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fix: Move NA values to end of table #124

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merged 7 commits into from
Oct 18, 2024
Merged

fix: Move NA values to end of table #124

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fb9239a
fix: Move NA values to end of table
fxwiegand Oct 16, 2024
f594b15
Update compare_diffexp.py
fxwiegand Oct 16, 2024
dca9161
Update compare_diffexp.py with dbg prints
fxwiegand Oct 16, 2024
69ef4d2
Update compare_diffexp.py
fxwiegand Oct 17, 2024
4776153
Update compare_diffexp.py
fxwiegand Oct 17, 2024
5f8dc17
refactor: Make meta comparison use proper logs
fxwiegand Oct 17, 2024
58d7cd5
Update compare_diffexp.py
fxwiegand Oct 17, 2024
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13 changes: 12 additions & 1 deletion workflow/scripts/compare_diffexp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,11 +46,20 @@ def prepare(df):
combined = combined.with_columns(
abs(pl.col(effect_x) - pl.col(effect_y)).alias("difference")
)
print(combined)
combined = (
combined.with_columns(
(-pl.col("pval_min").log(base=10) * pl.col("difference")).alias("pi_value")
)
.sort(pl.col("pi_value").abs(), descending=True)
.with_columns(
pl.col("pi_value").fill_nan(None),
pl.col("difference").fill_nan(None),
)
Comment on lines +53 to +56
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This seems convoluted, but at least it's well documented:
https://docs.pola.rs/user-guide/expressions/missing-data/#notanumber-or-nan-values

.sort(
pl.col("pi_value").abs(),
descending=True,
nulls_last=True,
)
.select(
pl.col(
"ext_gene",
Expand All @@ -64,6 +73,8 @@ def prepare(df):
)
.to_pandas()
)
)
print(combined)
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⚠️ Potential issue

Syntax error and additional print statement

There are two issues in this segment:

  1. There's an extra closing parenthesis at line 76, which is causing a syntax error. This needs to be removed.
  2. Another print statement is added at line 77, which might be useful for debugging but could clutter output in production.

To fix the syntax error and address the print statement, apply the following changes:

-)
-print(combined)
+print(combined)  # Consider removing or wrapping in a debug condition

This will resolve the syntax error and maintain the print statement. However, consider removing the print statement or wrapping it in a debug condition for production use.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
)
print(combined)
print(combined) # Consider removing or wrapping in a debug condition
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🪛 Ruff

76-76: SyntaxError: Expected a statement

76-77: SyntaxError: Expected a statement

combined.to_csv(snakemake.output[0], sep="\t", index=False)


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