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feat: added column in overview table for the clear name of the lineage #400

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merged 7 commits into from
Dec 14, 2021
Merged

feat: added column in overview table for the clear name of the lineage #400

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9672930
added the generation of a new column called 'WHO Label' in generate-o…
lenakinzel Dec 14, 2021
f65ab19
Update workflow/scripts/generate-overview-table.py
lenakinzel Dec 14, 2021
461f7be
Update workflow/scripts/generate-overview-table.py
lenakinzel Dec 14, 2021
76f781b
fill nan with "-"
thomasbtf Dec 14, 2021
af7c75f
replace nans
thomasbtf Dec 14, 2021
85c53dd
Merge branch 'master' into include-scorpio_call-in-overview-table
thomasbtf Dec 14, 2021
411ecd8
fmt
thomasbtf Dec 14, 2021
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8 changes: 7 additions & 1 deletion workflow/scripts/generate-overview-table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,6 +136,7 @@ def register_contig_lengths(assemblies, name):
pangolin_results.shape[0] == 1
), "unexpected number of rows (>1) in pangolin results"
lineage = pangolin_results.loc[0, "lineage"]
scorpio = pangolin_results.loc[0, "scorpio_call"]
if lineage == "None":
pangolin_call = "no strain called"
else:
Expand All @@ -152,7 +153,12 @@ def register_contig_lengths(assemblies, name):
# varcount = f" ({varcount})"
# pangolin_call = f"{lineage}{varcount}"
pangolin_call = f"{lineage}"
data.loc[sample, "Lineage"] = pangolin_call
data.loc[sample, "Pangolin Lineage"] = pangolin_call
if scorpio == "None":
scorpio_call = "no clear name because of missing strain"
else:
scorpio_call = f"{scorpio}"
data.loc[sample, "WHO Label"] = scorpio_call


# add variant calls
Expand Down