diff --git a/freyja/_cli.py b/freyja/_cli.py index 0397020..e4bf335 100644 --- a/freyja/_cli.py +++ b/freyja/_cli.py @@ -196,7 +196,8 @@ def update(outdir, noncl, buildlocal, pathogen): """ from freyja.updates import (convert_tree, download_barcodes, download_tree, get_cl_lineages, - get_curated_lineage_data) + get_curated_lineage_data, + download_config) from freyja.convert_paths2barcodes import sortFun locDir = os.path.abspath(os.path.join(os.path.realpath(__file__), os.pardir)) @@ -208,6 +209,7 @@ def update(outdir, noncl, buildlocal, pathogen): locDir = os.path.join(locDir, 'data') print('Getting outbreak data') + download_config(locDir) get_curated_lineage_data(locDir, pathogen) get_cl_lineages(locDir, pathogen) # # get data from UShER diff --git a/freyja/data/H5Nx_barcodes.csv b/freyja/data/H5Nx_barcodes.csv deleted file mode 100644 index 8791be1..0000000 --- a/freyja/data/H5Nx_barcodes.csv +++ /dev/null @@ -1,12 +0,0 @@ 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diff --git a/freyja/data/lineages.yml b/freyja/data/lineages.yml index 66bee20..82609d9 100644 --- a/freyja/data/lineages.yml +++ b/freyja/data/lineages.yml @@ -2861,6 +2861,7 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - JN.1.50 - JN.1.50.1 - JN.1.50.2 @@ -2952,6 +2953,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -2982,6 +2984,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -3029,6 +3035,8 @@ - KR.5 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 @@ -3089,6 +3097,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -3156,6 +3165,8 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MC.1 - MC.2 - MC.2.1 @@ -3168,6 +3179,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -3178,9 +3190,15 @@ - MC.16 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 - ME.1 - MF.1 - MF.2 @@ -3204,6 +3222,7 @@ - MT.1 - MU.1 - MV.1 + - MV.2 - MW.1 - MY.1 - MZ.1 @@ -3217,6 +3236,13 @@ - N.8 - N.9 - N.10 + - NA.1 + - NA.1.1 + - NC.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 - P.1 - P.1.1 - P.1.2 @@ -5856,6 +5882,7 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - JN.1.50 - JN.1.50.1 - JN.1.50.2 @@ -5947,6 +5974,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -5977,6 +6005,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -6024,6 +6056,8 @@ - KR.5 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 @@ -6084,6 +6118,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -6151,6 +6186,8 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MC.1 - MC.2 - MC.2.1 @@ -6163,6 +6200,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -6173,9 +6211,15 @@ - MC.16 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 - ME.1 - MF.1 - MF.2 @@ -6199,6 +6243,7 @@ - MT.1 - MU.1 - MV.1 + - MV.2 - MW.1 - MY.1 - MZ.1 @@ -6212,6 +6257,13 @@ - N.8 - N.9 - N.10 + - NA.1 + - NA.1.1 + - NC.