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Changeset 21:b3b775a4ae1f (2021-07-03)

Previous changeset 20:d8092fd69175 (2021-06-18) Next changeset 22:b044a346c00d (2021-10-05)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ec5db8349483b2cd46f9da23abe6cefcf65bc714"

modified:
scripts/hyphy_summary.py
test-data/summary/ORF6-segment.json
test-data/summary/merged-segment.json
test-data/summary/merged-site.json
test-data/summary/nsp7-segment.json
test-data/summary/nsp8-segment.json
test-data/summary/nsp8-site.json

diff -r d8092fd69175 -r b3b775a4ae1f scripts/hyphy_summary.py
--- a/scripts/hyphy_summary.py Fri Jun 18 15:29:34 2021 +0000
+++ b/scripts/hyphy_summary.py Sat Jul 03 08:59:00 2021 +0000

[

b'@@ -107,7 +107,7 @@\n if self.cfel is None:\n return\n node_tags = {}\n- _ = self._newick_parser(self.cfel[\'input\'][\'trees\'][\'0\'], False, node_tags, self.cfel)[\'json\']\n+ _ = newick_parser(self.cfel[\'input\'][\'trees\'][\'0\'], False, node_tags, self.cfel, self.arguments, self.labels)[\'json\']\n if self.summary_json is not None:\n omegas = {}\n T = {}\n@@ -191,7 +191,7 @@\n return defaultdict(int)\n compressed_subs = {}\n node_tags = {}\n- the_tree = self._newick_parser(self.slac[\'input\'][\'trees\'][\'0\'], False, node_tags, self.slac)[\'json\']\n+ the_tree = newick_parser(self.slac[\'input\'][\'trees\'][\'0\'], False, node_tags, self.slac, self.arguments, self.labels)\n root_node = None\n if self.summary_json is not None:\n for branch, info in self.slac[\'branch attributes\'][\'0\'].items():\n@@ -210,9 +210,9 @@\n if gs[0] >= 0:\n self.labels[root_node] = self.slac[\'branch attributes\'][\'0\'][root_node][\'codon\'][0][i]\n try:\n- self._traverse_tree_in_order(the_tree, self.slac[\'branch attributes\'][\'0\'], i, None, root_node)\n+ traverse_tree_in_order(the_tree, self.labels, self.slac[\'branch attributes\'][\'0\'], i, None, root_node)\n except Exception:\n- raise\n+ pass\n compressed_subs[gs[0]] = self.labels\n for k in set([k[0] for k in node_tags.values()]):\n if len(k):\n@@ -433,195 +433,201 @@\n gene_name = \'N/A\'\n return (genomic_site_coord, gene_name, gene_site)\n \n- def _traverse_tree_in_order(self, node, slac_data, i, parent_tag, root):\n- node_tag = None\n- if node is None:\n- return\n- try:\n- nn = root if node[\'name\'] == \'root\' else node[\'name\']\n- except Exception:\n- raise\n- if nn in slac_data:\n- node_tag = slac_data[nn][\'codon\'][0][i]\n- if (parent_tag != node_tag):\n- self.labels[nn] = node_tag\n- self.labels[node[\'name\']] = node_tag\n- if \'children\' in node:\n- for c in node[\'children\']:\n- if c is not None:\n- if \'name\' in c:\n- self._traverse_tree_in_order(c, slac_data, i, node_tag, root)\n-\n- def _match_node_names(self, qry_node, ref_node, mapping):\n- if \'children\' in qry_node and \'children\' in ref_node:\n- mapping[ref_node[\'name\']] = qry_node[\'name\']\n- if len(qry_node[\'children\']) != len(ref_node[\'children\']):\n- raise Exception(\'Internal topology mismatch\')\n- for i, n in enumerate(ref_node[\'children\']):\n- self._match_node_names(qry_node[\'children\'][i], n, mapping)\n- elif \'children\' in qry_node:\n- raise Exception(\'Topology mismatch\')\n- elif \'children\' in ref_node:\n- raise Exception(\'Topology mismatch\')\n- else:\n- if qry_node[\'name\'] != ref_node[\'name\']:\n- raise Exception(\'Leaf name mismatch\')\n-\n def _get_incoming_labels(self):\n json_data = self._load_json(self.arguments.labels)\n self.incoming_labels = json_data\n \n- def _newick_parser(self, nwk_str, bootstrap_values, track_tags, json_map):\n- clade_stack = []\n- automaton_state = 0\n- current_node_name = \'\'\n- current_node_attribute = \'\'\n- current_node_annotation = \'\'\n- quote_delimiter = None\n- name_quotes = {"\'": 1, \'"\': 1}\n \n- def add_new_tree_level():\n- new_level = {\'name\': None}\n- the_parent = clade_stack[len(clade_stack) - 1]\n- if (\'children\' not in the_parent):\n- the_parent[\'children\'] = []\n- clade_stack.append(new_level)\n- the_parent[\'children\'].append(clade_stack[len(clade_st'..b' automaton_state = 4\n else:\n- if (current_char == \'[\'):\n- if len(current_node_annotation):\n- return generate_error(char_index)\n- else:\n- automaton_state = 4\n+ if (automaton_state == 3):\n+ current_node_attribute += current_char\n else:\n- if (automaton_state == 3):\n- current_node_attribute += current_char\n- else:\n- if (space.search(current_char)):\n- continue\n- if (current_char == \';\'):\n- char_index = len(nwk_str)\n- break\n- current_node_name += current_char\n- elif automaton_state == 2:\n- # inside a quoted expression\n- if (current_char == quote_delimiter):\n- if (char_index < len(nwk_str - 1)):\n- if (nwk_str[char_index + 1] == quote_delimiter):\n- char_index += 1\n- current_node_name += quote_delimiter\n+ if (space.search(current_char)):\n continue\n- quote_delimiter = 0\n- automaton_state = 1\n+ if (current_char == ""):\n+ char_index = len(nwk_str)\n+ break\n+ current_node_name += current_char\n+ elif automaton_state == 2:\n+ # inside a quoted expression\n+ if (current_char == quote_delimiter):\n+ if (char_index < len(nwk_str - 1)):\n+ if (nwk_str[char_index + 1] == quote_delimiter):\n+ char_index += 1\n+ current_node_name += quote_delimiter\n continue\n- else:\n- current_node_name += current_char\n- elif automaton_state == 4:\n- # inside a comment / attribute\n- if (current_char == \']\'):\n- automaton_state = 3\n- else:\n- if (current_char == \'[\'):\n- 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+ quote_delimiter = 0\n+ automaton_state = 1\n+ continue\n+ else:\n+ current_node_name += current_char\n+ elif automaton_state == 4:\n+ # inside a comment / attribute\n+ if (current_char == "]"):\n+ automaton_state = 3\n+ else:\n+ if (current_char == "["):\n+ return generate_error(char_index)\n+ current_node_annotation += current_char\n+ except Exception as e:\n+ return generate_error(char_index)\n+ print(e)\n \n- if (len(current_node_name)):\n- tree_json[\'name\'] = current_node_name\n+ if (len(clade_stack) != 1):\n+ return generate_error(len(nwk_str) - 1)\n \n- return {\n- \'json\': tree_json,\n- \'error\': None\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'

