960857470568],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ '..b' "Node20":"B-1-617",\n+ "Node38":"Reference",\n+ "Node4":"B-1-617",\n+ "REFERENCE":"background",\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",\n+ "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+ "FEL analysis":{\n+ "order":2,\n+ "timer":9\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":14\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 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, 5.29728091323631, 0.9461773292547254, 0.9916852839786031],\n+ [2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [1.278267402694179, 5.298403086637607, 0.9461144831242657, 0.9904628995183751],\n+ [2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [1.030656170591586, 3.823727052389935, 0.942638374340996, 0.9270224239598963],\n+ [2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [3.975230885904575, 5.30388234857391, 0.9465622210338908, 0.9992343211968069],\n+ [2.137353792162707, 5.296766801760399, 0.9463136085589463, 0.9943458070207923],\n+ [20.84019273721462, 0.5473950512397699, 0.9262893422448674, 0.7088967010586273],\n+ [1.495447087063753, 5.29728091323631, 0.9461773292547254, 0.9916852839786031],\n+ [2.137353792162707, 5.296766801760397, 0.9463136085589462, 0.9943458070207902],\n+ [3.975230885904575, 5.30388234857391, 0.9465622210338908, 0.9992343211968069],\n+ [2.836411565163506, 5.6103649987489, 0.9482694123386571, 1.034072300241131],\n+ [1.61184502313527, 4.307287808565802, 0.9439296243666123, 0.9496700143349283],\n+ [2.836411565163506, 5.610364998748899, 0.9482694123386571, 1.034072300241131],\n+ [1.93832931318592, 5.295277139506894, 0.9462752504226483, 0.9935955925112926],\n+ [4.171010736958778, 5.303943343626898, 0.9466009523237737, 0.999999999999989],\n+ [1.498027303473378, 5.297339308476421, 0.9461742322151047, 0.9916249783486369],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [2.137353792162707, 5.296766801760399, 0.9463136085589463, 0.9943458070207923],\n+ [1.61184502313527, 4.307287808565802, 0.9439296243666123, 0.9496700143349283],\n+ [1.61184502313527, 4.307287808565802, 0.9439296243666123, 0.9496700143349283],\n+ [2.204874850677001, 5.296750969191259, 0.946323457164476, 0.9945386006007213],\n+ [2.340253562061947, 5.297091003298223, 0.9463485068063867, 0.9950292844312618],\n+ [20.67860679338684, 5.33473590231843, 0.9493492328909104, 1.057320253551461],\n+ [2.204874850677001, 5.296750969191259, 0.946323457164476, 0.9945386006007213],\n+ [2.340253562061947, 5.297091003298223, 0.9463485068063868, 0.995029284431264],\n+ [2.340253562061947, 5.297091003298223, 0.9463485068063867, 0.9950292844312618],\n+ [0.9796147027291616, 3.32238984355696, 0.9412466511136409, 0.9037272813595958],\n+ [2.204874850677001, 5.296750969191259, 0.946323457164476, 0.9945386006007213],\n+ [1.93832931318592, 5.295277139506894, 0.9462752504226483, 0.9935955925112926],\n+ [1.61184502313527, 4.307287808565802, 0.9439296243666123, 0.9496700143349283],\n+ [2.836411565163506, 5.6103649987489, 0.94826'..b'ANISM_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+ "Node1":"test",\n+ "Node10":"test",\n+ "Node12":"test",\n+ "Node13":"background",\n+ "Node16":"test",\n+ "Node19":"test",\n+ "Node2":"test",\n+ "Node20":"test",\n+ "Node23":"test",\n+ "Node24":"test",\n+ "Node27":"test",\n+ "Node28":"test",\n+ "Node29":"test",\n+ "Node3":"test",\n+ "Node30":"background",\n+ "Node33":"test",\n+ "Node34":"test",\n+ "Node35":"test",\n+ "Node36":"background",\n+ "Node38":"background",\n+ "Node4":"test",\n+ "Node40":"background",\n+ "Node43":"test",\n+ "Node44":"test",\n+ "Node47":"test",\n+ "Node50":"test",\n+ "Node54":"test",\n+ "Node57":"test",\n+ "Node58":"background",\n+ "Node8":"test",\n+ "REFERENCE":"background"\n+ }\n+ },\n+ "timers":{\n+ "Baseline Fit":{\n+ "order":1,\n+ "timer":202\n+ },\n+ "Overall":{\n+ "order":0,\n+ "timer":244\n+ },\n+ "Residue A analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue C analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue D analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue E analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue F analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue G analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue H analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue I analysis":{\n+ "order":21,\n+ "timer":2\n+ },\n+ "Residue K analysis":{\n+ "order":21,\n+ "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 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,581 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [3.195197959507056, 0, 3.205811877302111, 0.002772105520872259, 0.9580101497567953, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, -7.296727429917382e-05, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [3.238107125504523, 0, 3.213547473340999, 0.003030822331904659, 0.9560963156973498, 0],\n+ [0, 1.332038499257686, 0, -0.001332719656321757, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [6.598685982136248, 0.2251722656465092, 