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 - P.1 - P.1.1 - P.1.2 @@ -7913,6 +7965,7 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - JN.1.50 - JN.1.50.1 - JN.1.50.2 @@ -8004,6 +8057,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -8034,6 +8088,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -8081,6 +8139,8 @@ - KR.5 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 @@ -8141,6 +8201,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -8208,6 +8269,8 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MC.1 - MC.2 - MC.2.1 @@ -8220,6 +8283,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -8230,9 +8294,15 @@ - MC.16 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 - ME.1 - MF.1 - MF.2 @@ -8256,6 +8326,7 @@ - MT.1 - MU.1 - MV.1 + - MV.2 - MW.1 - MY.1 - MZ.1 @@ -8269,6 +8340,13 @@ - N.8 - N.9 - N.10 + - NA.1 + - NA.1.1 + - NC.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 - P.1 - P.1.1 - P.1.2 @@ -12445,6 +12523,7 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - JN.1.50 - JN.1.50.1 - JN.1.50.2 @@ -12533,6 +12612,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -12563,6 +12643,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -12610,6 +12694,8 @@ - KR.5 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 @@ -12666,6 +12752,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -12730,6 +12817,8 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MC.1 - MC.2 - MC.2.1 @@ -12742,6 +12831,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -12752,9 +12842,15 @@ - MC.16 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 - ME.1 - MF.1 - MF.2 @@ -12778,9 +12874,17 @@ - MT.1 - MU.1 - MV.1 + - MV.2 - MW.1 - MY.1 - MZ.1 + - NA.1 + - NA.1.1 + - NC.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: B.1.1 - name: BA.1 alias: B.1.1.529.1 @@ -13678,6 +13782,7 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - JN.1.50 - JN.1.50.1 - JN.1.50.2 @@ -13766,6 +13871,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -13796,6 +13902,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -13843,6 +13953,8 @@ - KR.5 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 @@ -13899,6 +14011,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -13963,6 +14076,8 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MC.1 - MC.2 - MC.2.1 @@ -13975,6 +14090,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -13985,9 +14101,15 @@ - MC.16 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 - ME.1 - MF.1 - MF.2 @@ -14011,9 +14133,17 @@ - MT.1 - MU.1 - MV.1 + - MV.2 - MW.1 - MY.1 - MZ.1 + - NA.1 + - NA.1.1 + - NC.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: B.1.1.529 - name: BA.2.1 alias: B.1.1.529.2.1 @@ -17438,6 +17568,7 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - JN.1.50 - JN.1.50.1 - JN.1.50.2 @@ -17520,6 +17651,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -17550,6 +17682,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -17597,6 +17733,8 @@ - KR.5 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 @@ -17653,6 +17791,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -17717,6 +17856,8 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MC.1 - MC.2 - MC.2.1 @@ -17729,6 +17870,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -17739,9 +17881,15 @@ - MC.16 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 - ME.1 - MF.1 - MF.2 @@ -17765,9 +17913,17 @@ - MT.1 - MU.1 - MV.1 + - MV.2 - MW.1 - MY.1 - MZ.1 + - NA.1 + - NA.1.1 + - NC.