Skip to content

fixing pepxml scores and spectrumID #122

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

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

fixing pepxml scores and spectrumID #122

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
28 changes: 17 additions & 11 deletions psm_utils/io/pepxml.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -112,13 +112,28 @@ def _parse_peptidoform(peptide: str, modifications: List[dict], charge: Optional

def _parse_psm(self, spectrum_query: dict, search_hit: dict) -> PSM:
"""Parse pepXML PSM to :py:class:`~psm_utils.psm.PSM`."""

psm_metadata = {
"num_matched_ions": str(search_hit["num_matched_ions"]),
"tot_num_ions": str(search_hit["tot_num_ions"]),
"num_missed_cleavages": str(search_hit["num_missed_cleavages"]),
}
psm_metadata.update(
{
f"search_score_{key.lower()}": str(search_hit["search_score"][key])
for key in search_hit["search_score"]
}
)

return PSM(
peptidoform=self._parse_peptidoform(
search_hit["peptide"],
search_hit["modifications"],
spectrum_query["assumed_charge"],
),
spectrum_id=spectrum_query["spectrum"],
spectrum_id=spectrum_query["spectrumNativeID"]
if "spectrumNativeID" in spectrum_query
else spectrum_query["spectrum"],
run=None,
collection=None,
spectrum=None,
Expand All @@ -143,15 +158,6 @@ def _parse_psm(self, spectrum_query: dict, search_hit: dict) -> PSM:
"start_scan": str(spectrum_query["start_scan"]),
"end_scan": str(spectrum_query["end_scan"]),
},
metadata={
"num_matched_ions": str(search_hit["num_matched_ions"]),
"tot_num_ions": str(search_hit["tot_num_ions"]),
"num_missed_cleavages": str(search_hit["num_missed_cleavages"]),
}.update(
{
f"search_score_{key.lower()}": str(search_hit["search_score"][key])
for key in search_hit["search_score"]
}
),
metadata=psm_metadata,
rescoring_features=dict(),
)
Loading