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PSM Data Class #368

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63 changes: 53 additions & 10 deletions casanovo/data/ms_io.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,18 +2,56 @@

import collections
import csv
import dataclasses
import operator
import os
import re
from pathlib import Path
from typing import List
from typing import List, Tuple, Iterable

import natsort

from .. import __version__
from ..config import Config


@dataclasses.dataclass
class PepSpecMatch:
"""
Peptide Spectrum Match (PSM) dataclass

Parameters
----------
sequence : str
The amino acid sequence of the peptide.
spectrum_id : Tuple[str, str]
A tuple containing the spectrum identifier in the form
(spectrum file name, spectrum file idx)
peptide_score : float
Score of the match between the full peptide sequence and the
spectrum.
charge : int
The precursor charge state of the peptide ion observed in the spectrum.
calc_mz : float
The calculated mass-to-charge ratio (m/z) of the peptide based on its
sequence and charge state.
exp_mz : float
The observed (experimental) precursor mass-to-charge ratio (m/z) of the
peptide as detected in the spectrum.
aa_scores : Iterable[float]
A list of scores for individual amino acids in the peptide
sequence, where len(aa_scores) == len(sequence)
"""

sequence: str
spectrum_id: Tuple[str, str]
peptide_score: float
charge: int
calc_mz: float
exp_mz: float
aa_scores: Iterable[float]


class MztabWriter:
"""
Export spectrum identifications to an mzTab file.
Expand Down Expand Up @@ -42,7 +80,7 @@ def __init__(self, filename: str):
),
]
self._run_map = {}
self.psms = []
self.psms: List[PepSpecMatch] = []

def set_metadata(self, config: Config, **kwargs) -> None:
"""
Expand Down Expand Up @@ -178,34 +216,39 @@ def save(self) -> None:
]
)
for i, psm in enumerate(
natsort.natsorted(self.psms, key=operator.itemgetter(1)), 1
natsort.natsorted(
self.psms, key=operator.attrgetter("spectrum_id")
),
1,
):
filename, idx = os.path.abspath(psm[1][0]), psm[1][1]
filename = os.path.abspath(psm.spectrum_id[0])
idx = psm.spectrum_id[1]
writer.writerow(
[
"PSM",
psm[0], # sequence
psm.sequence, # sequence
i, # PSM_ID
"null", # accession
"null", # unique
"null", # database
"null", # database_version
f"[MS, MS:1003281, Casanovo, {__version__}]",
psm[2], # search_engine_score[1]
psm.peptide_score, # search_engine_score[1]
# FIXME: Modifications should be specified as
# controlled vocabulary terms.
"null", # modifications
# FIXME: Can we get the retention time from the data
# loader?
"null", # retention_time
int(psm[3]), # charge
psm[4], # exp_mass_to_charge
psm[5], # calc_mass_to_charge
psm.charge, # charge
psm.exp_mz, # exp_mass_to_charge
psm.calc_mz, # calc_mass_to_charge
f"ms_run[{self._run_map[filename]}]:{idx}",
"null", # pre
"null", # post
"null", # start
"null", # end
psm[6], # opt_ms_run[1]_aa_scores
# opt_ms_run[1]_aa_scores
",".join(list(map("{:.5f}".format, psm.aa_scores))),
]
)
18 changes: 9 additions & 9 deletions casanovo/denovo/model.py
Original file line number Diff line number Diff line change
Expand Up @@ -914,15 +914,15 @@ def on_predict_batch_end(
if len(peptide) == 0:
continue
self.out_writer.psms.append(
(
peptide,
tuple(spectrum_i),
peptide_score,
charge,
precursor_mz,
self.peptide_mass_calculator.mass(peptide, charge),
",".join(list(map("{:.5f}".format, aa_scores))),
),
ms_io.PepSpecMatch(
sequence=peptide,
spectrum_id=tuple(spectrum_i),
peptide_score=peptide_score,
charge=int(charge),
calc_mz=precursor_mz,
exp_mz=self.peptide_mass_calculator.mass(peptide, charge),
aa_scores=aa_scores,
)
)

def _log_history(self) -> None:
Expand Down
2 changes: 1 addition & 1 deletion casanovo/denovo/model_runner.py
Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ def log_metrics(self, test_index: AnnotatedSpectrumIndex) -> None:
Index containing the annotated spectra used to generate model
predictions
"""
model_output = [psm[0] for psm in self.writer.psms]
model_output = [psm.sequence for psm in self.writer.psms]
spectrum_annotations = [
test_index[i][4] for i in range(test_index.n_spectra)
]
Expand Down
10 changes: 5 additions & 5 deletions casanovo/utils.py
Original file line number Diff line number Diff line change
@@ -1,13 +1,11 @@
"""Small utility functions"""

import heapq
import logging
import os
import platform
import re
import socket
import sys
import time
from datetime import datetime
from typing import Tuple, Dict, List, Optional

Expand All @@ -16,6 +14,8 @@
import psutil
import torch

from .data.ms_io import PepSpecMatch


SCORE_BINS = [0.0, 0.5, 0.9, 0.95, 0.99]

Expand Down Expand Up @@ -195,7 +195,7 @@ def log_run_report(


def log_sequencing_report(
predictions: Tuple[str, Tuple[str, str], float, float, float, float, str],
predictions: List[PepSpecMatch],
start_time: Optional[int] = None,
end_time: Optional[int] = None,
score_bins: List[float] = SCORE_BINS,
Expand All @@ -219,8 +219,8 @@ def log_sequencing_report(
run_report = get_report_dict(
pd.DataFrame(
{
"sequence": [psm[0] for psm in predictions],
"score": [psm[2] for psm in predictions],
"sequence": [psm.sequence for psm in predictions],
"score": [psm.peptide_score for psm in predictions],
}
),
score_bins=score_bins,
Expand Down
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