CoreMS 4.0.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (171) hide show
  1. corems/__init__.py +63 -0
  2. corems/chroma_peak/__init__.py +0 -0
  3. corems/chroma_peak/calc/ChromaPeakCalc.py +480 -0
  4. corems/chroma_peak/calc/__init__.py +0 -0
  5. corems/chroma_peak/calc/subset.py +196 -0
  6. corems/chroma_peak/factory/__init__.py +0 -0
  7. corems/chroma_peak/factory/chroma_peak_classes.py +1178 -0
  8. corems/encapsulation/__init__.py +0 -0
  9. corems/encapsulation/constant.py +1283 -0
  10. corems/encapsulation/factory/__init__.py +0 -0
  11. corems/encapsulation/factory/parameters.py +392 -0
  12. corems/encapsulation/factory/processingSetting.py +1244 -0
  13. corems/encapsulation/input/__init__.py +0 -0
  14. corems/encapsulation/input/parameter_from_json.py +579 -0
  15. corems/encapsulation/output/__init__.py +0 -0
  16. corems/encapsulation/output/parameter_to_dict.py +142 -0
  17. corems/encapsulation/output/parameter_to_json.py +332 -0
  18. corems/mass_spectra/__init__.py +0 -0
  19. corems/mass_spectra/calc/GC_Calc.py +84 -0
  20. corems/mass_spectra/calc/GC_Deconvolution.py +558 -0
  21. corems/mass_spectra/calc/GC_RI_Calibration.py +44 -0
  22. corems/mass_spectra/calc/MZSearch.py +249 -0
  23. corems/mass_spectra/calc/SignalProcessing.py +656 -0
  24. corems/mass_spectra/calc/__init__.py +0 -0
  25. corems/mass_spectra/calc/lc_calc.py +5790 -0
  26. corems/mass_spectra/calc/lc_calc_operations.py +1127 -0
  27. corems/mass_spectra/factory/GC_Class.py +791 -0
  28. corems/mass_spectra/factory/__init__.py +0 -0
  29. corems/mass_spectra/factory/chromat_data.py +51 -0
  30. corems/mass_spectra/factory/lc_class.py +2721 -0
  31. corems/mass_spectra/input/__init__.py +0 -0
  32. corems/mass_spectra/input/andiNetCDF.py +200 -0
  33. corems/mass_spectra/input/boosterHDF5.py +216 -0
  34. corems/mass_spectra/input/brukerSolarix.py +153 -0
  35. corems/mass_spectra/input/brukerSolarix_utils.py +73 -0
  36. corems/mass_spectra/input/corems_hdf5.py +1710 -0
  37. corems/mass_spectra/input/massList.py +133 -0
  38. corems/mass_spectra/input/mzml.py +668 -0
  39. corems/mass_spectra/input/parserbase.py +239 -0
  40. corems/mass_spectra/input/rawFileReader.py +1839 -0
  41. corems/mass_spectra/output/__init__.py +0 -0
  42. corems/mass_spectra/output/export.py +2800 -0
  43. corems/mass_spectrum/__init__.py +0 -0
  44. corems/mass_spectrum/calc/AutoRecalibration.py +237 -0
  45. corems/mass_spectrum/calc/Calibration.py +602 -0
  46. corems/mass_spectrum/calc/CalibrationCalc.py +253 -0
  47. corems/mass_spectrum/calc/KendrickGroup.py +239 -0
  48. corems/mass_spectrum/calc/MassErrorPrediction.py +436 -0
  49. corems/mass_spectrum/calc/MassSpectrumCalc.py +303 -0
  50. corems/mass_spectrum/calc/MeanResolvingPowerFilter.py +212 -0
  51. corems/mass_spectrum/calc/NoiseCalc.py +371 -0
  52. corems/mass_spectrum/calc/NoiseCalc_Bayes.py +93 -0
  53. corems/mass_spectrum/calc/PeakPicking.py +994 -0
  54. corems/mass_spectrum/calc/__init__.py +0 -0
  55. corems/mass_spectrum/factory/MassSpectrumClasses.py +1753 -0
  56. corems/mass_spectrum/factory/__init__.py +0 -0
  57. corems/mass_spectrum/input/__init__.py +0 -0
