diff --git a/quickstart-build/Snakefile b/quickstart-build/Snakefile index bccc9b3..3c9cf6f 100644 --- a/quickstart-build/Snakefile +++ b/quickstart-build/Snakefile @@ -20,15 +20,13 @@ rule all: """Specify all input files here. For this build, you'll start with input sequences from the example_data folder, which contain metadata information in the sequence header. Specify here files denoting specific strains to include or drop, -references sequences, and files for auspice visualization (lat_longs, colors)""" +references sequences, and files for auspice visualization""" rule files: params: input_sequences = "example_data/{subtype}_{segment}.fasta", dropped_strains = "config/dropped_strains_{subtype}.txt", include_strains = "config/include_strains_{subtype}.txt", reference = "config/reference_{subtype}_{segment}.gb", - colors = "config/colors_{subtype}.tsv", - lat_longs = "config/lat_longs_{subtype}.tsv", auspice_config = "config/auspice_config_{subtype}.json" @@ -305,8 +303,6 @@ rule export: tree = rules.refine.output.tree, metadata = rules.parse.output.metadata, node_data = node_data_by_wildcards, - colors = files.colors, - lat_longs = files.lat_longs, auspice_config = files.auspice_config output: auspice_json = "auspice/flu_avian_{subtype}_{segment}.json" @@ -316,8 +312,6 @@ rule export: --tree {input.tree} \ --metadata {input.metadata} \ --node-data {input.node_data}\ - --colors {input.colors} \ - --lat-longs {input.lat_longs} \ --auspice-config {input.auspice_config} \ --include-root-sequence \ --output {output.auspice_json} diff --git a/quickstart-build/auspice/flu_avian_h5n1_ha.json b/quickstart-build/auspice/flu_avian_h5n1_ha.json deleted file mode 100644 index 149465f..0000000 --- a/quickstart-build/auspice/flu_avian_h5n1_ha.json +++ /dev/null @@ -1,3146 +0,0 @@ -{ - "version": "v2", - "meta": { - "title": "Real-time tracking of influenza A/H5N1 virus evolution", - "updated": "2023-01-12", - "maintainers": [ - { - "name": "You!", - "url": "" - } - ], - "display_defaults": { - "map_triplicate": true, - "color_by": "region" - }, - "genome_annotations": { - "nuc": { - "end": 1760, - "start": 1, - "strand": "+", - "seqid": "config/reference_h5n1_ha.gb", - "type": "source" - }, - "HA": { - "end": 1728, - "seqid": "config/reference_h5n1_ha.gb", - "start": 22, - "strand": "+", - "type": "CDS" - } - }, - "colorings": [ - { - "key": "gt", - "title": "Genotype", - "type": "categorical" - }, - { - "key": "num_date", - "title": "Date", - "type": "continuous" - }, - { - "key": "country", - "title": "Country", - "type": "categorical" - }, - { - "key": "region", - "title": "Region", - "type": "categorical", - "scale": [ - [ - "China", - "#4042C7" - ], - [ - "Southeast Asia", - "#4274CE" - ], - [ - "South Asia", - "#5199B7" - ], - [ - "Japan Korea", - "#69B091" - ], - [ - "Africa", - "#CEB541" - ] - ] - }, - { - "key": "host", - "title": "Host", - "type": "categorical", - "scale": [ - [ - "Avian", - "#4066CF" - ], - [ - "Environment", - "#77B67F" - ], - [ - "Human", - "#DC2F24" - ] - ] - }, - { - "key": "furin_cleavage_motif", - "title": "furin cleavage motif", - "type": "categorical" - }, - { - "key": "cleavage_site_sequence", - "title": "cleavage site sequence", - "type": "categorical" - }, - { - "key": "cleavage_site_sequence", - "title": "cleavage site sequence", - "type": "categorical" - }, - { - "key": "furin_cleavage_motif", - "title": "furin cleavage motif", - "type": "categorical" - } - ], - "filters": [ - "host", - "region", - "country", - "submitting_lab" - ], - "geo_resolutions": [ - { - "key": "region", - "demes": { - "Africa": { - "latitude": 4.070194, - "longitude": 21.824559 - }, - "South Asia": { - "latitude": 24.485438, - "longitude": 76.513158 - }, - "China": { - "latitude": 35.000074, - "longitude": 104.999927 - }, - "Southeast Asia": { - "latitude": 3.020567, - "longitude": 112.390683 - }, - "Japan Korea": { - "latitude": 35.845119, - "longitude": 136.736386 - } - } - }, - { - "key": "country", - "demes": { - "Thailand": { - "latitude": 14.8971921, - "longitude": 100.83273 - }, - "China": { - "latitude": 35.000074, - "longitude": 104.999927 - }, - "Japan": { - "latitude": 35.68536, - "longitude": 139.75309 - }, - "Laos": { - "latitude": 20.0171109, - "longitude": 103.378253 - }, - "Egypt": { - "latitude": 26.2540493, - "longitude": 29.2675469 - }, - "Bangladesh": { - "latitude": 24.4768783, - "longitude": 90.2932426 - }, - "Vietnam": { - 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"nuc": "GCAGGGGTTCAATCTGTCAAAATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTGACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAATCCAGCCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAACTGAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCCCCAAAAGTTCTTGGTCCAATCATGAAGCCTCATTAGGGGTGAGCTCAGCATGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAATACATACCCAACAATAAAGAGGAGCTACAATAATACCAACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGGGACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCAAAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAACCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGAATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTGAATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCGATAAACTCTAGTATGCCATTCCACAACATACACCCTCTCACCATCGGGGAATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCAGAAATAGCCCTCAAAGAGAGAGAAGAAGAAGAAAGAGAGGACTATTTGGAGCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTGGTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACAAAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCGATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAATAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGATTCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAATGAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAAGGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTTTCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAACGGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGAGGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGTCAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTGGCTGGTCTATCTTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGAATTTGCATTTAAATTTGTGAGTTCAGATTGTAGTTAAAAACACC" -} \ No newline at end of file diff --git a/quickstart-build/config/colors_h5n1.tsv b/quickstart-build/config/colors_h5n1.tsv deleted file mode 100644 index d257479..0000000 --- a/quickstart-build/config/colors_h5n1.tsv +++ /dev/null @@ -1,56 +0,0 @@ -host avian #4066CF -host environment #77B67F -host nonhuman mammal #CEB541 -host human #DC2F24 -h5_label_clade 0 #5E1D9D -h5_label_clade 1 #521EA7 -h5_label_clade 1-8-9-like #4C24B0 -h5_label_clade 1.1 #472DB8 -h5_label_clade 1.1-like #4335C0 -h5_label_clade 1.1.1 #403EC6 -h5_label_clade 1.1.2 #3F48C9 -h5_label_clade 2-like #3F53CD -h5_label_clade 2.1.1 #3E5DD0 -h5_label_clade 2.1.2 #4066CF -h5_label_clade 2.1.3 #4270CE -h5_label_clade 2.1.3.1 #4379CD -h5_label_clade 2.1.3.2 #4682C9 -h5_label_clade 2.1.3.2a #4989C4 -h5_label_clade 2.1.3.2b #4C91C0 -h5_label_clade 2.1.3.3 #5097BA -h5_label_clade 2.2 #549DB3 -h5_label_clade 2.2.1 #58A2AC -h5_label_clade 2.2.1.1 #5CA7A5 -h5_label_clade 2.2.1.1a #61AB9D -h5_label_clade 2.2.1.2 #67AE95 -h5_label_clade 2.2.2 #6CB28D -h5_label_clade 2.2.2.1 #72B485 -h5_label_clade 2.3.1 #78B77D -h5_label_clade 2.3.2 #7FB976 -h5_label_clade 2.3.2.1 #85BA6E -h5_label_clade 2.3.2.1a #8CBB68 -h5_label_clade 2.3.2.1b #93BD62 -h5_label_clade 2.3.2.1c #9BBE5C -h5_label_clade 2.3.3 #A2BE57 -h5_label_clade 2.3.4 #A9BD53 -h5_label_clade 2.3.4-like #B1BD4E -h5_label_clade 2.3.4.1 #B8BC4B -h5_label_clade 2.3.4.2 #BFBB48 -h5_label_clade 2.3.4.3 #C5B945 -h5_label_clade 2.3.4.4 #CCB742 -h5_label_clade 2.4 #D1B340 -h5_label_clade 2.5 #D6AF3E -h5_label_clade 3 #DCAB3D -h5_label_clade 3-like #DFA53B -h5_label_clade 4 #E29E39 -h5_label_clade 5 #E49838 -h5_label_clade 5-6-like #E68F36 -h5_label_clade 6 #E68634 -h5_label_clade 7 #E67C33 -h5_label_clade 7.1 #E67231 -h5_label_clade 7.2 #E4652E -h5_label_clade 8 #E2592C -h5_label_clade 8-9-like #E04D29 -h5_label_clade 9 #DF4127 -h5_label_clade EA-nonGsGD #DD3425 -h5_label_clade Am-nonGsGD #891916 \ No newline at end of file diff --git a/quickstart-build/config/lat_longs_h5n1.tsv b/quickstart-build/config/lat_longs_h5n1.tsv deleted file mode 100644 index fc883d5..0000000 --- a/quickstart-build/config/lat_longs_h5n1.tsv +++ /dev/null @@ -1 +0,0 @@ -country tibet 31.129337 88.671049