6.592228961936009, 0.005547079257077314, 0.9406294756580599, 0],\n+ [0, 0, 0, -2.674095220811523e-06, 1, 0],\n+ [6.598685982136248, 0.2251722656465092, 6.592228961936009, 0.005547079257077314, 0.9406294756580599, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [6.158743797064303, 0.2592752451004765, 6.174124078617361, 0.005128927725017718, 0.9429070828447497, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 1.212374231203373, 0, -0.001087198701075209, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, -3.905098004963747e-07, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [6.138362004166043, 0.2445181781691473, 6.130401353642858, 0.005133217856357675, 0.9428832507411992, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0.5381482959007637, 0, -0.000478648432334694, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [20.56274947956719, 1.153771012915874, 20.31835550563158, 0.01485544411855955, 0.9029917493640262, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [12.332534670739, 3469.599471446826, 25.80735991393082, 7.940542096376955, 0.004833935152283808, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, -1.482836388788655e-06, 1, 0],\n+ [15.47421552854267, 0.1366859327111816, 15.4417258929309, 0.01080363925394323, 0.9172165220913007, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 1.464737792323401, 0, -0.001659709283721611, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [6.138362004166043, 0.2445181781691473, 6.130401363029468, 0.005133279629863097, 0.9428829076563918, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, -6.884674199625351e-07, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [10000, 0.0600875449979046, 0, 0.8876016225813821, 0.3461280740416711, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [15.57863687176358, 0.14470798181776, 15.40388468507432, 0.01200895125781898, 0.9127382212825174, 0],\n+ [0, 0.3002103330212254, 0, -0.0003012569440272728, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, -5.985593496404817e-07, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, -6.061155737313584e-06, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 1.362355024782405, 0, -0.00131370882900228, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, -5.257292201577002e-07, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, -4.991814819277351e-07, 1, 0],\n+ [0, 0, 0, -7.833423893544023e-06, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 1, 0],\n+ '..b'\n+ "Node20":"test",\n+ "Node38":"background",\n+ "Node4":"test",\n+ "REFERENCE":"background",\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",\n+ "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+ "FEL analysis":{\n+ "order":2,\n+ "timer":4\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":6\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":10\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,1796 @@\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+ [3.152554051843212, 0, 1, 4.728831077764818, 0, 0, 0.6666666666666666, 0, 0, -9.309130496877323, -9.309130496877323],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 0.01, 11.93617095556557, 0.99, 1.181448599931173, 0.286224560648385, 1, 0, -8.156494645925976, -8.156780324191693],\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+ [3.183060398629631, 0, 1, 4.774590597944442, 0, 0, 0.6666666666666666, 0, 0, -9.310784105780046, -9.310784105780046],\n+ [0, 0, 0.001542572549341103, 9.536088848783528, 0.9984574274506589, 1.956236477088911, 0.1864481881457208, 1, 0, -9.131573461237856, -9.131799448740075],\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+ [6.482349627924372, 0, 1, 22.11982471081377, 0, 0, 0.6666666666666666, 0, 0, -9.318773525114544, -9.318773525114544],\n+ [0, 0, 0.8, 0, 0.2, 0, 0.6666666666666666, 0, 0, -16.20540160629974, -16.20540160629974],\n+ [6.482349627924372, 0, 1, 22.11982471081377, 0, 0, 0.6666666666666666, 0, 0, -9.318773525114544, -9.318773525114544],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [6.13023477476708, 0, 1, 16.42683762241957, 0, 0, 0.6666666666666666, 0, 0, -8.426707996008661, -8.426657557593867],\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, 1e-08, 11.25009627466926, 0.9999999899999999, 2.140796075562884, 0.1687479724774007, 1, 0, -7.862288382502665, -7.862357593123471],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 0.7856630669500002, 0, 0.2143369330499998, 0, 0.6666666666666666, 0, 0, -8.300016389329704, -8.299995192895061],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [6.101386435319732, 0, 1, 19.61771276623135, 0, 0, 0.6666666666666666, 0, 0, -8.704315977164981, -8.704315977164981],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 0.75, 0, 0.25, 0, 0.6666666666666666, 0, 0, -9.195329163599508, -9.195329163599508],\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+ [19.9380473313024, 0, 1, 0.9373179694184103, 0, 0, 0.6666666666666666, 0, 0, -15.22014132048619, -15.22014132048619],\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+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [11.64306808727784, 