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: BA.2 - name: BA.2.86.1 alias: B.1.1.529.2.86.1 @@ -17897,6 +18053,7 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - JN.1.50 - JN.1.50.1 - JN.1.50.2 @@ -17974,6 +18131,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -18004,6 +18162,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -18051,6 +18213,8 @@ - KR.5 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 @@ -18107,6 +18271,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -18169,6 +18334,8 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MC.1 - MC.2 - MC.2.1 @@ -18181,6 +18348,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -18191,9 +18359,15 @@ - MC.16 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 - ME.1 - MF.1 - MF.2 @@ -18215,9 +18389,17 @@ - MT.1 - MU.1 - MV.1 + - MV.2 - MW.1 - MY.1 - MZ.1 + - NA.1 + - NA.1.1 + - NC.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: BA.2.86 - name: JN.1 alias: B.1.1.529.2.86.1.1 @@ -18346,6 +18528,7 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - JN.1.50 - JN.1.50.1 - JN.1.50.2 @@ -18392,6 +18575,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -18422,6 +18606,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -18469,6 +18657,8 @@ - KR.5 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 @@ -18525,6 +18715,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -18587,6 +18778,8 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MC.1 - MC.2 - MC.2.1 @@ -18599,6 +18792,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -18609,9 +18803,15 @@ - MC.16 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 - ME.1 - MF.1 - MF.2 @@ -18633,9 +18833,17 @@ - MT.1 - MU.1 - MV.1 + - MV.2 - MW.1 - MY.1 - MZ.1 + - NA.1 + - NA.1.1 + - NC.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: BA.2.86.1 - name: JN.1.1 alias: B.1.1.529.2.86.1.1.1 @@ -19332,6 +19540,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -19362,6 +19571,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -19419,6 +19632,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -19455,6 +19669,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -19485,6 +19700,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - KP.3 - KP.3.1 - KP.3.1.1 @@ -19542,6 +19761,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -19687,6 +19907,7 @@ - KP.2 - KP.2.1 - KP.2.2 + - KP.2.2.1 - KP.2.3 - KP.2.3.1 - KP.2.3.2 @@ -19717,6 +19938,10 @@ - KP.2.22 - KP.2.23 - KP.2.24 + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 - MW.1 parent: JN.1.11.1 - name: KP.2.1 @@ -19728,7 +19953,13 @@ alias: B.1.1.529.2.86.1.1.11.1.2.2 children: - KP.2.2 + - KP.2.2.1 parent: KP.2 +- name: KP.2.2.1 + alias: B.1.1.529.2.86.1.1.11.1.2.2.1 + children: + - KP.2.2.1 + parent: KP.2.2 - name: KP.2.3 alias: B.1.1.529.2.86.1.1.11.1.2.3 children: @@ -19895,6 +20126,29 @@ children: - KP.2.24 parent: KP.2 +- name: KP.2.25 + alias: B.1.1.529.2.86.1.1.11.1.2.25 + children: + - KP.2.25 + - KP.2.25.1 + - KP.2.25.2 + - KP.2.25.3 + parent: KP.2 +- name: KP.2.25.1 + alias: B.1.1.529.2.86.1.1.11.1.2.25.1 + children: + - KP.2.25.1 + parent: KP.2.25 +- name: KP.2.25.2 + alias: B.1.1.529.2.86.1.1.11.1.2.25.2 + children: + - KP.2.25.2 + parent: KP.2.25 +- name: KP.2.25.3 + alias: B.1.1.529.2.86.1.1.11.1.2.25.3 + children: + - KP.2.25.3 + parent: KP.2.25 - name: KP.3 alias: B.1.1.529.2.86.1.1.11.1.3 children: @@ -19938,6 +20192,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -19980,6 +20235,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -20011,6 +20267,7 @@ - MC.8.1 - MC.9 - MC.10 + - MC.10.1 - MC.11 - MC.11.1 - MC.12 @@ -20081,7 +20338,13 @@ alias: B.1.1.529.2.86.1.1.11.1.3.1.1.10 children: - MC.10 + - MC.10.1 parent: KP.3.1.1 +- name: MC.10.1 + alias: B.1.1.529.2.86.1.1.11.1.3.1.1.10.1 + children: + - MC.10.1 + parent: MC.10 - name: MC.11 alias: B.1.1.529.2.86.1.1.11.1.3.1.1.11 children: @@ -20405,9 +20668,12 @@ - JN.1.13.1 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 + - NC.1 parent: JN.1 - name: JN.1.13.1 alias: B.1.1.529.2.86.1.1.13.1 @@ -20415,24 +20681,49 @@ - JN.1.13.1 - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 + - NC.1 parent: JN.1.13 - name: KS.1 alias: B.1.1.529.2.86.1.1.13.1.1 children: - KS.1 - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 - KS.1.2 - KS.1.3 - KS.1.4 + - NC.1 parent: JN.1.13.1 - name: KS.1.1 alias: B.1.1.529.2.86.1.1.13.1.1.1 children: - KS.1.1 + - KS.1.1.1 + - KS.1.1.2 + - NC.1 parent: KS.1 +- name: KS.1.1.1 + alias: B.1.1.529.2.86.1.1.13.1.1.1.1 + children: + - KS.1.1.1 + - NC.1 + parent: KS.1.1 +- name: NC.1 + alias: B.1.1.529.2.86.1.1.13.1.1.1.1.1 + children: + - NC.1 + parent: KS.1.1.1 +- name: KS.1.1.2 + alias: B.1.1.529.2.86.1.1.13.1.1.1.2 + children: + - KS.1.1.2 + parent: KS.1.1 - name: KS.1.2 alias: B.1.1.529.2.86.1.1.13.1.1.2 children: @@ -20521,6 +20812,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -20538,6 +20830,10 @@ - LF.9 - LF.9.1 - MT.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: JN.1 - name: JN.1.16.1 alias: B.1.1.529.2.86.1.1.16.1 @@ -20550,6 +20846,7 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 - LF.4 - LF.4.1 - LF.5 @@ -20566,6 +20863,10 @@ - LF.8.1.1 - LF.9 - LF.9.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: JN.1.16 - name: LF.1 alias: B.1.1.529.2.86.1.1.16.1.1 @@ -20596,18 +20897,25 @@ - LF.3 - LF.3.1 - LF.3.1.1 + - LF.3.1.2 parent: JN.1.16.1 - name: LF.3.1 alias: B.1.1.529.2.86.1.1.16.1.3.1 children: - LF.3.1 - LF.3.1.1 + - LF.3.1.2 parent: LF.3 - name: LF.3.1.1 alias: B.1.1.529.2.86.1.1.16.1.3.1.1 children: - LF.3.1.1 parent: LF.3.1 +- name: LF.3.1.2 + alias: B.1.1.529.2.86.1.1.16.1.3.1.2 + children: + - LF.3.1.2 + parent: LF.3.1 - name: LF.4 alias: B.1.1.529.2.86.1.1.16.1.4 children: @@ -20678,18 +20986,51 @@ - LF.8 - LF.8.1 - LF.8.1.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: JN.1.16.1 - name: LF.8.1 alias: B.1.1.529.2.86.1.1.16.1.8.1 children: - LF.8.1 - LF.8.1.