libgunshotmatch 0.10.1__tar.gz → 0.11.1__tar.gz

{libgunshotmatch-0.10.1 → libgunshotmatch-0.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: libgunshotmatch
-Version: 0.10.1
+Version: 0.11.1
 Summary: Base library for GunShotMatch.
 Author-email: Dominic Davis-Foster <dominic@davis-foster.co.uk>
 License: MIT
@@ -135,7 +135,7 @@ libgunshotmatch
 .. |language| image:: https://img.shields.io/github/languages/top/GunShotMatch/libgunshotmatch
 	:alt: GitHub top language
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.10.1
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.11.1
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.10.1 → libgunshotmatch-0.11.1}/README.rst

@@ -91,7 +91,7 @@ libgunshotmatch
 .. |language| image:: https://img.shields.io/github/languages/top/GunShotMatch/libgunshotmatch
 	:alt: GitHub top language
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.10.1
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.11.1
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.10.1 → libgunshotmatch-0.11.1}/libgunshotmatch/__init__.py

@@ -29,5 +29,5 @@ Base library for GunShotMatch.
 __author__: str = "Dominic Davis-Foster"
 __copyright__: str = "2020-2023 Dominic Davis-Foster"
 __license__: str = "MIT License"
-__version__: str = "0.10.1"
+__version__: str = "0.11.1"
 __email__: str = "dominic@davis-foster.co.uk"

{libgunshotmatch-0.10.1 → libgunshotmatch-0.11.1}/libgunshotmatch/consolidate/__init__.py

@@ -27,7 +27,7 @@ Functions for combining peak identifications across aligned peaks into a single
 #
 
 # stdlib
-from collections import Counter
+from collections import Counter, defaultdict
 from fnmatch import fnmatch
 from itertools import permutations
 from multiprocessing import Pool
@@ -61,6 +61,7 @@ __all__ = (
 		"pairwise_ms_comparisons",
 		"ConsolidatedPeakFilter",
 		"InvertedFilter",
+		"combine_spectra",
 		)
 
 
@@ -476,10 +477,17 @@ class ConsolidatedPeak:
 		for hit in d["hits"]:
 			hits.append(ConsolidatedSearchResult.from_dict(hit))
 
+		ms_list: MutableSequence[Optional[MassSpectrum]] = []
+		for msd in d["ms_list"]:
+			if msd is None:
+				ms_list.append(None)
+			else:
+				ms_list.append(MassSpectrum.from_dict(msd))
+
 		return cls(
 				rt_list=d["rt_list"],
 				area_list=d["area_list"],
-				ms_list=[MassSpectrum.from_dict(msd) for msd in d["ms_list"]],
+				ms_list=ms_list,
 				meta=d["meta"],
 				ms_comparison=d["ms_comparison"],
 				hits=hits,
@@ -804,3 +812,31 @@ class InvertedFilter(ConsolidatedPeakFilter):
 				filtered_consolidated_peaks.append(cp)
 
 		return filtered_consolidated_peaks
+
+
+def combine_spectra(peak: ConsolidatedPeak) -> Tuple[List[int], List[float]]:
+	"""
+	Sum the intensities across all mass spectra in the given peak.
+
+	:param peak:
+
+	:returns: List of masses and list of corresponding intensities.
+
+	.. versionadded:: v0.11.0
+	"""
+
+	combined_ms_data: Dict[int, float] = defaultdict(float)
+
+	for ms in peak.ms_list:
+		if ms is not None:
+			for mass, intensity in zip(ms.mass_list, ms.intensity_list):
+				combined_ms_data[mass] += intensity
+
+	mass_list, intensity_list = [], []
+	for mass, intensity in combined_ms_data.items():
+		mass_list.append(mass)
+		intensity_list.append(intensity)
+
+	# mass_list, intensity_list = zip(*combined_ms_data.items())
+
+	return mass_list, intensity_list

{libgunshotmatch-0.10.1 → libgunshotmatch-0.11.1}/libgunshotmatch/peak.py

@@ -55,6 +55,7 @@ __all__ = (
 		"filter_peaks",
 		"peak_from_dict",
 		"write_alignment",
+		"base_peak_mass",
 		)
 
 
@@ -240,6 +241,10 @@ class PeakList(List[Peak]):
 
 		peaks_as_pure_list: List[Dict[str, Any]] = []
 		for peak in self:
+			if peak is None:
+				peaks_as_pure_list.append(None)
+				continue
+
 			try:
 				ion_areas = peak.ion_areas
 			except ValueError:
@@ -531,3 +536,25 @@ def _to_peak_list(a_list: List[Peak]) -> PeakList:
 		return a_list
 	else:
 		return PeakList(a_list)
+
+
+def base_peak_mass(peak: Peak) -> float:
+	"""
+	Returns the mass of the largest fragment in the peak's mass spectrum.
+
+	:param peak:
+
+	.. versionadded:: v0.11.0
+	"""
+
+	apex_mass_list = peak.mass_spectrum.mass_list
+	apex_mass_spec = peak.mass_spectrum.mass_spec
+
+	# Determine the intensity of the base peak in the mass spectrum
+	base_peak_intensity = max(apex_mass_spec)
+
+	# Determine the index of the base peak in the mass spectrum
+	base_peak_index = apex_mass_spec.index(base_peak_intensity)
+
+	# Finally, determine the mass of the base peak
+	return apex_mass_list[base_peak_index]

{libgunshotmatch-0.10.1 → libgunshotmatch-0.11.1}/libgunshotmatch/project.py

@@ -28,7 +28,7 @@ Represents a collection of repeat analyses.
 