diff -r d8092fd69175 -r b3b775a4ae1f test-data/summary/ORF6-segment.json
--- a/test-data/summary/ORF6-segment.json Fri Jun 18 15:29:34 2021 +0000
+++ b/test-data/summary/ORF6-segment.json Sat Jul 03 08:59:00 2021 +0000

[

b'@@ -1,7 +1,1135 @@\n {\n "ORF6": {\n- "map": [],\n+ "map": [\n+ 27201,\n+ 27204,\n+ 27207,\n+ 27210,\n+ 27213,\n+ 27216,\n+ 27219,\n+ 27222,\n+ 27225,\n+ 27228,\n+ 27231,\n+ 27234,\n+ 27237,\n+ 27240,\n+ 27243,\n+ 27246,\n+ 27249,\n+ 27252,\n+ 27255,\n+ 27258,\n+ 27261,\n+ 27264,\n+ 27267,\n+ 27270,\n+ 27273,\n+ 27276,\n+ 27279,\n+ 27282,\n+ 27285,\n+ 27288,\n+ 27291,\n+ 27294,\n+ 27297,\n+ 27300,\n+ 27303,\n+ 27306,\n+ 27309,\n+ 27312,\n+ 27315,\n+ 27318,\n+ 27321,\n+ 27324,\n+ 27327,\n+ 27330,\n+ 27333,\n+ 27336,\n+ 27339,\n+ 27342,\n+ 27345,\n+ 27348,\n+ 27351,\n+ 27354,\n+ 27357,\n+ 27360,\n+ 27363,\n+ 27366,\n+ 27369,\n+ 27372,\n+ 27375,\n+ 27378,\n+ 27381\n+ ],\n "tree": "(REFERENCE,(gb_MW505295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3142_2021_Segment_null_Host_Human,gb_MW586274_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_CDC_STM_000005611_2021_Segment_null_Host_Human)Node184,epi_isl_1533799_hCoV_19_India_MH_NCCS_9947_2021,gb_MW155738_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC11358_2020_Segment_null_Host_Human,gb_MW064840_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MI_QDX_825_2020_Segment_null_Host_Human,(gb_MW545306_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3723_2021_Segment_null_Host_Human,gb_MW547503_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_CUNCI_HGC09I039_2020_Segment_null_Host_Human)Node194,(epi_isl_1543980_hCoV_19_Singapore_490_2021,gb_MW565832_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0724_2021_Segment_null_Host_Human)Node198,(gb_MW093451_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_DSHS_0533_2020_Segment_null_Host_Human,gb_MT449654_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_1063_2020_Segment_null_Host_Human)Node201,(gb_MW586846_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_NY_QDX_4256_2021_Segment_null_Host_Human,gb_MW156732_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC10631_2020_Segment_null_Host_Human)Node206,epi_isl_1631286_hCoV_19_England_CAMC_14E7527_2021,gb_MW486406_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_2638_2020_Segment_null_Host_Human,gb_MW035934_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_2214_2020_Segment_null_Host_Human,gb_MW586670_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_CDC_STM_000003618_2021_Segment_null_Host_Human,gb_MW154411_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC6964_2020_Segment_null_Host_Human,gb_LC571023_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_DP0724_Segment_null_Host_Human,gb_MW134116_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_3258_2020_Segment_null_Host_Human,(gb_MW549937_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3900_2021_Segment_null_Host_Human,gb_MW549223_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S3727_2020_Segment_null_Host_Human)Node226,((gb_MW545248_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3654_2021_Segment_null_Host_Human,gb_MW578246_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MD_MDH_0808_2021_Segment_null_Host_Human)Node231,gb_MW549830_Organism_Severe_acute_respiratory_syndrome_'..b' "gb_MW064863_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_QDX_779_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005652737786801275\n+ ],\n+ "gb_MW155278_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC12385_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.00557872293700733\n+ ],\n+ "epi_isl_1442952_hCoV_19_Singapore_321_2021": [\n+ "Reference",\n+ false,\n+ 0.00557872293700733\n+ ],\n+ "gb_MW193966_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_nimh_12171_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005612858460151898\n+ ],\n+ "gb_MW462661_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MN_MDH_2263_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005587511279835753\n+ ],\n+ "epi_isl_1516887_hCoV_19_Australia_QLD1826_2021": [\n+ "Reference",\n+ false,\n+ 0.005608121500950802\n+ ],\n+ "gb_MW521810_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_QDX_3530_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005660233852045118\n+ ],\n+ "gb_MW490888_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_FL_BPHL_2295_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005585751083177282\n+ ],\n+ "gb_MW155642_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_AUS_VIC13394_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.00559169913114487\n+ ],\n+ "gb_MT847221_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BGD_BCSIR_NILMRC_283_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005610880832638092\n+ ],\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": [\n+ "Reference",\n+ false,\n+ 0.005650956888864765\n+ ],\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": [\n+ "Reference",\n+ false,\n+ 0.005579409632217661\n+ ],\n+ "gb_MT447156_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_THA_SI200383_NT_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005586721466300974\n+ ],\n+ "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": [\n+ "Reference",\n+ false,\n+ 0.005610810413765556\n+ ],\n+ "gb_MW545207_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_3609_2021_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005615097964869044\n+ ],\n+ "gb_MT873189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_DPH_00301_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005615096261285128\n+ ],\n+ "gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0\n+ ],\n+ "gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005592899537321293\n+ ],\n+ "Node100": [\n+ "Reference",\n+ true,\n+ 0.005590443923023665\n+ ],\n+ "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+ "Reference",\n+ false,\n+ 0.005587435112002911\n+ ]\n+ }\n }\n }\n\\ No newline at end of file\n'

diff -r d8092fd69175 -r b3b775a4ae1f test-data/summary/merged-segment.json
--- a/test-data/summary/merged-segment.json Fri Jun 18 15:29:34 2021 +0000
+++ b/test-data/summary/merged-segment.json Sat Jul 03 08:59:00 2021 +0000