0.4928820447193593, 1e-08, 14.25357030569616, 0.9999999899999999, 0.01166398299710281, 0.6387332196335862, 0, 0, -10.62917192283428, -10.62954649188683],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 0.8, 0, 0.2, 0, 0.6666666666666666, 0, 0, -6.450160374240846, -6.450160374240846],\n+ [15.41466934663608, 0, 1, 1.352835255829256, 0, 0, 0.6666666666666666, 0, 0, -8.173886747539196, -8.173829437988074],\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+ [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+ [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, 0.7916811160680001, 0, 0.2083188839319999, 0, 0.6666666666666666, 0, 0, -10.45989140432108, -10.45984658875252],\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+ [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+ [0, '..b'_2021,epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021)"\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Node20":"test",\n+ "Node38":"background",\n+ "Node4":"test",\n+ "REFERENCE":"background",\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":"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+ "MEME analysis":{\n+ "order":2,\n+ "timer":9\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":3\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":12\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 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, 0.6666666666666666, 0, 0, -9.287223836219399, -9.287223836219399],\n+ [0, 0, 1, 0.4712554259319698, 0, 0, 0.6666666666666666, 0, 0, -16.66043872325964, -16.66020536350117],\n+ [6.613018745603487, 0.9469109242998108, 1, 9.919528118405228, 0, 0, 0.6666666666666666, 0, 0, -9.287223836219399, -9.287223836219399],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [6.184493076847391, 0.9840443673414764, 1, 14.36467313781675, 0, 0, 0.6666666666666666, 0, 0, -8.397276622473779, -8.39727424153126],\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, 1.640491119619624, 0, 0, 0.6666666666666666, 0, 0, -9.354308226158436, -9.353594494276042],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0.501598063392769, 0, 0, 0.6666666666666666, 0, 0, -8.522470337679948, -8.522266927380841],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [6.183281758268945, 0.7526223661612934, 1, 20.13077820217984, 0, 0, 0.6666666666666666, 0, 0, -8.672432133180507, -8.672432133180507],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0.5512309724476928, 0, 0, 0.6666666666666666, 0, 0, -9.420342677733165, -9.420102843444187],\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+ [20.55396794793096, 0, 1, 30.83095192189643, 0, 0, 0.6666666666666666, 0, 0, -15.39183141266653, -15.39183141266653],\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+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [11.94069241655939, 1.294861562443251, 1e-08, 3408.05771887139, 0.9999999899999999, 8.386841845077999, 0.006668512759224421, 1, 0, -8.544833462621876, -8.54400349923981],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 2.667290430871263, 0, 0, 0.6666666666666666, 0, 0, -6.676160314084659, -6.675420533850337],\n+ [15.28765906802091, 0.5510526648388843, 1, 0.9197801610675972, 0, 0, 0.6666666666666666, 0, 0, -8.143971341837663, -8.143971341837663],\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+ [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+ [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, 0.7340000026600002, 1.664161295283797, 0.2659999973399998, -0.0004958679801596588, 0.6666666666666666, 0, 0, -10.6790535370286, -10.67690847747361],\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+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],\n+ [0, 0, 1, 0, 0, 0, 1, 0, 0, 0, '..b'+ "Node20":"test",\n+ "Node38":"background",\n+ "Node4":"test",\n+ "REFERENCE":"background",\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",\n+ "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+ "MEME analysis":{\n+ "order":2,\n+ "timer":5\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":10\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,596 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [3.250710398632764, 2.543979863949704, 0.000260278000831112, -9.279879778998792, -9.280586210458985, 1, -0.03083220306091588, 1, -9.279441534952744, 0.246012012715961, 1, -9.279441534952742, 0.3671614662852546, 1, -9.279441534952742, -0.1712639841078613, 1, -9.279441534952737, 0.2624930750589453, 1, -9.279441534952737],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0.5537159057721711, 1.458738094193731e-05, -9.653318580984834, -9.653547984340634, 1, 0.5104924519363182, 1, -9.653308651005229, -0.1367278481442925, 1, -9.653308651005229, 0.5919809397222774, 1, -9.653308651005229, -0.1178049485056483, 1, -9.653308651005229, 0.6168893659032167, 1, -9.653308651005229],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [3.120608327772482, 2.614421539287396, 0.0002691437601083932, -9.281874472112623, -9.282601939787694, 1, 0.04953574496877388, 