masster 0.2.5__py3-none-any.whl → 0.3.1__py3-none-any.whl

masster/study/study5_schema.json

@@ -1,241 +1,253 @@
-{
-  "consensus_df": {
-    "columns": {
-      "consensus_uid": {
-        "dtype": "pl.Int64"
-      },
-      "consensus_id": {
-        "dtype": "pl.Utf8"
-      },
-      "quality": {
-        "dtype": "pl.Float64"
-      },
-      "number_samples": {
-        "dtype": "pl.Int64"
-      },
-      "rt": {
-        "dtype": "pl.Float64"
-      },
-      "mz": {
-        "dtype": "pl.Float64"
-      },
-      "rt_min": {
-        "dtype": "pl.Float64"
-      },
-      "rt_max": {
-        "dtype": "pl.Float64"
-      },
-      "rt_mean": {
-        "dtype": "pl.Float64"
-      },
-      "rt_start_mean": {
-        "dtype": "pl.Float64"
-      },
-      "rt_end_mean": {
-        "dtype": "pl.Float64"
-      },
-      "rt_delta_mean": {
-        "dtype": "pl.Float64"
-      },
-      "mz_min": {
-        "dtype": "pl.Float64"
-      },
-      "mz_max": {
-        "dtype": "pl.Float64"
-      },
-      "mz_mean": {
-        "dtype": "pl.Float64"
-      },
-      "mz_start_mean": {
-        "dtype": "pl.Float64"
-      },
-      "mz_end_mean": {
-        "dtype": "pl.Float64"
-      },
-      "inty_mean": {
-        "dtype": "pl.Float64"
-      },
-      "bl": {
-        "dtype": "pl.Float64"
-      },
-      "chrom_coherence_mean": {
-        "dtype": "pl.Float64"
-      },
-      "chrom_prominence_mean": {
-        "dtype": "pl.Float64"
-      },
-      "chrom_prominence_scaled_mean": {
-        "dtype": "pl.Float64"
-      },
-      "chrom_height_scaled_mean": {
-        "dtype": "pl.Float64"
-      },
-      "iso_mean": {
-        "dtype": "pl.Float64"
-      },
-      "charge_mean": {
-        "dtype": "pl.Float64"
-      },
-      "number_ms2": {
-        "dtype": "pl.Int64"
-      }
-    }
-  },
-  "consensus_mapping_df": {
-    "columns": {
-      "consensus_uid": {
-        "dtype": "pl.Int64"
-      },
-      "feature_uid": {
-        "dtype": "pl.Int64"
-      },
-      "sample_uid": {
-        "dtype": "pl.Int64"
-      }
-    }
-  },
-  "consensus_ms2": {
-    "columns": {
-      "consensus_uid": {
-        "dtype": "pl.Int64"
-      },
-      "energy": {
-        "dtype": "pl.Float64"
-      },
-      "feature_uid": {
-        "dtype": "pl.Int64"
-      },
-      "number_frags": {
-        "dtype": "pl.Int64"
-      },
-      "prec_coherence": {
-        "dtype": "pl.Float64"
-      },
-      "prec_inty": {
-        "dtype": "pl.Float64"
-      },
-      "prec_prominence_scaled": {
-        "dtype": "pl.Float64"
-      },
-      "sample_uid": {
-        "dtype": "pl.Int64"
-      },
-      "scan_id": {
-        "dtype": "pl.Int64"
-      },
-      "spec": {
-        "dtype": "pl.Object"
-      }
-    }
-  },
-  "features_df": {
-    "columns": {
-      "feature_uid": {
-        "dtype": "pl.Int64"
-      },
-      "feature_id": {
-        "dtype": "pl.Utf8"
-      },
-      "sample_uid": {
-        "dtype": "pl.Int32"
-      },
-      "mz": {
-        "dtype": "pl.Float64"
-      },
-      "rt": {
-        "dtype": "pl.Float64"
-      },
-      "rt_original": {
-        "dtype": "pl.Float64"
-      },
-      "rt_start": {
-        "dtype": "pl.Float64"
-      },
-      "rt_end": {
-        "dtype": "pl.Float64"
-      },
-      "rt_delta": {
-        "dtype": "pl.Float64"
-      },