  58. corems/mass_spectrum/input/baseClass.py +531 -0
  59. corems/mass_spectrum/input/boosterHDF5.py +161 -0
  60. corems/mass_spectrum/input/coremsHDF5.py +475 -0
  61. corems/mass_spectrum/input/massList.py +402 -0
  62. corems/mass_spectrum/input/numpyArray.py +133 -0
  63. corems/mass_spectrum/output/__init__.py +0 -0
  64. corems/mass_spectrum/output/export.py +841 -0
  65. corems/molecular_formula/__init__.py +0 -0
  66. corems/molecular_formula/calc/MolecularFormulaCalc.py +885 -0
  67. corems/molecular_formula/calc/__init__.py +0 -0
  68. corems/molecular_formula/factory/MolecularFormulaFactory.py +895 -0
  69. corems/molecular_formula/factory/__init__.py +0 -0
  70. corems/molecular_formula/input/__init__.py +0 -0
  71. corems/molecular_formula/input/masslist_ref.py +355 -0
  72. corems/molecular_id/__init__.py +0 -0
  73. corems/molecular_id/calc/ClusterFilter.py +251 -0
  74. corems/molecular_id/calc/MolecularFilter.py +122 -0
  75. corems/molecular_id/calc/SpectralSimilarity.py +632 -0
  76. corems/molecular_id/calc/__init__.py +0 -0
  77. corems/molecular_id/calc/math_distance.py +1637 -0
  78. corems/molecular_id/data/FAMES_REF.msp +980 -0
  79. corems/molecular_id/data/PNNLMetV20191015.msp +157267 -0
  80. corems/molecular_id/factory/EI_SQL.py +650 -0
  81. corems/molecular_id/factory/MolecularLookupTable.py +914 -0
  82. corems/molecular_id/factory/__init__.py +0 -0
  83. corems/molecular_id/factory/classification.py +884 -0
  84. corems/molecular_id/factory/lipid_molecular_metadata.py +50 -0
  85. corems/molecular_id/factory/molecularSQL.py +827 -0
  86. corems/molecular_id/factory/spectrum_search_results.py +119 -0
  87. corems/molecular_id/input/__init__.py +0 -0
  88. corems/molecular_id/input/nistMSI.py +148 -0
  89. corems/molecular_id/search/__init__.py +0 -0
  90. corems/molecular_id/search/compoundSearch.py +214 -0
  91. corems/molecular_id/search/database_interfaces.py +1527 -0
  92. corems/molecular_id/search/findOxygenPeaks.py +330 -0
  93. corems/molecular_id/search/lcms_spectral_search.py +348 -0
  94. corems/molecular_id/search/molecularFormulaSearch.py +1117 -0
  95. corems/molecular_id/search/priorityAssignment.py +723 -0
  96. corems/ms_peak/__init__.py +0 -0
  97. corems/ms_peak/calc/MSPeakCalc.py +1010 -0
  98. corems/ms_peak/calc/__init__.py +0 -0
  99. corems/ms_peak/factory/MSPeakClasses.py +542 -0
  100. corems/ms_peak/factory/__init__.py +0 -0
  101. corems/transient/__init__.py +0 -0
  102. corems/transient/calc/TransientCalc.py +362 -0
  103. corems/transient/calc/__init__.py +0 -0
  104. corems/transient/factory/TransientClasses.py +457 -0
  105. corems/transient/factory/__init__.py +0 -0
  106. corems/transient/input/__init__.py +0 -0
  107. corems/transient/input/brukerSolarix.py +461 -0
  108. corems/transient/input/midasDatFile.py +172 -0
  109. corems-4.0.0.dist-info/METADATA +475 -0
  110. corems-4.0.0.dist-info/RECORD +171 -0
  111. corems-4.0.0.dist-info/WHEEL +5 -0
  112. corems-4.0.0.dist-info/licenses/LICENSE +22 -0
  113. corems-4.0.0.dist-info/top_level.txt +4 -0
  114. examples/archive/scripts/CoreMS_tutorial.py +94 -0
  115. examples/archive/scripts/DI HR-MS Halogens Bruker.py +196 -0
