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Merge pull request #54 from compomics/feature/pepxml
Feature: Add PepXMLReader
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,146 @@ | ||
| """Interface with TPP pepXML PSM files.""" | ||
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| from __future__ import annotations | ||
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| import logging | ||
| from collections import defaultdict | ||
| from pathlib import Path | ||
| from typing import List, Optional, Union | ||
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| from pyteomics import pepxml, proforma | ||
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| from psm_utils.io._base_classes import ReaderBase | ||
| from psm_utils.peptidoform import Peptidoform | ||
| from psm_utils.psm import PSM | ||
| from psm_utils.utils import mass_to_mz | ||
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| logger = logging.getLogger(__name__) | ||
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| STANDARD_SEARCHENGINE_SCORES = [ | ||
| "expect", | ||
| "EValue", | ||
| "Evalue", | ||
| "SpecEValue", | ||
| "xcorr", # Fallback if no e-value is present | ||
| "delta_dot", # SpectraST | ||
| "mzFidelity", | ||
| ] | ||
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| class PepXMLReader(ReaderBase): | ||
| def __init__(self, filename: Union[str, Path], *args, score_key: str = None, **kwargs) -> None: | ||
| """ | ||
| Reader for pepXML PSM files. | ||
| Parameters | ||
| ---------- | ||
| filename: str, pathlib.Path | ||
| Path to PSM file. | ||
| score_key: str, optional | ||
| Name of the score metric to use as PSM score. If not provided, the score metric is | ||
| inferred from a list of known search engine scores. | ||
| """ | ||
| super().__init__(filename, *args, **kwargs) | ||
| self.score_key = score_key or self._infer_score_name() | ||
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| def __iter__(self): | ||
| """Iterate over file and return PSMs one-by-one.""" | ||
| with pepxml.read(str(self.filename)) as reader: | ||
| for spectrum_query in reader: | ||
| for search_hit in spectrum_query["search_hit"]: | ||
| yield self._parse_psm(spectrum_query, search_hit) | ||
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| def _infer_score_name(self) -> str: | ||
| """Infer the score from the list of known PSM scores.""" | ||
| # Get scores from first PSM | ||
| with pepxml.read(str(self.filename)) as reader: | ||
| for spectrum_query in reader: | ||
| score_keys = spectrum_query["search_hit"][0]["search_score"].keys() | ||
| break | ||
|
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||
| # Infer score name | ||
| if not score_keys: | ||
| logger.warning("No pepXML scores found.") | ||
| return None | ||
| else: | ||
| for score in STANDARD_SEARCHENGINE_SCORES: # Check for known scores | ||
| if score in score_keys: | ||
| logger.debug(f"Using known pepXML score `{score}`.") | ||
| return score | ||
| else: | ||
| logger.warning(f"No known pepXML scores found. Defaulting to `{score_keys[0]}`.") | ||
| return score_keys[0] # Default to the first one if nothing found | ||
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| @staticmethod | ||
| def _parse_peptidoform(peptide: str, modifications: List[dict], charge: Optional[int] = None): | ||
| """Parse pepXML peptide to :py:class:`~psm_utils.peptidoform.Peptidoform`.""" | ||
| modifications_dict = defaultdict(list) | ||
| n_term = [] | ||
| c_term = [] | ||
| for mod in modifications: | ||
| mod_tag = proforma.process_tag_tokens(f"{mod['mass']:+}") | ||
| if mod["position"] == 0: | ||
| n_term.append(mod_tag) | ||
| elif mod["position"] == len(peptide) + 1: | ||
| c_term.append(mod_tag) | ||
| else: | ||
| modifications_dict[mod["position"]].append(mod_tag) | ||
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| sequence = [(aa, modifications_dict[i] or None) for i, aa in enumerate(peptide)] | ||
| properties = { | ||
| "n_term": n_term, | ||
| "c_term": c_term, | ||
| "charge_state": proforma.ChargeState(charge) if charge else None, | ||
| "unlocalized_modifications": [], | ||
| "labile_modifications": [], | ||
| "fixed_modifications": [], | ||
| "intervals": [], | ||
| "isotopes": [], | ||
| "group_ids": [], | ||
| } | ||
| return Peptidoform(proforma.ProForma(sequence, properties)) | ||
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| def _parse_psm(self, spectrum_query: dict, search_hit: dict) -> PSM: | ||
| """Parse pepXML PSM to :py:class:`~psm_utils.psm.PSM`.""" | ||
| return PSM( | ||
| peptidoform=self._parse_peptidoform( | ||
| search_hit["peptide"], | ||
| search_hit["modifications"], | ||
| spectrum_query["assumed_charge"], | ||
| ), | ||
| spectrum_id=spectrum_query["spectrum"], | ||
| run=None, | ||
| collection=None, | ||
| spectrum=None, | ||
| is_decoy=None, | ||
| score=search_hit["search_score"][self.score_key], | ||
| qvalue=None, | ||
| pep=None, | ||
| precursor_mz=mass_to_mz( | ||
| spectrum_query["precursor_neutral_mass"], spectrum_query["assumed_charge"] | ||
| ), | ||
| retention_time=spectrum_query["retention_time_sec"], | ||
| ion_mobility=spectrum_query["ion_mobility"] | ||
| if "ion_mobility" in spectrum_query | ||
| else None, | ||
| protein_list=[p["protein"] for p in search_hit["proteins"]], | ||
| rank=search_hit["hit_rank"], | ||
| source=None, | ||
| provenance_data={ | ||
| "pepxml_index": str(spectrum_query["index"]), | ||
| "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"] | ||
| } | ||
| ), | ||
| rescoring_features=None, | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| from psm_utils.peptidoform import Peptidoform | ||
| from psm_utils.io.pepxml import PepXMLReader | ||
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| class TestPepXMLReader: | ||
| def test_parse_peptidoform(self): | ||
| test_cases = [ | ||
| { | ||
| "in": { | ||
| "peptide": "ACDEK", | ||
| "modifications": [], | ||
| "charge": 2, | ||
| }, | ||
| "out": Peptidoform("ACDEK/2"), | ||
| }, | ||
| { | ||
| "in": { | ||
| "peptide": "STEEQNGGGQK", | ||
| "modifications": [ | ||
| {"position": 0, "mass": 43.017841151532004}, | ||
| {"position": 2, "mass": 181.014009}, | ||
| ], | ||
| "charge": 2, | ||
| }, | ||
| "out": Peptidoform("[+43.017841151532004]-STE[+181.014009]EQNGGGQK/2"), | ||
| }, | ||
| { | ||
| "in": { | ||
| "peptide": "ACDEK", | ||
| "modifications": [{"position": 6, "mass": 181.014009}], | ||
| "charge": 3, | ||
| }, | ||
| "out": Peptidoform("ACDEK-[+181.014009]/3"), | ||
| }, | ||
| ] | ||
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| for test_case in test_cases: | ||
| assert test_case["out"] == PepXMLReader._parse_peptidoform(**test_case["in"]) |