1, -9.281318510005244, -0.3536675776484469, 1, -9.28131851006073, 0.880962199708396, 1, -9.281317114729157, 0.4033925671419755, 1, -9.281318509947875, 0.1204188200792286, 1, -9.281318509962372],\n+ [0, 1.464518485321612, 2.65544170203544e-05, -10.62328331507694, -10.62393719801913, 1, -0.09951441286794899, 1, -10.62316666528899, 1.323879892092505, 1, -10.62316613327963, 0.2196172646873195, 1, -10.62316666528898, 0.1504288706197217, 1, -10.62316666528886, 0.1853325884628318, 1, -10.62316666528886],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [6.642049096285556, 0.9469109242998108, 0.0003620738332646705, -9.286905212837395, -9.287223838078173, 1, 0.4022344790431069, 1, -9.286810976596435, 1.197779080102599, 1, -9.286810976596437, 0.3589760978791438, 1, -9.286810976596435, 0.1410881301787622, 1, -9.286810976596435, -0.7850618321090115, 1, -9.286810976596435],\n+ [0, 0.3704419203686217, 2.210275222817499e-05, -16.66016944635797, -16.66043872464428, 1, 0.3930843395219109, 1, -16.6601383462611, 0.2146143946643995, 1, -16.6601383462611, 1.161538175214766, 1, -16.66013834626109, -0.02607298415665098, 1, -16.66013834627073, -0.8791189616882017, 1, -16.66013834626112],\n+ [6.642049096285556, 0.9469109242998108, 0.0003620738332646705, -9.286905212837395, -9.287223838078173, 1, 0.4022344790431069, 1, -9.286810976596435, 1.197779080102599, 1, -9.286810976596437, 0.3589760978791438, 1, -9.286810976596435, 0.1410881301787622, 1, -9.286810976596435, -0.7850618321090115, 1, -9.286810976596435],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [6.15200979587571, 0.7664418907442996, 0.0003241434681835816, -8.397013750003021, -8.397276621570359, 1, -0.2520353509836328, 1, -8.396847261582421, 0.1107366238822934, 1, -8.396847261582423, 0.1524040518249381, 1, -8.396847261582419, 0.5017067831730544, 1, -8.396847261582419, 0.1728359761835464, 1, -8.396847261582433],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 1.640491119619624, 4.530322293875232e-05, -9.354648574415357, -9.354308225168079, 1, 0.3464427721141255, 1, -9.353594756043833, 0.2276891704052981, 1, -9.353594756041785, 0.3556536075671364, 1, -9.353594755979932, 0.1068123231090358, 1, -9.353594756061817, 0.2571589515668457, 1, -9.353594756037198],\n+ [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],\n+ [0, 0.5015980633927689, 4.463668663386787e-06, -8.522225370219248, -8.522470343311889, 1, 0.634546397'..b' "Node20":"test",\n+ "Node38":"background",\n+ "Node4":"test",\n+ "REFERENCE":"background",\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":"background",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"background",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"background",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"background",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"background",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"background",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"background",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"background",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"background",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"background",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"background",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"background",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"background",\n+ "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"background",\n+ "epi_isl_1652105_hCoV_19_Singapore_561_2021":"background",\n+ "epi_isl_1652118_hCoV_19_Singapore_575_2021":"background",\n+ "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"background",\n+ "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"background",\n+ "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"background",\n+ "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"background",\n+ "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"background",\n+ "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"background",\n+ "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"background",\n+ "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"background",\n+ "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"background",\n+ "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"background",\n+ "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"background",\n+ "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"background",\n+ "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"background",\n+ "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"background",\n+ "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"background"\n+ }\n+ },\n+ "timers":{\n+ "Model fitting":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "PRIME analysis":{\n+ "order":2,\n+ "timer":19\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":25\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,557 @@\n+{\n+ "Synonymous site-posteriors": [\n+[1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 0.9999999999999999, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.9999999999999999, 