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fixed bugs #5

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merged 2 commits into from
Dec 18, 2024
Merged

fixed bugs #5

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251db6a
fixed bugs
daichengxin Dec 18, 2024
3a16a96
Update __init__.py
daichengxin Dec 18, 2024
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2 changes: 1 addition & 1 deletion quantmsrescore/__init__.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "0.0.2"
__version__ = "0.0.3"
11 changes: 9 additions & 2 deletions quantmsrescore/ms2rescore.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ def __init__(self, filename: Union[Path, str], *args, **kwargs) -> None:
self.user_params_metadata = self._get_userparams_metadata(self.peptide_ids[0].getHits()[0])
self.rescoring_features = self._get_rescoring_features(self.peptide_ids[0].getHits()[0])
self.skip_invalid_psm = 0
self.new_peptide_ids = []

def __iter__(self) -> Iterable[PSM]:
"""
Expand Down Expand Up @@ -63,12 +64,16 @@ def __iter__(self) -> Iterable[PSM]:

"""
for peptide_id in self.peptide_ids:
new_hits = []
for peptide_hit in peptide_id.getHits():
psm = self._parse_psm(self.protein_ids, peptide_id, peptide_hit)
if psm is not None:
new_hits.append(peptide_hit)
yield psm
else:
self.skip_invalid_psm += 1
peptide_id.setHits(new_hits)
self.new_peptide_ids.append(peptide_id)

def _parse_psm(
self,
Expand Down Expand Up @@ -239,12 +244,14 @@ def rescore_idxml(input_file, output_file, config) -> None:
logging.warning(
f"Removed {reader.skip_invalid_psm} PSMs without search engine features!"
)

peptide_ids = reader.new_peptide_ids
else:
peptide_ids = reader.peptide_ids
# Rescore
rescore(config, psm_list)

# Filter out PeptideHits within PeptideIdentification(s) that could not be processed by all feature generators
peptide_ids_filtered = filter_out_artifact_psms(psm_list, reader.peptide_ids)
peptide_ids_filtered = filter_out_artifact_psms(psm_list, peptide_ids)

# Write
writer = IdXMLWriter(output_file, reader.protein_ids, peptide_ids_filtered)
Expand Down
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