[

b'@@ -1,11 +1,1460 @@\n {\n "nsp7": {\n- "map": [],\n+ "map": [\n+ 11842,\n+ 11845,\n+ 11848,\n+ 11851,\n+ 11854,\n+ 11857,\n+ 11860,\n+ 11863,\n+ 11866,\n+ 11869,\n+ 11872,\n+ 11875,\n+ 11878,\n+ 11881,\n+ 11884,\n+ 11887,\n+ 11890,\n+ 11893,\n+ 11896,\n+ 11899,\n+ 11902,\n+ 11905,\n+ 11908,\n+ 11911,\n+ 11914,\n+ 11917,\n+ 11920,\n+ 11923,\n+ 11926,\n+ 11929,\n+ 11932,\n+ 11935,\n+ 11938,\n+ 11941,\n+ 11944,\n+ 11947,\n+ 11950,\n+ 11953,\n+ 11956,\n+ 11959,\n+ 11962,\n+ 11965,\n+ 11968,\n+ 11971,\n+ 11974,\n+ 11977,\n+ 11980,\n+ 11983,\n+ 11986,\n+ 11989,\n+ 11992,\n+ 11995,\n+ 11998,\n+ 12001,\n+ 12004,\n+ 12007,\n+ 12010,\n+ 12013,\n+ 12016,\n+ 12019,\n+ 12022,\n+ 12025,\n+ 12028,\n+ 12031,\n+ 12034,\n+ 12037,\n+ 12040,\n+ 12043,\n+ 12046,\n+ 12049,\n+ 12052,\n+ 12055,\n+ 12058,\n+ 12061,\n+ 12064,\n+ 12067,\n+ 12070,\n+ 12073,\n+ 12076,\n+ 12079,\n+ 12082,\n+ 12085,\n+ 12088\n+ ],\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'..b' 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"Reference",\n+ false,\n+ 0.005615097964869044\n+ ],\n+ "gb_MT873189_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_DPH_00301_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005615096261285128\n+ ],\n+ "gb_MW564882_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CZB_14886_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0\n+ ],\n+ "gb_MT811295_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_SEARCH_0657_IPL_2020_Segment_null_Host_Human": [\n+ "Reference",\n+ false,\n+ 0.005592899537321293\n+ ],\n+ "Node100": [\n+ "Reference",\n+ true,\n+ 0.005590443923023665\n+ ],\n+ "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+ "Reference",\n+ false,\n+ 0.005587435112002911\n+ ]\n+ }\n }\n }\n\\ No newline at end of file\n'

diff -r d8092fd69175 -r b3b775a4ae1f test-data/summary/merged-site.json
--- a/test-data/summary/merged-site.json Fri Jun 18 15:29:34 2021 +0000
+++ b/test-data/summary/merged-site.json Sat Jul 03 08:59:00 2021 +0000

