libgunshotmatch 0.10.0__py3-none-any.whl → 0.11.0__py3-none-any.whl

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 = "0.10.0"
+__version__: str = "0.11.0"
 __email__: str = "dominic@davis-foster.co.uk"

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",
 		)
 
 
@@ -804,3 +805,31 @@ 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/peak.py

@@ -55,6 +55,7 @@ __all__ = (
 		"filter_peaks",
 		"peak_from_dict",
 		"write_alignment",
+		"base_peak_mass",
 		)
 
 
@@ -429,11 +430,11 @@ def write_alignment(
 
 	rt_alignment = alignment.get_peak_alignment(require_all_expr=require_all_datafiles)
 	rt_alignment_filename = output_dir_p / f"{project_name}_alignment_rt.json"
-	rt_alignment_filename.write_clean(rt_alignment)
+	rt_alignment_filename.write_clean(rt_alignment.to_json())
 
 	area_alignment = alignment.get_area_alignment(require_all_expr=require_all_datafiles)
 	area_alignment_filename = output_dir_p / f"{project_name}_alignment_area.json"
-	area_alignment_filename.write_clean(area_alignment)
+	area_alignment_filename.write_clean(area_alignment.to_json())
 
 	ms_alignment = alignment.get_ms_alignment(require_all_expr=require_all_datafiles)
 	# ms_alignment.to_json(output_dir_p / 'alignment_ms.json')
@@ -531,3 +532,25 @@ 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-0.10.0.dist-info → libgunshotmatch-0.11.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: libgunshotmatch
-Version: 0.10.0
+Version: 0.11.0
 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/v0.10.0
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v0.11.0
 	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
 	:alt: GitHub commits since tagged version
 

{libgunshotmatch-0.10.0.dist-info → libgunshotmatch-0.11.0.dist-info}/RECORD

@@ -2,21 +2,21 @@ libgunshotmatch/comparison/__init__.py,sha256=g-KDfzG-oyRf2aeXlMaJJ3aWfQtQkr5-bG
 libgunshotmatch/comparison/_utils.py,sha256=aZ6fnFM4M_vTsKq5t79V4tfven1eVdG4EUCuYFuXMVs,1895
 libgunshotmatch/comparison/projects.py,sha256=Dq294cDndmQI2FnIcVXwleCQF0mF2m8U5wWnO5_aD9A,3356
 libgunshotmatch/comparison/unknowns.py,sha256=kvJJDtfpMp-c3hjCOz7YtvuuDR0YksWmyUuaSBC_5Jg,2710
-libgunshotmatch/consolidate/__init__.py,sha256=zdnqx7YzV3MiW5IVFEiPSJZT43BdcOmlRqkIKOEBqPg,23816
+libgunshotmatch/consolidate/__init__.py,sha256=ezF2MwUykNSzB5s3X8HiPohTef_kS4gXtRBKG1p6zwc,24567
 libgunshotmatch/consolidate/_fields.py,sha256=0kfPXJ0EG7GhdFiNzvcmd6W4i1x6Y0s2Y58z3RltPiA,2759
 libgunshotmatch/consolidate/_spectra.py,sha256=24aDoPwGWEyIFCH-fwRa4nifNMPqUyd-qTogk3BMeLY,2319
 libgunshotmatch/method/__init__.py,sha256=TP_3rvv3WEbV6Y5E_QWd2lcORPFnbXV4YRKGwXDa4ds,9423
 libgunshotmatch/method/_fields.py,sha256=HBFl0XmHBaAOHYdABs2NRbjtngGEw7kY0xP6D2Fl7h4,4941
-libgunshotmatch/__init__.py,sha256=_8fk8Y_s16QckNbYhOXc8zxn6HIK0f_3TRYEIkYEYr4,1434
+libgunshotmatch/__init__.py,sha256=OXM6TubGh5_DlwFy9SnXURf9fzbaz9cy-gNRZIAhimw,1434
 libgunshotmatch/datafile.py,sha256=4C4BiR95PBfIUbiUKQzVfh57tgZu_l6rLS8bIgrgPUs,16246
 libgunshotmatch/gzip_util.py,sha256=PcfT4QC4TM0KI3uCGetRpjChbTXTGmNEJBr7BghO3i8,2414
-libgunshotmatch/peak.py,sha256=huZ1hObIFcQpMPXyU6lYe7B-FFT-djSeG4jII7CgWAE,16923
+libgunshotmatch/peak.py,sha256=qe3-y0EsA37W2qMlMVruEOFRRxSG7NVWDcd8TvjZaqY,17546
 libgunshotmatch/project.py,sha256=ch8v8egvcULjYk7_40KywgM-_j3mf2tvRTzAsIC6Kp0,6904
 libgunshotmatch/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 libgunshotmatch/search.py,sha256=GMP7_DMnXFq3TG8AT1WARIn4ObCfOGfTDakpGeKzJYw,3123
 libgunshotmatch/utils.py,sha256=8wrdSk1ZWIgIu6eN9QEDF23goxN7z2VszxcDYZZ8ov0,5729
-libgunshotmatch-0.10.0.dist-info/LICENSE,sha256=bFtJt-lyVJHV-88FeFa_r3BEOsmpna5qG2KOl9JUNfU,1064
-libgunshotmatch-0.10.0.dist-info/METADATA,sha256=B26beZpWIdl-1YRu3Bl51SqsjWIOd0Y4vy2C1Osy7oA,6394
-libgunshotmatch-0.10.0.dist-info/WHEEL,sha256=3vSnEhs48RUlSXcCXKCl4DOHs_qqaP2dU3IGkMqN2oI,84
-libgunshotmatch-0.10.0.dist-info/entry_points.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-libgunshotmatch-0.10.0.dist-info/RECORD,,
+libgunshotmatch-0.11.0.dist-info/LICENSE,sha256=bFtJt-lyVJHV-88FeFa_r3BEOsmpna5qG2KOl9JUNfU,1064
+libgunshotmatch-0.11.0.dist-info/METADATA,sha256=8TbC-eZngXagQbCQ_G5iStuzriCjYSvGD5umtsxjkAo,6394
+libgunshotmatch-0.11.0.dist-info/WHEEL,sha256=pUf8gZsdmDXXTtqZfolZFpfoEwFoEdADIuUvQVl5qAY,83
+libgunshotmatch-0.11.0.dist-info/entry_points.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+libgunshotmatch-0.11.0.dist-info/RECORD,,

{libgunshotmatch-0.10.0.dist-info → libgunshotmatch-0.11.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: whey (0.0.24)
+Generator: whey (0.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any