  116. examples/archive/scripts/DI HR-MS MassList.py +385 -0
  117. examples/archive/scripts/GC-MS MetabRef.py +213 -0
  118. examples/archive/scripts/GC-MS NetCDF.py +217 -0
  119. examples/archive/scripts/HR-MS Thermo Raw 21T.py +136 -0
  120. examples/archive/scripts/LC-ICPMS_metal_peaks.py +297 -0
  121. examples/archive/scripts/LCMS-Thermo.py +460 -0
  122. examples/archive/scripts/LCMS_isotopes.py +283 -0
  123. examples/archive/scripts/MSParams_example.py +21 -0
  124. examples/archive/scripts/Molecular Formula Data Aggreation.py +84 -0
  125. examples/archive/scripts/Single Mz Search.py +69 -0
  126. examples/test_notebooks.py +145 -0
  127. ext_lib/ChemstationMSFileReader.dll +0 -0
  128. ext_lib/ChemstationMSFileReader.xml +126 -0
  129. ext_lib/RawFileReaderLicense.doc +0 -0
  130. ext_lib/ThermoFisher.CommonCore.BackgroundSubtraction.dll +0 -0
  131. ext_lib/ThermoFisher.CommonCore.BackgroundSubtraction.xml +2307 -0
  132. ext_lib/ThermoFisher.CommonCore.Data.dll +0 -0
  133. ext_lib/ThermoFisher.CommonCore.Data.xml +28974 -0
  134. ext_lib/ThermoFisher.CommonCore.MassPrecisionEstimator.dll +0 -0
  135. ext_lib/ThermoFisher.CommonCore.MassPrecisionEstimator.xml +241 -0
  136. ext_lib/ThermoFisher.CommonCore.RawFileReader.dll +0 -0
  137. ext_lib/ThermoFisher.CommonCore.RawFileReader.xml +31174 -0
  138. ext_lib/__init__.py +0 -0
  139. ext_lib/dotnet/OpenMcdf.Extensions.dll +0 -0
  140. ext_lib/dotnet/OpenMcdf.dll +0 -0
  141. ext_lib/dotnet/OpenMcdf.xml +1154 -0
  142. ext_lib/dotnet/System.IO.FileSystem.AccessControl.dll +0 -0
  143. ext_lib/dotnet/System.IO.FileSystem.AccessControl.xml +506 -0
  144. ext_lib/dotnet/System.Security.AccessControl.dll +0 -0
  145. ext_lib/dotnet/System.Security.AccessControl.xml +2043 -0
  146. ext_lib/dotnet/System.Security.Principal.Windows.dll +0 -0
  147. ext_lib/dotnet/System.Security.Principal.Windows.xml +1011 -0
  148. ext_lib/dotnet/ThermoFisher.CommonCore.BackgroundSubtraction.dll +0 -0
  149. ext_lib/dotnet/ThermoFisher.CommonCore.BackgroundSubtraction.xml +2307 -0
  150. ext_lib/dotnet/ThermoFisher.CommonCore.Data.dll +0 -0
  151. ext_lib/dotnet/ThermoFisher.CommonCore.Data.xml +29148 -0
  152. ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.dll +0 -0
  153. ext_lib/dotnet/ThermoFisher.CommonCore.MassPrecisionEstimator.xml +241 -0
  154. ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.dll +0 -0
  155. ext_lib/dotnet/ThermoFisher.CommonCore.RawFileReader.xml +31492 -0
  156. ext_lib/version +18 -0
  157. support_code/atom_parsers/AtomsDescription.py +359 -0
  158. support_code/atom_parsers/CreateAtomsDescription.py +56 -0
  159. support_code/nmdc/filefinder.py +90 -0
  160. support_code/nmdc/lipidomics/lipidomics_workflow.py +748 -0
  161. support_code/nmdc/lipidomics/manifest_examples.py +49 -0
  162. support_code/nmdc/metabolomics/gcms_workflow.py +158 -0
  163. support_code/nmdc/metabolomics/lcms_metabolomics_targeted_search.py +59 -0
  164. support_code/nmdc/metabolomics/lcms_metabolomics_workflow.py +248 -0
  165. support_code/nmdc/metabolomics/metabolomics_collection.py +628 -0
  166. support_code/nmdc/metadata/dms_api.py +42 -0