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: LF.8 - name: LF.8.1.1 alias: B.1.1.529.2.86.1.1.16.1.8.1.1 children: - LF.8.1.1 + - ND.1 + - ND.1.1 + - ND.2 + - ND.3 parent: LF.8.1 +- name: ND.1 + alias: B.1.1.529.2.86.1.1.16.1.8.1.1.1 + children: + - ND.1 + - ND.1.1 + parent: LF.8.1.1 +- name: ND.1.1 + alias: B.1.1.529.2.86.1.1.16.1.8.1.1.1.1 + children: + - ND.1.1 + parent: ND.1 +- name: ND.2 + alias: B.1.1.529.2.86.1.1.16.1.8.1.1.2 + children: + - ND.2 + parent: LF.8.1.1 +- name: ND.3 + alias: B.1.1.529.2.86.1.1.16.1.8.1.1.3 + children: + - ND.3 + parent: LF.8.1.1 - name: LF.9 alias: B.1.1.529.2.86.1.1.16.1.9 children: @@ -21299,10 +21640,16 @@ - JN.1.49 - JN.1.49.1 - JN.1.49.2 + - JN.1.49.3 - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MV.1 + - MV.2 + - NA.1 + - NA.1.1 parent: JN.1 - name: JN.1.49.1 alias: B.1.1.529.2.86.1.1.49.1 @@ -21311,7 +21658,12 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MV.1 + - MV.2 + - NA.1 + - NA.1.1 parent: JN.1.49 - name: MB.1 alias: B.1.1.529.2.86.1.1.49.1.1 @@ -21319,31 +21671,75 @@ - MB.1 - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MV.1 + - MV.2 + - NA.1 + - NA.1.1 parent: JN.1.49.1 - name: MB.1.1 alias: B.1.1.529.2.86.1.1.49.1.1.1 children: - MB.1.1 - MB.1.1.1 + - MB.1.1.2 + - MB.1.1.3 - MV.1 + - MV.2 + - NA.1 + - NA.1.1 parent: MB.1 - name: MB.1.1.1 alias: B.1.1.529.2.86.1.1.49.1.1.1.1 children: - MB.1.1.1 - MV.1 + - MV.2 parent: MB.1.1 - name: MV.1 alias: B.1.1.529.2.86.1.1.49.1.1.1.1.1 children: - MV.1 parent: MB.1.1.1 +- name: MV.2 + alias: B.1.1.529.2.86.1.1.49.1.1.1.1.2 + children: + - MV.2 + parent: MB.1.1.1 +- name: MB.1.1.2 + alias: B.1.1.529.2.86.1.1.49.1.1.1.2 + children: + - MB.1.1.2 + - NA.1 + - NA.1.1 + parent: MB.1.1 +- name: NA.1 + alias: B.1.1.529.2.86.1.1.49.1.1.1.2.1 + children: + - NA.1 + - NA.1.1 + parent: MB.1.1.2 +- name: NA.1.1 + alias: B.1.1.529.2.86.1.1.49.1.1.1.2.1.1 + children: + - NA.1.1 + parent: NA.1 +- name: MB.1.1.3 + alias: B.1.1.529.2.86.1.1.49.1.1.1.3 + children: + - MB.1.1.3 + parent: MB.1.1 - name: JN.1.49.2 alias: B.1.1.529.2.86.1.1.49.2 children: - JN.1.49.2 parent: JN.1.49 +- name: JN.1.49.3 + alias: B.1.1.529.2.86.1.1.49.3 + children: + - JN.1.49.3 + parent: JN.1.49 - name: JN.1.50 alias: B.1.1.529.2.86.1.1.50 children: @@ -21555,9 +21951,15 @@ - JN.1.64.1 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 parent: JN.1 - name: JN.1.64.1 alias: B.1.1.529.2.86.1.1.64.1 @@ -21565,20 +21967,39 @@ - JN.1.64.1 - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 - MD.2 - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 parent: JN.1.64 - name: MD.1 alias: B.1.1.529.2.86.1.1.64.1.1 children: - MD.1 - MD.1.1 + - MD.1.1.1 + - MD.1.2 parent: JN.1.64.1 - name: MD.1.1 alias: B.1.1.529.2.86.1.1.64.1.1.1 children: - MD.1.1 + - MD.1.1.1 + parent: MD.1 +- name: MD.1.1.1 + alias: B.1.1.529.2.86.1.1.64.1.1.1.1 + children: + - MD.1.1.1 + parent: MD.1.1 +- name: MD.1.2 + alias: B.1.1.529.2.86.1.1.64.1.1.2 + children: + - MD.1.2 parent: MD.1 - name: MD.2 alias: B.1.1.529.2.86.1.1.64.1.2 @@ -21590,12 +22011,40 @@ children: - MD.3 - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 parent: JN.1.64.1 - name: MD.3.1 alias: B.1.1.529.2.86.1.1.64.1.3.1 