-      "mz_start": {
-        "dtype": "pl.Float64"
-      },
-      "mz_end": {
-        "dtype": "pl.Float64"
-      },
-      "inty": {
-        "dtype": "pl.Float64"
-      },
-      "quality": {
-        "dtype": "pl.Float64"
-      },
-      "charge": {
-        "dtype": "pl.Int32"
-      },
-      "iso": {
-        "dtype": "pl.Int64"
-      },
-      "iso_of": {
-        "dtype": "pl.Int64"
-      },
-      "adduct": {
-        "dtype": "pl.Utf8"
-      },
-      "adduct_mass": {
-        "dtype": "pl.Float64"
-      },
-      "adduct_group": {
-        "dtype": "pl.Int64"
-      },
-      "chrom": {
-        "dtype": "pl.Object"
-      },
-      "filled": {
-        "dtype": "pl.Boolean"
-      },
-      "chrom_area": {
-        "dtype": "pl.Float64"
-      },
-      "chrom_coherence": {
-        "dtype": "pl.Float64"
-      },
-      "chrom_prominence": {
-        "dtype": "pl.Float64"
-      },
-      "chrom_prominence_scaled": {
-        "dtype": "pl.Float64"
-      },
-      "chrom_height_scaled": {
-        "dtype": "pl.Float64"
-      },
-      "ms2_scans": {
-        "dtype": "pl.Object"
-      },
-      "ms2_specs": {
-        "dtype": "pl.Object"
-      }
-    }
-  },
-  "samples_df": {
-    "columns": {
-      "map_id": {
-        "dtype": "pl.Utf8"
-      },
-      "sample_name": {
-        "dtype": "pl.Utf8"
-      },
-      "sample_path": {
-        "dtype": "pl.Utf8"
-      },
-      "sample_type": {
-        "dtype": "pl.Utf8"
-      },
-      "sample_uid": {
-        "dtype": "pl.Int64"
-      },
-      "size": {
-        "dtype": "pl.Int64"
-      }
-    }
-  }
-}
+{
+  "consensus_df": {
+    "columns": {
+      "consensus_uid": {
+        "dtype": "pl.Int64"
+      },
+      "consensus_id": {
+        "dtype": "pl.Utf8"
+      },
+      "quality": {
+        "dtype": "pl.Float64"
+      },
+      "number_samples": {
+        "dtype": "pl.Int64"
+      },
+      "rt": {
+        "dtype": "pl.Float64"
+      },
+      "mz": {
+        "dtype": "pl.Float64"
+      },
+      "rt_min": {
+        "dtype": "pl.Float64"
+      },
+      "rt_max": {
+        "dtype": "pl.Float64"
+      },
+      "rt_mean": {
+        "dtype": "pl.Float64"
+      },
+      "rt_start_mean": {
+        "dtype": "pl.Float64"
+      },
+      "rt_end_mean": {
+        "dtype": "pl.Float64"
+      },
+      "rt_delta_mean": {
+        "dtype": "pl.Float64"
+      },
+      "mz_min": {
+        "dtype": "pl.Float64"
+      },
+      "mz_max": {
+        "dtype": "pl.Float64"
+      },
+      "mz_mean": {
+        "dtype": "pl.Float64"
+      },
+      "mz_start_mean": {
+        "dtype": "pl.Float64"
+      },
+      "mz_end_mean": {
+        "dtype": "pl.Float64"
+      },
+      "inty_mean": {
+        "dtype": "pl.Float64"
+      },
+      "bl": {
+        "dtype": "pl.Float64"
+      },
+      "chrom_coherence_mean": {
+        "dtype": "pl.Float64"
+      },
+      "chrom_prominence_mean": {
+        "dtype": "pl.Float64"
+      },
+      "chrom_prominence_scaled_mean": {
+        "dtype": "pl.Float64"
+      },
+      "chrom_height_scaled_mean": {
+        "dtype": "pl.Float64"
+      },
+      "iso_mean": {
+        "dtype": "pl.Float64"
+      },
+      "charge_mean": {
+        "dtype": "pl.Float64"
+      },
+      "number_ms2": {
+        "dtype": "pl.Int64"
+      },
+      "adducts": {
