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major changes in mztab for large datasets #43

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merged 4 commits into from
Dec 20, 2024
Merged

major changes in mztab for large datasets #43

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9627216
Merge pull request #2 from bigbio/dev
daichengxin Dec 1, 2024
dfe2fd4
Merge pull request #3 from bigbio/dev
daichengxin Dec 16, 2024
f316ae2
make diann2mztab optional for large-scale datasets
daichengxin Dec 16, 2024
1ee7ee8
Merge pull request #42 from daichengxin/dev
ypriverol Dec 16, 2024
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2 changes: 1 addition & 1 deletion quantmsutils/__init__.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "0.0.17"
__version__ = "0.0.18"
23 changes: 13 additions & 10 deletions quantmsutils/diann/diann2mztab.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@
@click.option("--charge", "-c")
@click.option("--missed_cleavages", "-m")
@click.option("--qvalue_threshold", "-q", type=float)
@click.option("--enable_diann2mztab", "-e", is_flag=True)
@click.pass_context
def diann2mztab(
ctx,
Expand All @@ -55,6 +56,7 @@ def diann2mztab(
charge,
missed_cleavages,
qvalue_threshold,
enable_diann2mztab
):
"""
Convert DIA-NN output to MSstats, Triqler or mzTab.
Expand Down Expand Up @@ -177,16 +179,17 @@ def diann2mztab(
logger.info(f"Triqler input file is saved as {exp_out_prefix}_triqler_in.tsv")
del out_triqler

mztab_out = f"{Path(exp_design).stem}_out.mzTab"
# Convert to mzTab
diann_directory.convert_to_mztab(
report=report,
f_table=f_table,
charge=charge,
missed_cleavages=missed_cleavages,
dia_params=dia_params,
out=mztab_out,
)
if enable_diann2mztab:
mztab_out = f"{Path(exp_design).stem}_out.mzTab"
# Convert to mzTab
diann_directory.convert_to_mztab(
report=report,
f_table=f_table,
charge=charge,
missed_cleavages=missed_cleavages,
dia_params=dia_params,
out=mztab_out,
Comment on lines +185 to +191
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🛠️ Refactor suggestion

Improve error handling in convert_to_mztab

The function should handle potential errors during file operations and data processing.

 diann_directory.convert_to_mztab(
     report=report,
     f_table=f_table,
     charge=charge,
     missed_cleavages=missed_cleavages,
     dia_params=dia_params,
     out=mztab_out,
+    try:
+        diann_directory.convert_to_mztab(
+            report=report,
+            f_table=f_table,
+            charge=charge,
+            missed_cleavages=missed_cleavages,
+            dia_params=dia_params,
+            out=mztab_out,
+        )
+    except Exception as e:
+        logger.error(f"Failed to convert to mzTab format: {str(e)}")
+        raise

Committable suggestion skipped: line range outside the PR's diff.

)


def _true_stem(x):
Expand Down
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