  167. support_code/nmdc/nom/archived_scripts/nmdc_metadata_gen.py +288 -0
  168. support_code/nmdc/nom/archived_scripts/nom_grow_workflow.py +209 -0
  169. support_code/nmdc/nom/nom_workflow.py +312 -0
  170. support_code/windows_only_importers/BrukerCompassXtract.py +180 -0
  171. support_code/windows_only_importers/ThermoMSFileReader.py +405 -0
ext_lib/ChemstationMSFileReader.xml ADDED
@@ -0,0 +1,126 @@
1
+ <?xml version="1.0"?>
2
+ <doc>
3
+ <assembly>
4
+ <name>
5
+ ChemstationMSFileReader
6
+ </name>
7
+ </assembly>
8
+ <members>
9
+ <member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.#ctor(System.String)">
10
+ <summary>
11
+ Open the specified data file and read the data headers
12
+ </summary>
13
+ <param name="sDatafilePath">Path to the file to read</param>
14
+ <remarks></remarks>
15
+ </member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.GetSpectrum(System.Int32,ChemstationMSFileReader.clsSpectralRecord@,System.Int32@)">
16
+ <summary>
17
+ Returns the mass spectrum at the specified index
18
+ </summary>
19
+ <param name="intSpectrumIndex">0-based spectrum index</param>
20
+ <param name="oSpectrum">Spectrum object (output)</param>
21
+ <param name="intTotalSignalRawFromIndex">TIC value as reported by the Index; this value has been scaled down by some sort of polynomial transformation</param>
22
+ <returns>True if success, false if an error</returns>
23
+ </member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadHeaders(System.String)">
24
+ <summary>
25
+ Open the data file and read the header sections from the data file
26
+ </summary>
27
+ <param name="sDataFilePath">Path to the file to read</param>
28
+ <returns>True if success, false if an error</returns>
29
+ <remarks>The file handle will remain open until this class is disposed of</remarks>
30
+ </member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadIndexRecords(System.IO.FileStream@)">
31
+ <summary>
32
+ Reads the index entries (aka directory records)
33
+ </summary>
34
+ <param name="fsDatafile"></param>
35
+ <returns>True if success, false if an error</returns>
36
+ </member><member name="M:ChemstationMSFileReader.clsChemstationDataMSFileReader.ReadNormalizationRecords(System.IO.FileStream@)">
37
+ <summary>
38
+ Reads the 10 normalization records from the data file
39
+ </summary>
40
+ <param name="fsDatafile"></param>
41
+ <returns>True if success, false if an error</returns>
42
+ </member><member name="M:ChemstationMSFileReader.clsSpectralRecord.#ctor">
43
+ <summary>
44
+ Instantiate a new spectrum object
45
+ </summary>
46
+ <remarks></remarks>
47
+ </member><member name="M:ChemstationMSFileReader.clsSpectralRecord.#ctor(System.IO.FileStream@,System.Int32)">
48
+ <summary>
49
+ Populate a spectrum object with the data at the specified byte offset
50
+ </summary>
51
+ </member><member name="M:ChemstationMSFileReader.clsSpectralRecord.Clear">
52
+ <summary>
53
+ Initialize the variables and data structures
54
+ </summary>
55
+ <remarks></remarks>
56
+ </member><member name="M:ChemstationMSFileReader.clsSpectralRecord.ReadFromFile(System.IO.FileStream@,System.Int32)">
57
+ <summary>
58
+ Read the spectrum at the specified byte offset
59
+ </summary>