+        "dtype": "pl.Object"
+      }
+    }
+  },
+  "consensus_mapping_df": {
+    "columns": {
+      "consensus_uid": {
+        "dtype": "pl.Int64"
+      },
+      "feature_uid": {
+        "dtype": "pl.Int64"
+      },
+      "sample_uid": {
+        "dtype": "pl.Int64"
+      }
+    }
+  },
+  "consensus_ms2": {
+    "columns": {
+      "consensus_uid": {
+        "dtype": "pl.Int64"
+      },
+      "energy": {
+        "dtype": "pl.Float64"
+      },
+      "feature_uid": {
+        "dtype": "pl.Int64"
+      },
+      "number_frags": {
+        "dtype": "pl.Int64"
+      },
+      "prec_coherence": {
+        "dtype": "pl.Float64"
+      },
+      "prec_inty": {
+        "dtype": "pl.Float64"
+      },
+      "prec_prominence_scaled": {
+        "dtype": "pl.Float64"
+      },
+      "sample_uid": {
+        "dtype": "pl.Int64"
+      },
+      "scan_id": {
+        "dtype": "pl.Int64"
+      },
+      "spec": {
+        "dtype": "pl.Object"
+      }
+    }
+  },
+  "features_df": {
+    "columns": {
+      "feature_uid": {
+        "dtype": "pl.Int64"
+      },
+      "sample_uid": {
+        "dtype": "pl.Int32"
+      },
+      "feature_id": {
+        "dtype": "pl.Utf8"
+      },
+      "mz": {
+        "dtype": "pl.Float64"
+      },
+      "rt": {
+        "dtype": "pl.Float64"
+      },
+      "rt_original": {
+        "dtype": "pl.Float64"
+      },
+      "rt_start": {
+        "dtype": "pl.Float64"
+      },
+      "rt_end": {
+        "dtype": "pl.Float64"
+      },
+      "rt_delta": {
+        "dtype": "pl.Float64"
+      },
+      "mz_start": {
+        "dtype": "pl.Float64"
+      },
+      "mz_end": {
+        "dtype": "pl.Float64"
+      },
+      "inty": {
+        "dtype": "pl.Float64"
+      },
+      "quality": {
+        "dtype": "pl.Float64"
+      },
+      "charge": {
+        "dtype": "pl.Int32"
+      },
+      "iso": {
+        "dtype": "pl.Int64"
+      },
+      "iso_of": {
+        "dtype": "pl.Int64"
+      },
+      "adduct_group": {
+        "dtype": "pl.Int64"
+      },
+      "adduct": {
+        "dtype": "pl.Utf8"
+      },
+      "adduct_mass": {
+        "dtype": "pl.Float64"
+      },
+      "filled": {
+        "dtype": "pl.Boolean"
+      },
+      "chrom_area": {
+        "dtype": "pl.Float64"
+      },
+      "chrom": {
+        "dtype": "pl.Object"
+      },
+      "chrom_coherence": {
+        "dtype": "pl.Float64"
+      },
+      "chrom_prominence": {
+        "dtype": "pl.Float64"
+      },
+      "chrom_prominence_scaled": {
+        "dtype": "pl.Float64"
+      },
+      "chrom_height_scaled": {
+        "dtype": "pl.Float64"
+      },
+      "ms2_scans": {
+        "dtype": "pl.Object"
+      },
+      "ms2_specs": {
+        "dtype": "pl.Object"
+      }
+    }
+  },
+  "samples_df": {
+    "columns": {
+      "map_id": {
+        "dtype": "pl.Utf8"
+      },
+      "sample_name": {
+        "dtype": "pl.Utf8"
+      },
+      "sample_path": {
+        "dtype": "pl.Utf8"
+      },
+      "file_source": {
+        "dtype": "pl.Utf8"
+      },
+      "sample_type": {
+        "dtype": "pl.Utf8"
+      },
+      "sample_uid": {
+        "dtype": "pl.Int64"
+      },
+      "size": {
+        "dtype": "pl.Int64"
+      },
+      "ms1": {
+        "dtype": "pl.Int64"
+      },
+      "ms2": {
+        "dtype": "pl.Int64"
+      }
+    }
+  }
+}

