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make json format readable #240

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merged 1 commit into from
Jun 10, 2024
Merged

make json format readable #240

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11 changes: 6 additions & 5 deletions freyja/_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -224,15 +224,16 @@ def update(outdir, noncl, buildlocal):
os.path.join(locDir, 'usher_barcodes.feather'))

dictMuts = {}
for lin in df.index:
muts = sorted([df.columns[m0] for m0, v in enumerate(df.loc[lin])
if v > 0], key=sortFun)
for lin in df_barcodes.index:
muts = sorted([df_barcodes.columns[m0]
for m0, v in enumerate(df_barcodes.loc[lin])
if v > 0], key=sortFun)
dictMuts[lin] = muts

import json
jpath = os.path.join(locDir, "lineage_mutations.json")
with open(jpath, "w") as outfile:
json.dump(dictMuts, outfile)
json.dump(dictMuts, outfile, indent=4)

# delete files generated along the way that aren't needed anymore
print('Cleaning up')
Expand Down Expand Up @@ -310,7 +311,7 @@ def barcode_build(pb, outdir, noncl):
import json
jpath = os.path.join(locDir, "lineage_mutations.json")
with open(jpath, "w") as outfile:
json.dump(dictMuts, outfile)
json.dump(dictMuts, outfile, indent=4)

# delete files generated along the way that aren't needed anymore
print('Cleaning up')
Expand Down
2 changes: 1 addition & 1 deletion freyja/data/curated_lineages.json
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253,124 changes: 253,123 additions & 1 deletion freyja/data/lineage_mutations.json
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29 changes: 29 additions & 0 deletions freyja/data/lineages.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2786,6 +2786,7 @@
- JN.1.13.1
- JN.1.14
- JN.1.15
- JN.1.15.1
- JN.1.16
- JN.1.16.1
- JN.1.16.2
Expand Down Expand Up @@ -3029,6 +3030,7 @@
- LR.2
- LS.1
- LT.1
- LU.1
- M.1
- M.2
- M.3
Expand Down Expand Up @@ -5606,6 +5608,7 @@
- JN.1.13.1
- JN.1.14
- JN.1.15
- JN.1.15.1
- JN.1.16
- JN.1.16.1
- JN.1.16.2
Expand Down Expand Up @@ -5849,6 +5852,7 @@
- LR.2
- LS.1
- LT.1
- LU.1
- M.1
- M.2
- M.3
Expand Down Expand Up @@ -7488,6 +7492,7 @@
- JN.1.13.1
- JN.1.14
- JN.1.15
- JN.1.15.1
- JN.1.16
- JN.1.16.1
- JN.1.16.2
Expand Down Expand Up @@ -7731,6 +7736,7 @@
- LR.2
- LS.1
- LT.1
- LU.1
- M.1
- M.2
- M.3
Expand Down Expand Up @@ -11845,6 +11851,7 @@
- JN.1.13.1
- JN.1.14
- JN.1.15
- JN.1.15.1
- JN.1.16
- JN.1.16.1
- JN.1.16.2
Expand Down Expand Up @@ -12081,6 +12088,7 @@
- LR.2
- LS.1
- LT.1
- LU.1
parent: B.1.1
- name: BA.1
alias: B.1.1.529.1
Expand Down Expand Up @@ -12903,6 +12911,7 @@
- JN.1.13.1
- JN.1.14
- JN.1.15
- JN.1.15.1
- JN.1.16
- JN.1.16.1
- JN.1.16.2
Expand Down Expand Up @@ -13139,6 +13148,7 @@
- LR.2
- LS.1
- LT.1
- LU.1
parent: B.1.1.529
- name: BA.2.1
alias: B.1.1.529.2.1
Expand Down Expand Up @@ -16488,6 +16498,7 @@
- JN.1.13.1
- JN.1.14
- JN.1.15
- JN.1.15.1
- JN.1.16
- JN.1.16.1
- JN.1.16.2
Expand Down Expand Up @@ -16718,6 +16729,7 @@
- LR.2
- LS.1
- LT.1
- LU.1
parent: BA.2
- name: BA.2.86.1
alias: B.1.1.529.2.86.1
Expand Down Expand Up @@ -16773,6 +16785,7 @@
- JN.1.13.1
- JN.1.14
- JN.1.15
- JN.1.15.1
- JN.1.16
- JN.1.16.1
- JN.1.16.2
Expand Down Expand Up @@ -16999,6 +17012,7 @@
- LR.2
- LS.1
- LT.1
- LU.1
parent: BA.2.86
- name: JN.1
alias: B.1.1.529.2.86.1.1
Expand Down Expand Up @@ -17053,6 +17067,7 @@
- JN.1.13.1
- JN.1.14
- JN.1.15
- JN.1.15.1
- JN.1.16
- JN.1.16.1
- JN.1.16.2
Expand Down Expand Up @@ -17248,6 +17263,7 @@
- LR.2
- LS.1
- LT.1
- LU.1
parent: BA.2.86.1
- name: JN.1.1
alias: B.1.1.529.2.86.1.1.1
Expand Down Expand Up @@ -18177,7 +18193,20 @@
alias: B.1.1.529.2.86.1.1.15
children:
- JN.1.15
- JN.1.15.1
- LU.1
parent: JN.1
- name: JN.1.15.1
alias: B.1.1.529.2.86.1.1.15.1
children:
- JN.1.15.1
- LU.1
parent: JN.1.15
- name: LU.1
alias: B.1.1.529.2.86.1.1.15.1.1
children:
- LU.1
parent: JN.1.15.1
- name: JN.1.16
alias: B.1.1.529.2.86.1.1.16
children:
Expand Down
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