diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/clade-labeling/add-clades.py b/clade-labeling/add-clades.py old mode 100644 new mode 100755 diff --git a/clade-labeling/update-clades.py b/clade-labeling/update-clades.py old mode 100644 new mode 100755 index 0f55ffd..a1a74c0 --- a/clade-labeling/update-clades.py +++ b/clade-labeling/update-clades.py @@ -84,7 +84,7 @@ def append_new_clades(new_clades, old_clades): """run label and reformat the output""" print("\nrunning LABEL to assign clades to", len(new_strains), "new strains of", subtype) -os.system('flu-amd/LABEL -D {new_strains_fasta} {label_output} H5v2015'.format(new_strains_fasta=new_strains_fasta, label_output=label_output)) +os.system('flu-amd/./LABEL -D {new_strains_fasta} {label_output} H5v2015'.format(new_strains_fasta=new_strains_fasta, label_output=label_output)) os.system('python clade-labeling/check-LABEL-annotations.py --label_output {label_output}_final.txt --output {new_clades_file}'.format(new_clades_file=new_clades_file, label_output=label_output)) diff --git a/config/auspice_config_h5n1.json b/config/auspice_config_h5n1.json old mode 100644 new mode 100755 index d7d5e3e..5497b96 --- a/config/auspice_config_h5n1.json +++ b/config/auspice_config_h5n1.json @@ -1,78 +1,108 @@ -{ - "title": "Real-time tracking of influenza A/H5N1 virus evolution", - "maintainers": [ - {"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"} - ], - "build_url": "https://github.com/nextstrain/avian-flu", - "data_provenance": [ - { - "name": "GISAID" - } - ], - "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" - }, - { - "key": "host", - "title": "Host", - "type": "categorical" - }, - { - "key": "domestic_status", - "title": "Domestic or Wild", - "type": "categorical" - }, - { - "key": "h5_label_clade", - "title": "H5 clade", - "type": "categorical" - }, - { - "key": "furin_cleavage_motif", - "title": "furin cleavage motif", - "type": "categorical" - }, - { - "key": "cleavage_site_sequence", - "title": "cleavage site sequence", - "type": "categorical" - }, - { - "key": "submitting_lab", - "title": "Submitting lab", - "type": "categorical" - } - ], - "geo_resolutions": [ - "region", - "country" - ], - "display_defaults": { - "map_triplicate": true, - "color_by": "region" - }, - "filters": [ - "host", - "region", - "country", - "submitting_lab" - ] -} +{ + "title": "Real-time tracking of influenza A/H5N1 virus evolution", + "maintainers": [ + {"name": "Louise Moncla", "url": "http://bedford.io/team/louise-moncla/"} + ], + "build_url": "https://github.com/nextstrain/avian-flu", + "data_provenance": [ + { + "name": "GISAID" + } + ], + "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" + }, + { + "key": "host", + "title": "Host", + "type": "categorical" + }, + { + "key": "domestic_status", + "title": "Domestic or Wild", + "type": "categorical" + }, + { + "key": "subtype", + "title": "Subtype", + "type": "categorical" + }, + { + "key": "h5_label_clade", + "title": "LABEL clade", + "type": "categorical" + }, + { + "key": "gisaid_clade", + "title": "GISAID clade", + "type": "categorical" + }, + { + "key": "furin_cleavage_motif", + "title": "furin