{masster-0.2.5.dist-info → masster-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.2.5
+Version: 0.3.1
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -676,6 +676,7 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: >=3.11
@@ -732,9 +733,10 @@ Description-Content-Type: text/markdown
 
 **MASSter** is a comprehensive Python package for mass spectrometry data analysis, designed for metabolomics and LC-MS data processing. It provides tools for feature detection, alignment, consensus building, and interactive visualization of mass spectrometry datasets. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. 
 
-Most core processing functions are derived from OpenMS. We use the same nomenclature and refer to their documentation for an explanation of the parameters. To a large extent, however, you should be able to use the defaults (=no parameters) when calling processing steps.
+This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. 
+
+Some of the core processing functions are derived from OpenMS. We use the same nomenclature and refer to their documentation for an explanation of the parameters. To a large extent, however, you should be able to use the defaults (=no parameters) when calling processing steps.
 
-This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. Novel functionalities will be added based on need and requests.
 
 ## Installation
 
@@ -751,23 +753,26 @@ import masster
 study = masster.Study(default_folder=r'D:\...\mylcms')
 
 # Load data from folder with raw data, here: WIFF
-study.add_folder(r'D:\...\...\...\*.wiff')
+study.add(r'D:\...\...\...\*.wiff')
 
-# Align maps
+# Perform retention time correction
 study.align(rt_max_diff=2.0)
+study.plot_alignment()
 
 # Find consensus features
-study.find_consensus(min_samples=3)
+study.merge(min_samples=3)
+study.plot_consensus_2d()
 
 # Retrieve missing data for quantification
-study.fill_chrom(abs_)
+study.fill()
 
 # Integrate according to consensus metadata
-study.integrate_chrom()
+study.integrate()
 
-# link MS2 across the whole study and export them
-study.find_ms2()
+# export results
 study.export_mgf()
+study.export_mztab()
+study.export_consensus()
 
