diff --git a/LICENSE b/LICENSE index 9e0ecdf..b451fbf 100644 --- a/LICENSE +++ b/LICENSE @@ -2,14 +2,14 @@ Canopy™ -Copyright © 2020 SomaLogic, Inc. +Copyright © 2022 SomaLogic Operating Company, Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of the Canopy software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions outlined below. Further, Canopy and SomaLogic are trademarks -owned by SomaLogic, Inc. No license is hereby granted to these trademarks other than for purposes of +owned by SomaLogic Operating Company, Inc. No license is hereby granted to these trademarks other than for purposes of identifying the origin or source of the Software. The above copyright notice and this permission notice shall be included in all copies or substantial diff --git a/README.md b/README.md index 3bf373b..55b9de9 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://choosealicense. ## Overview -This document accompanies the Python package `canopy`, which loads the SomaLogic, Inc. proprietary data file called an `*.adat`. The package provides auxiliary functions for extracting relevant information from the ADAT object once in the Python environment. Basic familiarity with the Python environment is assumed, as is the ability to install contributed packages from the Python Package Installer (pip) +This document accompanies the Python package `canopy`, which loads the SomaLogic Operating Company, Inc. proprietary data file called an `*.adat`. The package provides auxiliary functions for extracting relevant information from the ADAT object once in the Python environment. Basic familiarity with the Python environment is assumed, as is the ability to install contributed packages from the Python Package Installer (pip) ----- diff --git a/canopy/annotations.py b/canopy/annotations.py new file mode 100644 index 0000000..93b21ae --- /dev/null +++ b/canopy/annotations.py @@ -0,0 +1,185 @@ +from __future__ import annotations +import pandas as pd +from canopy import Adat +from . import errors +from copy import deepcopy +import re + + +LIFTING_COLUMN_REGEX = r'\w+ Scalar v\d+.\d+ to v\d+.\d+' + + +class Annotations(pd.DataFrame): + """A Pandas `DataFrame` object with additional functionality to help with annotations specific needs. + + + Modeled after: + https://github.com/geopandas + + On subclassing the pandas dataframe: + https://pandas.pydata.org/pandas-docs/stable/development/extending.html#subclassing-pandas-data-structures + """ + + _metadata = [ + 'supported_lifting_matrices', + 'supported_lifting_signal_space', + ] + + def __init__(self, *args, **kwargs) -> None: + super(Annotations, self).__init__(*args, **kwargs) + self._update_supported_lifting_options() + + @property + def _constructor(self) -> Adat: + self._update_supported_lifting_options() + return Annotations + + def __setitem__(self, key, val): + super().__setitem__(key, val) + if re.match(LIFTING_COLUMN_REGEX, key): + self._update_supported_lifting_options() + + def __delitem__(self, key) -> None: + super().__delitem__(key) + if re.match(LIFTING_COLUMN_REGEX, key): + self._update_supported_lifting_options() + + def _update_supported_lifting_options(self): + self.supported_lifting_matrices = set() + self.supported_lifting_signal_space = set() + + for name in self.columns: + if re.match(LIFTING_COLUMN_REGEX, name): + supported_info = name.split(' ') + self.supported_lifting_matrices.add(supported_info[0]) + self.supported_lifting_signal_space.add((supported_info[2], supported_info[4])) + + def update_adat_column_meta(self, adat: Adat) -> Adat: + """Utility to update a provided adat's column metadata to match the annotations object. + + Attempts to update the following column metadata in the adat: + - SomaId + - Target + - TargetFullName + - UniProt + - Type + - Organism + - EntrezGeneSymbol + - ExtrezGeneID + + Parameters + ---------- + adat : Adat + Canopy Adat object + + Returns + ------- + updated_adat : Adat + Canopy Adat object with updated column metadata + + Examples + -------- + >>> updated_adat = Annotations.update_adat_column_meta(adat) + """ + + xlsx_to_adat_column_map = { + 'SomaId': 'SomaId', + 'Target Name': 'Target', + 'Target Full Name': 'TargetFullName', + 'UniProt ID': 'UniProt', + 'Type': 'Type', + 'Organism': 'Organism', + 'Entrez Gene Name': 'EntrezGeneSymbol', + 'Entrez Gene ID': 'EntrezGeneID', + } + + seq_ids = self.index.get_level_values('SeqId') + mod_adat = adat.copy() + for xlsx_col, adat_col in xlsx_to_adat_column_map.items(): + if adat_col not in adat.columns.names: + continue + values_dict = {seq_id: col_meta for seq_id, col_meta in zip(seq_ids, self[xlsx_col].values)} + mod_adat = mod_adat.replace_keyed_meta( + axis=1, + replaced_meta_name=adat_col, + key_meta_name='SeqId', + values_dict=values_dict + ) + return mod_adat + + def supported_lifting_space_str(self): + ret_str = '' + for space in self.supported_lifting_signal_space: + ret_str += f'from "{space[0]}" to "{space[1]}"' + return ret_str + + def lift_adat(self, adat: Adat, lift_to_version: str = None) -> Adat: + """Utility to perform lifting on an adat. + + Parameters + ---------- + adat : Adat + Canopy Adat object + + Returns + ------- + lifted_adat : Adat + Canopy Adat object with scaled RFU + + Examples + -------- + >>> lifted_adat = Annotations.lift_adat(adat=adat) + """ + self._update_supported_lifting_options() + + # Perform checks to see if this bridging is appropriate for this adat + adat = adat.copy() + process_steps = adat.header_metadata['!ProcessSteps'] + scalable_norm_steps = 'Raw RFU, Hyb Normalization, medNormInt (SampleId), plateScale, Calibration, anmlQC, qcCheck, anmlSMP' + if not process_steps.startswith(scalable_norm_steps): + raise errors.AnnotationsLiftingError(f'ANML normalized SOMAscan data is required for lifting. Provided norm steps: "{process_steps}"') + + # Get matrix from adat header metdata + matrix = adat.header_metadata['StudyMatrix'] + if matrix == 'EDTA Plasma': # Takes care of the EDTA Plasma --> Plasma conversion so we can look up the column in the annotations df + matrix = 'Plasma' + if matrix not in self.supported_lifting_matrices: + raise errors.AnnotationsLiftingError(f'Unsupported matrix: "{matrix}". Supported matrices: {", ".join(self.supported_lifting_matrices)}.') + + # Get assay version from adat header metadata. Prefer SignalSpace (created by lifting apps) if it exists + if 'SignalSpace' in adat.header_metadata: + signal_space = adat.header_metadata['SignalSpace'] + else: + signal_space = adat.header_metadata['!AssayVersion'] + if signal_space.lower() == 'v4': # Takes care of the v4 and V4 --> v4.0 conversion so we can look up the column in the annotations df + signal_space = 'v4.0' + + # Check to see if we can perform this lifting with the assay version(s) provided + if lift_to_version: + if (signal_space, lift_to_version) not in self.supported_lifting_signal_space: + raise errors.AnnotationsLiftingError(f'Unsupported lifting from "{signal_space}" to "{lift_to_version}". Supported lifting: {self.supported_lifting_space_str()}.') + else: + possible_lifts = [lift for lift in self.supported_lifting_signal_space if lift[0] == signal_space] + if not possible_lifts: + raise errors.AnnotationsLiftingError(f'Unsupported lifting from: "{signal_space}". Supported lifting: {self.supported_lifting_space_str()}.') + elif len(possible_lifts) > 1: + raise errors.AnnotationsLiftingError(f'Too many lifting options. Please provide a value for the argument "lift_to_version". Supported lifting: {self.supported_lifting_space_str()}.') + else: + lift_to_version = possible_lifts[0][1] + + # Build column name & get scalars + an_lifting_column = f'{matrix} Scalar {signal_space} to {lift_to_version}' + scalars = self[an_lifting_column] + + # Check if seq ids will broadcast between adat & annotations (symmetric difference) + sym_diff = set(scalars.index) ^ set(adat.columns.get_level_values('SeqId')) + if sym_diff: + raise errors.AnnotationsLiftingError('Unable to perform lifting due to analyte mismatch between adat & annotations. Has either file been modified?') + + # Scale adat + scaled_adat = adat.multiply(scalars, axis='columns', level='SeqId') + scaled_adat.header_metadata = deepcopy(adat.header_metadata) + scaled_adat.header_metadata['!ProcessSteps'] += f', Annotation Lift ({signal_space} to {lift_to_version})' + scaled_adat.header_metadata['SignalSpace'] = lift_to_version + + return scaled_adat diff --git a/canopy/base/adat_math_helpers.py b/canopy/base/adat_math_helpers.py index cb83628..e18dc0f 100644 --- a/canopy/base/adat_math_helpers.py +++ b/canopy/base/adat_math_helpers.py @@ -1,31 +1,25 @@ import numpy as np import pandas as pd +def calcELOD(x:pd.Series): # x is a pandas series + med = np.median(x) + absDiff = np.abs(x-med) + medDiff = np.median(absDiff) + eLOD = med+3*(1.4826*medDiff) + return