Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix: change status to qc_status #527

Merged
merged 1 commit into from
Apr 13, 2022
Merged

fix: change status to qc_status #527

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion workflow/notebooks/plot-all-strains-pangolin.py.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
"\n",
"for f in snakemake.input:\n",
" calls = pd.read_csv(f)\n",
" calls = calls[calls[\"status\"] != \"fail\"]\n",
" calls = calls[calls[\"qc_status\"] != \"fail\"]\n",
" all_calls.append(calls)\n",
"\n",
"all_calls = pd.concat(all_calls)\n",
Expand Down
2 changes: 1 addition & 1 deletion workflow/scripts/aggregate-pangolin-calls-per-stage.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@

pangolin_calls_by_stage = pd.concat(pangolin_calls, axis=0, ignore_index=True)

failed_called = (pangolin_calls_by_stage["status"] == "fail") | (
failed_called = (pangolin_calls_by_stage["qc_status"] == "fail") | (
pangolin_calls_by_stage["lineage"] == "None"
)
pangolin_calls_by_stage.loc[failed_called, "lineage"] = (
Expand Down
2 changes: 1 addition & 1 deletion workflow/scripts/evaluate-strain-call-error.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def load_pangolin_df(i, path):
inplace=True,
)
pangolin_df.drop(
columns=["taxon", "pangoLEARN_version", "status", "note"], inplace=True
columns=["taxon", "pangoLEARN_version", "qc_status", "note"], inplace=True
)
pangolin_df["mix"] = i
return pangolin_df
Expand Down
4 changes: 2 additions & 2 deletions workflow/scripts/summarize-non-cov2.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,10 @@ def analyize_pangolin(sm_input, accessions):
pango_df = pd.read_csv(pango_file)
if pango_df.loc[0, "note"] == "seq_len:1":
temp_dict[sample] = "assembly failed"
elif pango_df.loc[0, "status"] == "fail":
elif pango_df.loc[0, "qc_status"] == "fail":
temp_dict[sample] = "is non-sars-cov-2"
elif (
pango_df.loc[0, "status"] == "pass"
pango_df.loc[0, "qc_status"] == "pass"
and pango_df.loc[0, "lineage"] == "None"
):
temp_dict[sample] = "is non-sars-cov-2"
Expand Down