cleavage motif", + "type": "categorical" + }, + { + "key": "cleavage_site_sequence", + "title": "cleavage site sequence", + "type": "categorical" + }, + { + "key": "authors", + "title": "Authors", + "type": "categorical" + }, + { + "key": "PMID", + "title": "Pubmed ID", + "type": "categorical" + }, + { + "key": "submitting_lab", + "title": "Submitting lab", + "type": "categorical" + }, + { + "key": "originating_lab", + "title": "Originating lab", + "type": "categorical" + } + ], + "geo_resolutions": [ + "region", + "country" + ], + "display_defaults": { + "map_triplicate": true, + "color_by": "region" + }, + "filters": [ + "host", + "domestic_status", + "region", + "country", + "submitting_lab", + "subtype", + "h5_label_clade", + "gisaid_clade", + "authors" + ] +} diff --git a/config/auspice_config_h5nx.json b/config/auspice_config_h5nx.json old mode 100644 new mode 100755 index f4abdde..68b1946 --- a/config/auspice_config_h5nx.json +++ b/config/auspice_config_h5nx.json @@ -47,7 +47,12 @@ }, { "key": "h5_label_clade", - "title": "H5 clade", + "title": "LABEL clade", + "type": "categorical" + }, + { + "key": "gisaid_clade", + "title": "GISAID clade", "type": "categorical" }, { @@ -60,6 +65,16 @@ "title": "cleavage site sequence", "type": "categorical" }, + { + "key": "authors", + "title": "Authors", + "type": "categorical" + }, + { + "key": "PMID", + "title": "Pubmed ID", + "type": "categorical" + }, { "key": "submitting_lab", "title": "Submitting lab", @@ -81,10 +96,13 @@ }, "filters": [ "host", + "domestic_status", "region", "country", "submitting_lab", "subtype", - "h5_label_clade" + "h5_label_clade", + "gisaid_clade", + "authors" ] } diff --git a/config/auspice_config_h7n9.json b/config/auspice_config_h7n9.json old mode 100644 new mode 100755 diff --git a/config/auspice_config_h9n2.json b/config/auspice_config_h9n2.json old mode 100644 new mode 100755 diff --git a/config/colors_h5n1.tsv b/config/colors_h5n1.tsv old mode 100644 new mode 100755 index d257479..e011cd4 --- a/config/colors_h5n1.tsv +++ b/config/colors_h5n1.tsv @@ -53,4 +53,56 @@ 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 +h5_label_clade Am-nonGsGD #891916 +gisaid_clade 0 #5E1D9D +gisaid_clade 1 #521EA7 +gisaid_clade 1-8-9-like #4C24B0 +gisaid_clade 1.1 #472DB8 +gisaid_clade 1.1-like #4335C0 +gisaid_clade 1.1.1 #403EC6 +gisaid_clade 1.1.2 #3F48C9 +gisaid_clade 2.1.1 #3F53CD +gisaid_clade 2.1.2 #3E5DD0 +gisaid_clade 2.1.3 #4066CF +gisaid_clade 2.1.3.1 #4270CE +gisaid_clade 2.1.3.2 #4379CD +gisaid_clade 2.1.3.2a #4682C9 +gisaid_clade 2.1.3.2b #4989C4 +gisaid_clade 2.1.3.3 #4C91C0 +gisaid_clade 2.2 #5097BA +gisaid_clade 2.2.1 #549DB3 +gisaid_clade 2.2.1.1 #58A2AC +gisaid_clade 2.2.1.1a #5CA7A5 +gisaid_clade 2.2.1.2 #61AB9D +gisaid_clade 2.2.2 #67AE95 +gisaid_clade 2.2.2.1 #6CB28D +gisaid_clade 2.3.1 #72B485 +gisaid_clade 2.3.2 #78B77D +gisaid_clade 2.3.2.1 #7FB976 +gisaid_clade 2.3.2.1a #85BA6E +gisaid_clade 2.3.2.1b #8CBB68 +gisaid_clade 2.3.2.1c #93BD62 +gisaid_clade 2.3.3 #9BBE5C +gisaid_clade 2.3.4 #A2BE57 +gisaid_clade 2.3.4-like #A9BD53 +gisaid_clade 2.3.4.1 #B1BD4E +gisaid_clade 2.3.4.2 #B8BC4B +gisaid_clade 2.3.4.3 #BFBB48 +gisaid_clade 2.3.4.4 #C5B945 +gisaid_clade 2.3.4.4b #CCB742 +gisaid_clade 2.3.4.4c #D1B340 +gisaid_clade 2.3.4.4g #D6AF3E +gisaid_clade 2.3.4.4e #DCAB3D +gisaid_clade 2.3.4.4h #DFA53B +gisaid_clade 2.5 #E29E39 +gisaid_clade 3 #E49838 +gisaid_clade 4 #E68F36 +gisaid_clade 5 #E68634 +gisaid_clade 6 #E67C33 +gisaid_clade 7 #E67231 +gisaid_clade 7.1 #E4652E +gisaid_clade 7.2 #E2592C +gisaid_clade 8 #E04D29 +gisaid_clade 9 #DF4127 +gisaid_clade EA_nonGsGD #DD3425 +gisaid_clade Am_nonGsGD #891916 diff --git a/config/colors_h5nx.tsv b/config/colors_h5nx.tsv old mode 100644 new mode 100755 index ab08aab..bc18661 --- a/config/colors_h5nx.tsv +++ b/config/colors_h5nx.tsv @@ -63,4 +63,55 @@ h5_label_clade 8-9-like #E04D29 h5_label_clade 9 #DF4127 h5_label_clade EA-nonGsGD #DD3425 h5_label_clade Am-nonGsGD #891916 - +gisaid_clade 0 #5E1D9D +gisaid_clade 1 #521EA7 +gisaid_clade 1-8-9-like #4C24B0 +gisaid_clade 1.1 #472DB8 +gisaid_clade 1.1-like #4335C0 +gisaid_clade 1.1.1 #403EC6 +gisaid_clade 1.1.2 #3F48C9 +gisaid_clade 2.1.1 #3F53CD +gisaid_clade 2.1.2 #3E5DD0 +gisaid_clade 2.1.3 #4066CF +gisaid_clade 2.1.3.1 #4270CE +gisaid_clade 2.1.3.2 #4379CD +gisaid_clade 2.1.3.2a #4682C9 +gisaid_clade 2.1.3.2b #4989C4 +gisaid_clade 2.1.3.3 #4C91C0 +gisaid_clade 2.2 #5097BA +gisaid_clade 2.2.1 #549DB3 +gisaid_clade 2.2.1.1 #58A2AC +gisaid_clade 2.2.1.1a #5CA7A5 +gisaid_clade 2.2.1.2 #61AB9D +gisaid_clade 2.2.2 #67AE95 +gisaid_clade 2.2.2.1 #6CB28D +gisaid_clade 2.3.1 #72B485 +gisaid_clade 2.3.2 #78B77D +gisaid_clade 2.3.2.1 #7FB976 +gisaid_clade 2.3.2.1a #85BA6E +gisaid_clade 2.3.2.1b #8CBB68 +gisaid_clade 2.3.2.1c #93BD62 +gisaid_clade 2.3.3 #9BBE5C +gisaid_clade 2.3.4 #A2BE57 +gisaid_clade 2.3.4-like #A9BD53 +gisaid_clade 2.3.4.1 #B1BD4E +gisaid_clade 2.3.4.2 #B8BC4B +gisaid_clade 2.3.4.3 #BFBB48 +gisaid_clade 2.3.4.4 #C5B945 +gisaid_clade 2.3.4.4b #CCB742 +gisaid_clade 2.3.4.4c #D1B340 +gisaid_clade 2.3.4.4g #D6AF3E +gisaid_clade 2.3.4.4e #DCAB3D +gisaid_clade 2.3.4.4h #DFA53B +gisaid_clade 2.5 #E29E39 +gisaid_clade 3 #E49838 +gisaid_clade 4 #E68F36 +gisaid_clade 5 #E68634 +gisaid_clade 6 #E67C33 +gisaid_clade 7 #E67231 +gisaid_clade 7.1 #E4652E +gisaid_clade 7.2 #E2592C +gisaid_clade 8 #E04D29 +gisaid_clade 9 #DF4127 +gisaid_clade EA_nonGsGD #DD3425 +gisaid_clade Am_nonGsGD #891916 diff --git a/config/colors_h7n9.tsv b/config/colors_h7n9.tsv old mode 100644 new mode 100755 diff --git a/config/colors_h9n2.tsv b/config/colors_h9n2.tsv old mode 100644 new mode 100755 diff --git a/config/dropped_strains_h5n1.txt b/config/dropped_strains_h5n1.txt old mode 100644 new mode 100755 diff --git a/config/dropped_strains_h5nx.txt b/config/dropped_strains_h5nx.txt old mode 100644 new mode 100755 diff --git a/config/dropped_strains_h7n9.txt b/config/dropped_strains_h7n9.txt old mode 100644 new mode 100755 diff --git a/config/dropped_strains_h9n2.txt b/config/dropped_strains_h9n2.txt old mode 100644 new mode 100755 diff --git a/config/lat_longs_h5n1.tsv 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