circular import bug

casanovo/data/ms_io.py

@@ -13,43 +13,7 @@
 
 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]
+from .pep_spec_match import PepSpecMatch
 
 
 class MztabWriter:

casanovo/data/pep_spec_match.py

@@ -0,0 +1,41 @@
+"""Peptide spectrum match dataclass"""
+
+import dataclasses
+from typing import Tuple, Iterable
+
+
+@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]

casanovo/denovo/model.py

@@ -15,7 +15,7 @@
 
 from . import evaluate
 from .. import config
-from ..data import ms_io
+from ..data import ms_io, pep_spec_match
 from ..denovo.transformers import SpectrumEncoder, PeptideDecoder
 
 logger = logging.getLogger("casanovo")
@@ -1035,7 +1035,7 @@ def on_predict_batch_end(
             )
 
             self.out_writer.psms.append(
-                ms_io.PepSpecMatch(
+                pep_spec_match.PepSpecMatch(
                     sequence=peptide,
                     spectrum_id=tuple(spectrum_i),
                     peptide_score=peptide_score,

casanovo/utils.py

@@ -15,7 +15,7 @@
 import psutil
 import torch
 
-from .data.ms_io import PepSpecMatch
+from .data.pep_spec_match import PepSpecMatch
 
 
 SCORE_BINS = [0.0, 0.5, 0.9, 0.95, 0.99]