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add intensities as new variable/parameter
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@maim02
maim02 committed Oct 18, 2023
1 parent cbf31c8 commit 7fb1465
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Showing 2 changed files with 14 additions and 11 deletions.
17 changes: 10 additions & 7 deletions spectrum_fundamentals/annotation/annotation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ def match_peaks(
tmt_n_term: int,
unmod_sequence: str,
charge: int,
) -> List[Dict[str, Union[str, int, float]]]:
) -> Tuple[List[Dict[str, Union[str, int, float]]], float]:
"""
Matching experimental peaks with theoretical fragment ions.
Expand All @@ -28,9 +28,11 @@ def match_peaks(
:param unmod_sequence: Unmodified peptide sequence
:param charge: Precursor charge
:return: List of matched/annotated peaks
:return: float with sum of experimental peaks intensities
"""
start_peak = 0
no_of_peaks = len(peaks_intensity)
sum_intensities = sum(peaks_intensity)
max_intensity = 1.0
row_list = []
temp_list = []
Expand Down Expand Up @@ -77,7 +79,7 @@ def match_peaks(
for row in row_list:
row["intensity"] = float(row["intensity"]) / max_intensity
temp_list.append(row)
return temp_list
return temp_list, sum_intensities


def handle_multiple_matches(
Expand Down Expand Up @@ -134,6 +136,7 @@ def annotate_spectra(
- MZ: a NumPy array containing the m/z values of each peak in the annotated spectrum
- CALCULATED_MASS: a float representing the calculated mass of the spectrum
- removed_peaks: a NumPy array containing the indices of any peaks that were removed during the annotation process
- sum_intensities: a float representing the sum of experimental peak intensities
:param un_annot_spectra: a Pandas DataFrame containing the raw peaks and metadata to be annotated
:param mass_tolerance: mass tolerance to calculate min and max mass
Expand All @@ -148,7 +151,7 @@ def annotate_spectra(
continue
raw_file_annotations.append(results)
results_df = pd.DataFrame(raw_file_annotations)
results_df.columns = ["INTENSITIES", "MZ", "CALCULATED_MASS", "removed_peaks"]
results_df.columns = ["INTENSITIES", "MZ", "CALCULATED_MASS", "removed_peaks", "sum_intensities"]
logger.info(f"Removed {results_df['removed_peaks'].describe()} redundant peaks")

return results_df
Expand Down Expand Up @@ -214,7 +217,7 @@ def parallel_annotate(
index_columns: dict,
mass_tolerance: Optional[float] = None,
unit_mass_tolerance: Optional[str] = None,
) -> Optional[Tuple[np.ndarray, np.ndarray, float, int]]:
) -> Optional[Tuple[np.ndarray, np.ndarray, float, int, float]]:
"""
Perform parallel annotation of a spectrum.
Expand Down Expand Up @@ -244,7 +247,7 @@ def parallel_annotate(
)
if not unmod_sequence:
return None
matched_peaks = match_peaks(
matched_peaks, sum_intensities = match_peaks(
fragments_meta_data,
spectrum[index_columns["INTENSITIES"]],
spectrum[index_columns["MZ"]],
Expand All @@ -255,9 +258,9 @@ def parallel_annotate(
if len(matched_peaks) == 0:
intensity = np.full(174, 0.0)
mass = np.full(174, 0.0)
return intensity, mass, calc_mass, 0
return intensity, mass, calc_mass, 0, sum_intensities
matched_peaks, removed_peaks = handle_multiple_matches(matched_peaks)
intensities, mass = generate_annotation_matrix(
matched_peaks, unmod_sequence, spectrum[index_columns["PRECURSOR_CHARGE"]]
)
return intensities, mass, calc_mass, removed_peaks
return intensities, mass, calc_mass, removed_peaks, sum_intensities
8 changes: 4 additions & 4 deletions tests/unit_tests/data/spectrum_output.csv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
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