 # stdlib
 import os
-from typing import Any, Dict, List, Mapping, Optional, Type
+from typing import Any, Dict, List, Mapping, MutableSequence, Optional, Type
 
 # 3rd party
 import attr
@@ -131,14 +131,15 @@ class Project:
 		"""
 
 		alignment_as_dict = d["alignment"]
-		alignment_peaks: List[List[Peak]] = []
+		alignment_peaks: List[MutableSequence[Optional[Peak]]] = []
 		for row in alignment_as_dict["peaks"]:
 			alignment_peaks.append([])
 			for peak in row:
 				# print(peak)
-				peak_obj = peak_from_dict(peak)
-
-				alignment_peaks[-1].append(peak_obj)
+				if peak is None:
+					alignment_peaks[-1].append(None)
+				else:
+					alignment_peaks[-1].append(peak_from_dict(peak))
 
 		alignment = create_alignment(
 				alignment_peaks,

{libgunshotmatch-0.10.1 → libgunshotmatch-0.11.1}/libgunshotmatch/utils.py

@@ -171,7 +171,11 @@ def get_rt_range(project: "Project") -> Tuple[float, float]:
 	return min_rt, max_rt
 
 
-def create_alignment(peakpos: Sequence[Sequence[Peak]], expr_code: List[str], similarity: float = 0) -> Alignment:
+def create_alignment(
+		peakpos: Sequence[Sequence[Optional[Peak]]],
+		expr_code: List[str],
+		similarity: float = 0,
+		) -> Alignment:
 	"""
 	Create a new :class:`pyms.DPA.Alignment.Alignment` object.
 
@@ -185,7 +189,7 @@ def create_alignment(peakpos: Sequence[Sequence[Peak]], expr_code: List[str], si
 	"""
 
 	alignment = Alignment(None)
-	alignment.peakpos = [list(p) for p in peakpos]
+	alignment.peakpos = [list(p) for p in peakpos]  # type: ignore[arg-type]
 	alignment.peakalgt = numpy.transpose(alignment.peakpos).tolist()  # type: ignore[arg-type]
 	alignment.expr_code = expr_code
 	alignment.similarity = similarity

{libgunshotmatch-0.10.1 → libgunshotmatch-0.11.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "whey"
 
 [project]
 name = "libgunshotmatch"
-version = "0.10.1"
+version = "0.11.1"
 description = "Base library for GunShotMatch."
 readme = "README.rst"
 keywords = []
@@ -42,14 +42,13 @@ classifiers = [
 ]
 requires-python = ">=3.8"
 
+[project.license]
+file = "LICENSE"
+
 [[project.authors]]
 name = "Dominic Davis-Foster"
 email = "dominic@davis-foster.co.uk"
 
-
-[project.license]
-file = "LICENSE"
-
 [project.urls]
 Homepage = "https://github.com/GunShotMatch/libgunshotmatch"
 "Issue Tracker" = "https://github.com/GunShotMatch/libgunshotmatch/issues"
@@ -92,6 +91,16 @@ show_error_codes = true
 [tool.snippet-fmt]
 directives = [ "code-block",]
 
+[tool.snippet-fmt.languages.python]
+reformat = true
+
+[tool.snippet-fmt.languages.TOML]
+reformat = true
+
+[tool.snippet-fmt.languages.ini]
+
+[tool.snippet-fmt.languages.json]
+
 [tool.sphinx-pyproject]
 github_username = "GunShotMatch"
 github_repository = "libgunshotmatch"
@@ -113,7 +122,6 @@ extensions = [
     "sphinx.ext.mathjax",
     "sphinxcontrib.extras_require",
     "sphinx.ext.todo",
-    "sphinxemoji.sphinxemoji",
     "notfound.extension",
     "sphinx_copybutton",
     "sphinxcontrib.default_values",
@@ -126,7 +134,6 @@ extensions = [
     "remove_factory_defaults",
     "sphinx_toolbox.more_autosummary.column_widths",
 ]
-sphinxemoji_style = "twemoji"
 gitstamp_fmt = "%d %b %Y"
 templates_path = [ "_templates",]
 html_static_path = [ "_static",]
@@ -192,13 +199,3 @@ include = false
 [tool.dependency-dash."tests/requirements.txt"]
 order = 20
 include = false
-
-[tool.snippet-fmt.languages.python]
-reformat = true
-
-[tool.snippet-fmt.languages.TOML]
-reformat = true
-
-[tool.snippet-fmt.languages.ini]
-
-[tool.snippet-fmt.languages.json]