children: - MD.3.1 + - MD.3.1.1 + - MD.3.1.2 + - MD.3.1.3 + - MD.3.1.4 parent: MD.3 +- name: MD.3.1.1 + alias: B.1.1.529.2.86.1.1.64.1.3.1.1 + children: + - MD.3.1.1 + parent: MD.3.1 +- name: MD.3.1.2 + alias: B.1.1.529.2.86.1.1.64.1.3.1.2 + children: + - MD.3.1.2 + parent: MD.3.1 +- name: MD.3.1.3 + alias: B.1.1.529.2.86.1.1.64.1.3.1.3 + children: + - MD.3.1.3 + parent: MD.3.1 +- name: MD.3.1.4 + alias: B.1.1.529.2.86.1.1.64.1.3.1.4 + children: + - MD.3.1.4 + parent: MD.3.1 - name: JN.1.65 alias: B.1.1.529.2.86.1.1.65 children: @@ -43587,6 +44036,7 @@ - name: XDV alias: XDV children: + - NB.1 - XDV - XDV.1 - XDV.1.1 @@ -43595,6 +44045,7 @@ - XDV.1.3 - XDV.1.4 - XDV.1.5 + - XDV.1.5.1 - XDV.1.6 - XDV.1.7 - XDV.1.7.1 @@ -43607,6 +44058,7 @@ - name: XDV.1 alias: XDV.1 children: + - NB.1 - XDV.1 - XDV.1.1 - XDV.1.2 @@ -43614,6 +44066,7 @@ - XDV.1.3 - XDV.1.4 - XDV.1.5 + - XDV.1.5.1 - XDV.1.6 - XDV.1.7 - XDV.1.7.1 @@ -43652,8 +44105,21 @@ - name: XDV.1.5 alias: XDV.1.5 children: + - NB.1 - XDV.1.5 + - XDV.1.5.1 parent: XDV.1 +- name: XDV.1.5.1 + alias: XDV.1.5.1 + children: + - NB.1 + - XDV.1.5.1 + parent: XDV.1.5 +- name: NB.1 + alias: XDV.1.5.1.1 + children: + - NB.1 + parent: XDV.1.5.1 - name: XDV.1.6 alias: XDV.1.6 children: @@ -43773,3 +44239,8 @@ children: - XEK recombinant_parents: KP.2.3,XEC +- name: XEL + alias: XEL + children: + - XEL + recombinant_parents: KS.1.1.2,JN.1 diff --git a/freyja/data/mpox_barcodes.csv b/freyja/data/mpox_barcodes.csv deleted file mode 100644 index 50bf9dd..0000000 --- a/freyja/data/mpox_barcodes.csv +++ /dev/null @@ -1,39 +0,0 @@ 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diff --git a/freyja/data/mpox_lineages.yml b/freyja/data/mpox_lineages.yml deleted file mode 100644 index 4640dae..0000000 --- a/freyja/data/mpox_lineages.yml +++ /dev/null @@ -1,355 +0,0 @@ -- name: MPX-I - alias: MPX-I - children: - - MPX-Ia - - MPX-Ib - - MPX-I -- name: MPX-II - alias: MPX-II - children: - - MPX-IIa - - MPX-IIb - - MPX-IIb.A - - MPX-IIb.A.2 - - MPX-IIb.A.3 - - MPX-IIb.A.1 - - MPX-IIb.A.1.1 - - MPX-IIb.B.1 - - MPX-IIb.B.1.1 - - MPX-IIb.B.1.2 - - MPX-IIb.B.1.3 - - MPX-IIb.B.1.4 - - MPX-IIb.B.1.5 - - MPX-IIb.B.1.6 - - MPX-IIb.B.1.7 - - MPX-IIb.B.1.8 - - MPX-IIb.B.1.9 - - MPX-IIb.B.1.10 - - MPX-IIb.B.1.11 - - MPX-IIb.B.1.12 - - MPX-IIb.B.1.13 - - MPX-IIb.B.1.14 - - MPX-IIb.B.1.15 - - MPX-IIb.B.1.16 - - MPX-IIb.B.1.17 - - MPX-IIb.B.1.18 - - MPX-IIb.B.1.19 - - MPX-IIb.B.1.20 - - MPX-IIb.B.1.21 - - MPX-IIb.B.1.22 - - MPX-II -- name: MPX-Ia - alias: MPX-I.a - parent: MPX-I - children: - - MPX-Ia -- name: MPX-Ib - alias: MPX-I.b - parent: MPX-I - children: - - MPX-Ib -- name: MPX-IIa - alias: MPX-II.a - parent: MPX-II - children: - - MPX-IIa -- name: MPX-IIb - alias: MPX-II.b - parent: MPX-II - children: - - MPX-IIb.A - - MPX-IIb.A.2 - - MPX-IIb.A.3 - - MPX-IIb.A.1 - - MPX-IIb.A.1.1 - - MPX-IIb.B.1 - - MPX-IIb.B.1.1 - - MPX-IIb.B.1.2 - - MPX-IIb.B.1.3 - - MPX-IIb.B.1.4 - - MPX-IIb.B.1.5 - - MPX-IIb.B.1.6 - - MPX-IIb.B.1.7 - - MPX-IIb.B.1.8 - - MPX-IIb.B.1.9 - - MPX-IIb.B.1.10 - - MPX-IIb.B.1.11 - - MPX-IIb.B.1.12 - - MPX-IIb.B.1.13 - - MPX-IIb.B.1.14 - - MPX-IIb.B.1.15 - - MPX-IIb.B.1.16 - - MPX-IIb.B.1.17 - - MPX-IIb.B.1.18 - - MPX-IIb.B.1.19 - - MPX-IIb.B.1.20 - - MPX-IIb.B.1.21 - - MPX-IIb.B.1.22 - - MPX-IIb -- name: MPX-IIb.A - alias: MPX-II.b.A - parent: MPX-IIb - children: - - MPX-IIb.A.2 - - MPX-IIb.A.3 - - MPX-IIb.A.1 - - MPX-IIb.A.1.1 - - MPX-IIb.B.1 - - MPX-IIb.B.1.1 - - MPX-IIb.B.1.2 - - MPX-IIb.B.1.3 - - MPX-IIb.B.1.4 - - MPX-IIb.B.1.5 - - MPX-IIb.B.1.6 - - MPX-IIb.B.1.7 - - MPX-IIb.B.1.8 - - MPX-IIb.B.1.9 - - MPX-IIb.B.1.10 - - MPX-IIb.B.1.11 - - MPX-IIb.B.1.12 - - MPX-IIb.B.1.13 - - MPX-IIb.B.1.14 - - MPX-IIb.B.1.15 - - MPX-IIb.B.1.16 - - MPX-IIb.B.1.17 - - MPX-IIb.B.1.18 - - MPX-IIb.B.1.19 - - MPX-IIb.B.1.20 - - MPX-IIb.B.1.21 - - MPX-IIb.B.1.22 - - MPX-IIb.A -- name: MPX-IIb.A.2 - alias: MPX-II.b.A.2 - parent: MPX-IIb.A - children: - - MPX-IIb.A.2.1 - - MPX-IIb.A.2.2 - - MPX-IIb.A.2.3 - - MPX-IIb.A.2 -- name: MPX-IIb.A.2.1 - alias: MPX-II.b.A.2.1 - parent: MPX-IIb.A.2 - children: - - MPX-IIb.A.2.1 -- name: MPX-IIb.A.2.2 - alias: MPX-II.b.A.2.2 - parent: MPX-IIb.A.2 - children: - - MPX-IIb.A.2.2 -- name: MPX-IIb.A.2.3 - alias: MPX-II.b.A.2.3 - parent: MPX-IIb.A.2 - children: - - MPX-IIb.A.2.3 -- name: MPX-IIb.A.3 - alias: MPX-II.b.A.3 - parent: MPX-IIb.A - children: - - MPX-IIb.A.3 -- name: MPX-IIb.A.1 - alias: MPX-II.b.A.1 - parent: MPX-IIb.A - children: - - MPX-IIb.A.1.1 - - MPX-IIb.B.1 - - MPX-IIb.B.1.1 - - MPX-IIb.B.1.2 - - MPX-IIb.B.1.3 - - MPX-IIb.B.1.4 - - MPX-IIb.B.1.5 - - MPX-IIb.B.1.6 - - MPX-IIb.B.1.7 - - MPX-IIb.B.1.8 - - MPX-IIb.B.1.9 - - MPX-IIb.B.1.10 - - MPX-IIb.B.1.11 - - MPX-IIb.B.1.12 - - MPX-IIb.B.1.13 - - MPX-IIb.B.1.14 - - MPX-IIb.B.1.15 - - MPX-IIb.B.1.16 - - MPX-IIb.B.1.17 - - MPX-IIb.B.1.18 - - MPX-IIb.B.1.19 - - MPX-IIb.B.1.20 - - MPX-IIb.B.1.21 - - MPX-IIb.B.1.22 - - MPX-IIb.A.1 -- name: MPX-IIb.A.1.1 - alias: MPX-II.b.A.1.1 - parent: MPX-IIb.A.1 - children: - - MPX-IIb.B.1 - - MPX-IIb.B.1.1 - - MPX-IIb.B.1.2 - - MPX-IIb.B.1.3 - - MPX-IIb.B.1.4 - - MPX-IIb.B.1.5 - - MPX-IIb.B.1.6 - - MPX-IIb.B.1.7 - - MPX-IIb.B.1.8 - - MPX-IIb.B.1.9 - - MPX-IIb.B.1.10 - - MPX-IIb.B.1.11 - - MPX-IIb.B.1.12 - - MPX-IIb.B.1.13 - - MPX-IIb.B.1.14 - - MPX-IIb.B.1.15 - - MPX-IIb.B.1.16 - - MPX-IIb.B.1.17 - - MPX-IIb.B.1.18 - - MPX-IIb.B.1.19 - - MPX-IIb.B.1.20 - - MPX-IIb.B.1.21 - - MPX-IIb.B.1.22 - - MPX-IIb.A.1.1 -- name: MPX-IIb.B.1 - alias: MPX-II.b.B.1 - parent: MPX-IIb.A.1.1 - children: - - MPX-IIb.B.1.1 - - MPX-IIb.B.1.2 - - MPX-IIb.B.1.3 - - MPX-IIb.B.1.4 - - MPX-IIb.B.1.5 - - MPX-IIb.B.1.6 - - MPX-IIb.B.1.7 - - MPX-IIb.B.1.8 - - MPX-IIb.B.1.9 - - MPX-IIb.B.1.10 - - MPX-IIb.B.1.11 - - MPX-IIb.B.1.12 - - MPX-IIb.B.1.13 - - MPX-IIb.B.1.14 - - MPX-IIb.B.1.15 - - MPX-IIb.B.1.16 - - MPX-IIb.B.1.17 - - MPX-IIb.B.1.18 - - MPX-IIb.B.1.19 - - MPX-IIb.B.1.20 - - MPX-IIb.B.1.21 - - MPX-IIb.B.1.22 - - MPX-IIb.B.1 -- name: MPX-IIb.B.1.1 - alias: MPX-II.b.B.1.1 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.1 -- name: MPX-IIb.B.1.2 - alias: MPX-II.b.B.1.2 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.2 -- name: MPX-IIb.B.1.3 - alias: MPX-II.b.B.1.3 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.C.1 - - MPX-IIb.C.1.1 - - MPX-IIb.B.1.3 -- name: MPX-IIb.C.1 - alias: MPX-II.b.C.1 - parent: MPX-IIb.B.1.3 - children: - - MPX-IIb.C.1.1 - - MPX-IIb.C.1 -- name: MPX-IIb.C.1.1 - alias: MPX-II.b.C.1.1 - parent: MPX-IIb.C.1 - children: - - MPX-IIb.C.1.1 -- name: MPX-IIb.B.1.4 - alias: MPX-II.b.B.1.4 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.4 -- name: MPX-IIb.B.1.5 - alias: MPX-II.b.B.1.5 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.5 -- name: MPX-IIb.B.1.6 - alias: MPX-II.b.B.1.6 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.6 -- name: MPX-IIb.B.1.7 - alias: MPX-II.b.B.1.7 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.7 -- name: MPX-IIb.B.1.8 - alias: MPX-II.b.B.1.8 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.8 -- name: MPX-IIb.B.1.9 - alias: MPX-II.b.B.1.9 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.9 -- name: MPX-IIb.B.1.10 - alias: MPX-II.b.B.1.10 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.10 -- name: MPX-IIb.B.1.11 - alias: MPX-II.b.B.1.11 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.11 -- name: MPX-IIb.B.1.12 - alias: MPX-II.b.B.1.12 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.12 -- name: MPX-IIb.B.1.13 - alias: MPX-II.b.B.1.13 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.13 -- name: MPX-IIb.B.1.14 - alias: MPX-II.b.B.1.14 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.14 -- name: MPX-IIb.B.1.15 - alias: MPX-II.b.B.1.15 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.15 -- name: MPX-IIb.B.1.16 - alias: MPX-II.b.B.1.16 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.16 -- name: MPX-IIb.B.1.17 - alias: MPX-II.b.B.1.17 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.17 -- name: MPX-IIb.B.1.18 - alias: MPX-II.b.B.1.18 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.18 -- name: MPX-IIb.B.1.19 - alias: MPX-II.b.B.1.19 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.19 -- name: MPX-IIb.B.1.20 - alias: MPX-II.b.B.1.20 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.20 -- name: MPX-IIb.B.1.21 - alias: MPX-II.b.B.1.21 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.21 -- name: MPX-IIb.B.1.22 - alias: MPX-II.b.B.1.22 - parent: MPX-IIb.B.1 - children: - - MPX-IIb.B.1.22 diff --git a/freyja/updates.py b/freyja/updates.py index 58956ad..e53452f 100644 --- a/freyja/updates.py +++ b/freyja/updates.py @@ -15,12 +15,12 @@ def get_pathogen_config(locDir): return pathogen_config -# def download_config(locDir): -# url = "https://raw.githubusercontent.com/andersen-lab/"\ -# "Freyja/main/freyja/data/pathogen_config.yml" -# lpath = os.path.join(locDir, 'pathogen_config.yml') -# urllib.request.urlretrieve(url, lpath) -# return lpath +def download_config(locDir): + url = "https://raw.githubusercontent.com/andersen-lab/"\ + "Freyja/main/freyja/data/pathogen_config.yml" + lpath = os.path.join(locDir, 'pathogen_config.yml') + urllib.request.urlretrieve(url, lpath) + return lpath def download_tree(locDir):