1, 1, 1],\n+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] \n+ ],\n+ "analysis":0,\n+ "branch attributes":{\n+ "0":{\n+ "Node20":{\n+ "MG94xREV with separate rates for branch sets":0.001634892352012191,\n+ "Nucleotide GTR":0.001684521619549293,\n+ "RELAX alternative":0.001888715982590274,\n+ "RELAX null":0.001729201145341893\n+ },\n+ "Node38":{\n+ "MG94xREV with separate rates for branch sets":0.001919664136946674,\n+ "Nucleotide GTR":0.00168484920326581,\n+ "RELAX alternative":0.001886373803275281,\n+ "RELAX null":0.001757668602191916\n+ },\n+ "Node4":{\n+ "MG94xREV with separate rates for branch sets":0.001634608725455373,\n+ "Nucleotide GTR":0.001683801387489096,\n+ "RELAX alternative":0.001736927843216757,\n+ "RELAX null":0.001719649158870973\n+ },\n+ "REFERENCE":{\n+ "MG94xREV with separate rates for branch sets":0,\n+ "Nucleotide GTR":0,\n+ "RELAX alternative":0,\n+ "RELAX null":0,\n+ "original name":"REFERENCE"\n+ },\n+ "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{\n+ "MG94xREV with separate rates for branch sets":0,\n+ "Nucleotide GTR":0,\n+ "RELAX alternative":0,\n+ "RELAX null":0,\n+ "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021"\n+ },\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{\n+ "MG94xREV with separate rates for branch sets":0.001728428276944542,\n+ "Nucleotide GTR":0.001682745450340891,\n+ "RELAX alternative":0.001737560358174388,\n+ "RELAX null":0.001737701430364698,\n+ "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021"\n+ },\n+ "epi_'..b'Unclassified",\n+ "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":"Unclassified",\n+ "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":"Unclassified",\n+ "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":"Unclassified",\n+ "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":"Unclassified",\n+ "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":"Unclassified",\n+ "epi_isl_1543980_hCoV_19_Singapore_490_2021":"Unclassified",\n+ "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":"Unclassified",\n+ "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":"Unclassified",\n+ "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":"Unclassified",\n+ "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":"Unclassified",\n+ "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":"Unclassified",\n+ "epi_isl_1615709_hCoV_19_England_CAMC_14E792B_2021":"Unclassified",\n+ "epi_isl_1632256_hCoV_19_England_RAND_14E1D70_2021":"Unclassified",\n+ "epi_isl_1652105_hCoV_19_Singapore_561_2021":"Unclassified",\n+ "epi_isl_1652118_hCoV_19_Singapore_575_2021":"Unclassified",\n+ "gb_LR757997_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_UNKNOWN_LR757997_Segment_null_Host_Human":"Unclassified",\n+ "gb_MT226610_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_CHN_KMS1_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MT326179_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_UW_1572_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MT745751_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_DNAS_isl_BRB_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW154124_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC7567_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW345265_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0448_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW486334_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2535_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW523870_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_LA_CDC_STM_A100279_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW525063_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_CDC_STM_0000013_D10_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW540189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01215_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW562702_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2102128070_2020_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW583322_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_AL_CDC_STM_000001665_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW585851_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_CDC_STM_000004152_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW585867_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000003621_2021_Segment_null_Host_Human":"Unclassified",\n+ "gb_MW593074_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2645_2021_Segment_null_Host_Human":"Unclassified"\n+ }\n+ },\n+ "timers":{\n+ "Overall":{\n+ "order":0,\n+ "timer":67\n+ },\n+ "Preliminary model fitting":{\n+ "order":1,\n+ "timer":5\n+ },\n+ "RELAX alternative model fitting":{\n+ "order":3,\n+ "timer":50\n+ },\n+ "RELAX null model fitting":{\n+ "order":4,\n+ "timer":12\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 1fb98a84e86d -r 70de001b6768 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 07:08:44 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 |