 # Save the study to .study5
 study.save()

masster-0.3.1.dist-info/RECORD

@@ -0,0 +1,59 @@
+masster/__init__.py,sha256=G7hbKO8F_o1wFwQlvO25M8JYGka_YSAVU2_O__2rjlI,697
+masster/_version.py,sha256=ioQa4W_2pWdKSoU7hw7Pn6WMBm3nMuuLKfSR4f8171A,256
+masster/chromatogram.py,sha256=NgPr1uLGJHjRu6PWZZGOrS3pCl7sye1yQCJjlRi9ZSY,19305
+masster/logger.py,sha256=iJGDtqR0nzW4cMb_fPOwoytpgrpnlSkuH5MIhgK90Xk,14733
+masster/spectrum.py,sha256=LuDa7qP_JInctzkmxC9c5468opHOholy321KpUgyW2U,47550
+masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.featureXML,sha256=033IjCWBaYVymnPhVHneytilC-XIa6T-6wkeBB0BXvc,10980374
+masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.mzML,sha256=3RS_crLN-aoPSacMYaQ45sxszmp_EcQElrg8tiuAQyA,39741920
+masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.sample5,sha256=T3LxClfe3Uaqx4Rb7lY57e2uWpuJHzPy-VEl3cy4b7k,11109448
+masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data,sha256=01vC6m__Qqm2rLvlTMZoeKIKowFvovBTUnrNl8Uav3E,24576
+masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
+masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff.scan,sha256=ahi1Y3UhAj9Bj4Q2MlbgPekNdkJvMOoMXVOoR6CeIxc,13881220
+masster/data/examples/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff2,sha256=TFB0HW4Agkig6yht7FtgjUdbXax8jjKaHpSZSvuU5vs,3252224
+masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
+masster/sample/h5.py,sha256=aGj3vJsM08wiWFKryRCn5ROKBSRX85vE0Z-jiPSqLjI,63817
+masster/sample/helpers.py,sha256=OEgvR3bptA-tEqHAFVPjWpbagKXAU1h0bePPi9ttHa4,34842
+masster/sample/lib.py,sha256=9r2XlF_BaJ4WNAsQo8hElieRLwsAv0yrbYq4DJ0iVOM,33496
+masster/sample/load.py,sha256=y-KUJ2nCFX_06FHPUOh-CzRRvaTx14xNcXoL19bU8qY,47562
+masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
+masster/sample/plot.py,sha256=wd-4OosFT8MoO0fM8PSMskZK_yg8i8vfbiTieAzgrv4,62831
+masster/sample/processing.py,sha256=NjNLt47Fy0UF3Xs35NBhADg57qTC6Lfa4Xz8Y30v83A,58250
+masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
+masster/sample/sample.py,sha256=UlyA7cZtV_IMO8PRaYaUqf8cfAGfavVVfNDo0g_6OJw,16185
+masster/sample/sample5_schema.json,sha256=3SPFQZH4SooLYUt_lW-PCOE9rHnl56Vhc2XG-r1nyEQ,3586
+masster/sample/save.py,sha256=o9eFSqqr7KYwvCD3gOJt_nZ4h3pkflWqs0n0oSLM-sU,31970
+masster/sample/sciex.py,sha256=q6PdcjCtV2PWnJiXuvfISu09zjkaTR_fvHvWN9OvOcM,46870
+masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
+masster/sample/defaults/find_adducts_def.py,sha256=6CcGRlz4VeosoBT_W0bkR1Kjj11Rq3QvuuOnkizIZyk,11630
+masster/sample/defaults/find_features_def.py,sha256=d9LQsS7QEj2SIvhz_N55Zk80V2MOI5HlB4EylGDgG_4,13878
+masster/sample/defaults/find_ms2_def.py,sha256=KTELMAnioGLYbhzAwOgK14TZqboPEvzeBN0HC-v0Z5A,9872
+masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2AtQDHcPu-O-YoQPs,11460
+masster/sample/defaults/sample_def.py,sha256=t8vrb8MoBBsFQcRzlaT0-q0hAssOxWO7vhCAJU3_THs,14068
+masster/study/__init__.py,sha256=Zspv6U8jFqjkHGYdNdDy1rfUnCSolCzUdgSSg98PRgE,166
+masster/study/export.py,sha256=bm3e6AEwkXqBO6Pwd-2pWhxOmzQTFlOSauXFnaiSJDI,29019
+masster/study/h5.py,sha256=EcpyYfMknDzzdA6XTyMU_ppY92_DsPSPYGE0kpVN7T8,66429
+masster/study/helpers.py,sha256=SeW17rA3BIM2I2Whiye6wegRRSCabIpQoCsjOCafjKw,74888
+masster/study/helpers_optimized.py,sha256=EgOgPaL3c2LA8jDhnlEHvzb7O9Um-vnMIcnNaoH90gA,13620
+masster/study/load.py,sha256=TLxVhXu0HHb51lGggXitQLtfNxz2JJfKMkAXJbxhvhM,46880
+masster/study/parameters.py,sha256=0elaF7YspTsB7qyajWAbRNL2VfKlGz5GJLifmO8IGkk,3276
+masster/study/plot.py,sha256=hOG8bBT3mYV63FieEk-gYKtOyIXWppkTu21VeGbRnGk,21918
+masster/study/processing.py,sha256=BQuSBO7O8iTlCjXenECyg0_PAsPF1NNiUllypuemPZI,46101
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