[

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5.651971820557556,\n+ "B-1-617": 0,\n+ "Reference": 0\n+ },\n+ "pi": {\n+ "overall": 0.9946823441693979\n+ },\n+ "pp": -1,\n+ "s": {\n+ "B-1-617": 0,\n+ "Reference": 0\n+ },\n+ "q": 1\n+ },\n+ "cdn": {\n+ "Reference": {\n+ "CAG": 30,\n+ "CAC": 1,\n+ "CAT": 1\n+ }\n+ },\n+ "aa": {\n+ "Reference": {\n+ "Q": 30,\n+ "H": 2\n+ }\n+ },\n+ "bFEL": {\n+ "a": 0,\n+ "b": 0,\n+ "p": 1\n+ },\n+ "bMEME": {\n+ "p": 0.6666666666666666,\n+ "a": 0.0001047939488656373,\n+ "b+": 1.231388513343972,\n+ "w+": 0,\n+ "b-": 2.619848721640933e-05,\n+ "w-": 1,\n+ "br": 0\n+ },\n+ "lMEME": {\n+ "p": 0.3226010900378987,\n+ "a": 0,\n+ "b+": 12.0318826699798,\n+ "w+": 0.99999999,\n+ "b-": 0,\n+ "w-": 1e-08,\n+ "br": 1\n+ },\n+ "prime": {\n+ "p": [\n+ 1,\n+ 1,\n+ 1,\n+ 1,\n+ 1,\n+ 1\n+ ],\n+ "lambda": [\n+ 0.03644798756061563,\n+ -0.3104805457700024,\n+ 0.2357212180710769,\n+ -0.03138277695602196,\n+ -0.005528760550374304\n+ ]\n+ },\n+ "fade": {\n+ "A": {\n+ "rate": 5.308678043450536,\n+ "BF": 1.055716315319722\n+ },\n+ "C": {\n+ "rate": 5.485855194240376,\n+ "BF": 1.055201214399417\n+ },\n+ "D": {\n+ "rate": 5.446266138134284,\n+ "BF": 1.055385899378762\n+ },\n+ "E": {\n+ "rate": 5.500499331126934,\n+ "BF": 1.054475503345003\n+ },\n+ "F": {\n+ "rate": 5.518132842032017,\n+ "BF": 1.055000371827809\n+ },\n+ "G": {\n+ "rate": 5.631290855192524,\n+ "BF": 1.056763207313764\n+ },\n+ "H": {\n+ "rate": 17.73708239321951,\n+ "BF": 3.307358513643126\n+ },\n+ "I": {\n+ "rate": 5.343982030446722,\n+ "BF": 1.049931891253796\n+ },\n+ "K": {\n+ "rate": 5.45735425836756,\n+ "BF": 1.053932665571368\n+ },\n+ "L": {\n+ "rate": 5.39639482035181,\n+ "BF": 1.0545826854226\n+ },\n+ "M": {\n+ "rate": 5.362035570007507,\n+ "BF": 1.052316695364487\n+ },\n+ "N": {\n+ "rate": 5.458974630132252,\n+ "BF": 1.056085864838289\n+ },\n+ "P": {\n+ "rate": 5.511453174502486,\n+ "BF": 1.052535778634476\n+ },\n+ "Q": {\n+ "rate": 0.4589403382528013,\n+ "BF": 0.5346342422907141\n+ },\n+ "R": {\n+ "rate": 5.244347172461493,\n+ "BF": 1.044187416807419\n+ },\n+ "S": {\n+ "rate": 5.129448615617326,\n+ "BF": 1.044038260812914\n+ },\n+ "T": {\n+ "rate": 5.25116626823532,\n+ "BF": 1.05380623570147\n+ },\n+ "V": {\n+ "rate": 5.32619888389831,\n+ "BF": 1.050191753850974\n+ },\n+ "W": {\n+ "rate": 5.631290855192524,\n+ "BF": 1.056763207313764\n+ },\n+ "Y": {\n+ "rate": 5.533472866110234,\n+ "BF": 1.057326684928253\n+ }\n+ }\n+ }\n+}\n\\ No newline at end of file\n'

diff -r d8092fd69175 -r b3b775a4ae1f test-data/summary/nsp7-segment.json
--- a/test-data/summary/nsp7-segment.json Fri Jun 18 15:29:34 2021 +0000
+++ b/test-data/summary/nsp7-segment.json Sat Jul 03 08:59:00 2021 +0000

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diff -r d8092fd69175 -r b3b775a4ae1f test-data/summary/nsp8-segment.json
--- a/test-data/summary/nsp8-segment.json Fri Jun 18 15:29:34 2021 +0000
+++ b/test-data/summary/nsp8-segment.json Sat Jul 03 08:59:00 2021 +0000

[

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diff -r d8092fd69175 -r b3b775a4ae1f test-data/summary/nsp8-site.json
--- a/test-data/summary/nsp8-site.json Fri Jun 18 15:29:34 2021 +0000
+++ b/test-data/summary/nsp8-site.json Sat Jul 03 08:59:00 2021 +0000

[