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Replace exit(1) with ModificationNotSupportedError exception in dianncfg.py #61

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Replace exit(1) with ModificationNotSupportedError exception in dianncfg.py #61

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ae574bf
Initial plan
Copilot Nov 27, 2025
a319a84
Replace exit(1) with ModificationNotSupportedError exception
Copilot Nov 27, 2025
ff608dc
Remove generated diann_config.cfg and add to .gitignore
Copilot Nov 27, 2025
135e8c7
Fix grammar error in error message (support -> supports)
Copilot Nov 27, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -169,3 +169,4 @@ cython_debug/

.qodo
/tests/test_data/RD139_Narrow_UPS1_0_1fmol_inj1.mzML
diann_config.cfg
23 changes: 16 additions & 7 deletions quantmsutils/diann/dianncfg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,12 @@
unimod_database = UnimodDatabase()


class ModificationNotSupportedError(Exception):
"""Exception raised when a modification is not supported for DIA-NN processing."""

pass


@click.command("dianncfg", short_help="Create DIA-NN config file with enzyme and PTMs")
@click.option("--enzyme", "-e", help="")
@click.option("--fix_mod", "-f", help="")
Expand Down Expand Up @@ -64,11 +70,12 @@ def get_mod(mod, mod_type):
break

if tag == 0:
logging.error(
error_msg = (
"Currently only supported unimod modifications for DIA pipeline. Skipped: "
+ mod
)
exit(1)
logging.error(error_msg)
raise ModificationNotSupportedError(error_msg)

# TODO support DIA multiplex
if (
Expand All @@ -78,11 +85,12 @@ def get_mod(mod, mod_type):
or "mTRAQ" in diann_mod_name
or "Dimethyl:" in diann_mod_name
):
logging.error(
"quantms DIA-NN workflow only support LFQ now! Unsupported modifications: "
error_msg = (
"quantms DIA-NN workflow only supports LFQ now! Unsupported modifications: "
+ mod
)
exit(1)
logging.error(error_msg)
raise ModificationNotSupportedError(error_msg)
elif diann_mod_accession is not None:
site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
if site == "Protein N-term":
Expand All @@ -103,11 +111,12 @@ def get_mod(mod, mod_type):
logging.warning("Restricting to certain terminal AAs isn't directly supported. Please see https://github.com/vdemichev/DiaNN/issues/1791")
return diann_mod_accession, site
else:
logging.error(
error_msg = (
"Currently only supported unimod modifications for DIA pipeline. Skipped: "
+ mod
)
exit(1)
logging.error(error_msg)
raise ModificationNotSupportedError(error_msg)


def convert_mod(fix_mod: str, var_mod: str) -> Tuple[List, List]:
Expand Down
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