60
+ <param name="fsDatafile"></param>
61
+ <param name="intByteOffsetStart"></param>
62
+ <remarks></remarks>
63
+ </member><member name="M:ChemstationMSFileReader.clsSpectralRecord.ReadPackedAbundance(System.IO.FileStream@)">
64
+ <summary>
65
+ Read packed abundance stored as 2-bit scale with 14 bit mantissa
66
+ </summary>
67
+ <param name="fs">FileStream object</param>
68
+ <returns>Unpacked abundance</returns>
69
+ </member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadInt16SwapBytes(System.IO.FileStream@)">
70
+ <summary>
71
+ Reads an Int16 from the filestream
72
+ Swaps bytes prior to converting
73
+ </summary>
74
+ <param name="fs">FileStream object</param>
75
+ <returns>The value, as an Int16 number</returns>
76
+ </member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadUInt16SwapBytes(System.IO.FileStream@)">
77
+ <summary>
78
+ Reads an UInt16 from the filestream
79
+ Swaps bytes prior to converting
80
+ </summary>
81
+ <param name="fs">FileStream object</param>
82
+ <returns>The value, as an Int32 number</returns>
83
+ </member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadInt32SwapBytes(System.IO.FileStream@)">
84
+ <summary>
85
+ Reads an Int32 from the filestream
86
+ Swaps bytes prior to converting
87
+ </summary>
88
+ <param name="fs">FileStream object</param>
89
+ <returns>The value, as an Int32 number</returns>
90
+ </member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadSingleSwapBytes(System.IO.FileStream@)">
91
+ <summary>
92
+ Reads a 4-byte single (real) from the filestream
93
+ Swaps bytes prior to converting
94
+ </summary>
95
+ <param name="fs">FileStream object</param>
96
+ <returns>The value, as a single-precision number</returns>
97
+ </member><member name="M:ChemstationMSFileReader.clsByteConverter.ReadString(System.IO.FileStream@,System.Int32,System.Boolean)">
98
+ <summary>
99
+ Reads a fixed-length string from the filestream
100
+ Optionally advances the reader one byte after reading the string
101
+ </summary>
102
+ <param name="fs">FileStream object</param>
103
+ <param name="iStringLength">String length</param>
104
+ <param name="bAdvanceExtraByte">If true, then advances the read an extra byte after reading the string</param>
105
+ <returns>The string read</returns>
106
+ </member><member name="M:ChemstationMSFileReader.clsByteConverter.WordOffsetToBytes(System.Int32)">
107
+ <summary>
108
+ Convert byte-offset stored in words into bytes
109
+ </summary>
110
+ <param name="iOffsetWords"></param>
111
+ <returns>The byte offset, in bytes</returns>
112
+ </member><member name="M:ChemstationMSFileReader.clsDataHeader.#ctor(System.IO.FileStream@)">
113
+ <summary>
114
+ Read header from the specified file
115
+ </summary>
116
+ <param name="fsDatafile"></param>
117
+ <remarks></remarks>
118
+ </member><member name="M:ChemstationMSFileReader.clsDataHeader.ReadFromFile(System.IO.FileStream@)">
119
+ <summary>
120
+ Read header from the specified file
121
+ </summary>
122
+ <param name="fs">Input file stream</param>
123
+ <returns>True if success, false if an error</returns>
124
+ </member>
125
+ </members>
126
+ </doc>
ext_lib/RawFileReaderLicense.doc ADDED
Binary file