eLOD + class AdatMathHelpers: """A collection of methods to help with performing common and standard computations on the adat. """ - def e_lod(self, groupby=None): - """Computes estimated limit of detection of the buffer samples by plate as defined by median(somamer_rfu) + 4.9 * mad(somamer_rfu). - - Parameters - ---------- - groupby : List(str) - - Returns - ------- - e_lod_df : pd.DataFrame - - Examples - -------- - >>> e_lod_df = adat.e_lod() - >>> e_lod_df = adat.e_lod(groupby='SampleId') - """ - groupby = groupby or 'PlateId' - e_lod_df = self.groupby(groupby).apply(lambda x: x.median() + 4.9 * x.mad()) + def e_lod_by_reagent(self): + df = self.pick_on_meta(axis=0, name='SampleType', values=['Buffer']) + df.columns = df.columns.get_level_values('SeqId') + e_lod_df = df.apply(calcELOD) return e_lod_df + @staticmethod def _compute_intra_cv(adat, groupby): sums = {} diff --git a/docs/source/conf.py b/docs/source/conf.py index 52e0fe0..649903e 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -19,8 +19,8 @@ # -- Project information ----------------------------------------------------- project = 'canopy' -copyright = '2020, SomaLogic' -author = 'SomaLogic, Inc.' +copyright = '2022, SomaLogic Operating Company, Inc' +author = 'SomaLogic Operating Company, Inc.' # The full version, including alpha/beta/rc tags release = pkg_resources.require('canopy')[0].version diff --git a/setup.py b/setup.py index ee6bc5a..50e4f2f 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ setup( name='canopy', python_requires='>3.8.0', - version='0.3', + version='0.4', packages=find_packages(), url='http://confluence.sladmin.com/display/INGEN/Canopy', license='', diff --git a/tests/data/control_data.adat b/tests/data/control_data.adat index 039f0cf..905e45c 100644 --- a/tests/data/control_data.adat +++ b/tests/data/control_data.adat @@ -1,4 +1,4 @@ -!Checksum 7463a71b89e9aaea981d2ab0dfb7af9cf9118456 +!Checksum ^HEADER AdatId GID-bdac44fe-cdd7-4fc0-a1d1-f62df3fe34d4 !Version 1.2 @@ -8,17 +8,15 @@ AdatId GID-bdac44fe-cdd7-4fc0-a1d1-f62df3fe34d4 !Legal SOMALOGIC - CONFIDENTIAL INFORMATION !CreatedBy PharmaServices !CreatedDate 2020-02-06 -!EnteredBy ekasyon !ExpDate 2019-12-08 !GeneratedBy Px (Build: : ) Notes None !ProcessSteps Raw RFU, Hyb Normalization, medNormInt (SampleId), plateScale, Calibration, anmlQC, qcCheck, anmlSMP, Filtered !ProteinEffectiveDate 2020-02-06 -RunNotes None StudyMatrix EDTA Plasma PlateType Prod LabLocation SLUS -StudyOrganism +StudyOrganism !Title P0024405 AssaySite V4 CalibratorId 170261 @@ -69,7 +67,7 @@ PlateTailTest_P0024405 PASS QcReference_170259 460.4 221.1 117.7 697.0 515.5 2553.7 1622.8 492.9 911.1 433.7 856.7 192.5 488.2 799.2 220.5 3163.5 574.3 3543.3 244.2 354.7 49026.0 715.3 434.1 939.6 412.6 839.9 1810.6 1814.3 447.0 3004.9 421.5 738.9 4673.6 512.9 1469.8 551.7 493.1 790.7 119.0 878.9 619.1 418.9 565.2 1068.0 2615.6 1728.5 374.2 392.0 346.0 486.0 7610.8 331.5 4009.7 4842.4 1645.3 365.1 319.6 2963.2 1234.3 974.2 2034.9 197.7 449.7 2365.5 512.8 945.3 287.1 1091.6 2018.9 6069.1 479.5 579.0 141.7 1065.8 2261.3 128.0 115.6 640.2 1120.7 1285.1 269.8 807.6 2375.5 2563.4 2298.0 844.9 94.7 191.5 335.7 186.8 302.9 1202.5 704.8 469.2 10783.0 163.7 27.9 149.8 3473.5 2080.9 200.1 148.6 517.0 359.0 176.3 16.7 636.5 761.7 285.7 978.9 181.1 146.1 198.2 237.9 808.0 12640.2 57.4 76.8 388.0 8438.1 299.7 327.3 294.5 1550.9 202.7 240.6 183.9 460.4 676.3 379.5 1831.8 402.8 3077.2 376.8 2022.6 19.9 2295.1 3987.9 188.5 574.0 916.6 127.0 2367.1 920.9 393.1 10993.2 1933.4 4825.7 309.5 326.0 200.7 5076.4 240.5 381.6 45.0 6581.5 1862.0 155.1 3341.1 28.7 552.3 826.5 1771.0 1869.6 1849.9 395.6 423.8 7665.2 249.6 127.6 359.6 264.8 947.0 751.4 243.9 155.3 2418.7 308.2 1675.6 3574.7 1424.8 46.6 438.6 126.9 243.2 126.7 384.4 1159.5 684.4 151.0 763.5 230.0 320.5 169.3 3685.1 4588.8 682.5 316.1 332.3 1401.9 1629.7 4198.4 618.4 162.3 207.7 187.4 65.0 118.8 903.9 4599.4 707.4 7572.5 2110.6 1327.3 1443.0 887.4 3986.2 515.3 3042.9 768.6 13853.0 1691.3 895.7 2975.5 12460.6 565.8 896.6 745.9 390.2 4690.1 798.4 110.8 463.9 770.4 2900.1 349.8 890.7 270.4 5665.1 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0.000 0.000 QcReference_170260 619.2 211.0 153.7 621.0 550.2 2413.0 1792.6 538.8 834.8 465.9 801.6 175.7 538.5 886.9 252.3 3364.2 572.8 3081.8 392.6 402.0 54561.5 754.3 547.3 941.7 398.8 756.4 524.2 1512.8 513.9 1694.0 270.9 693.7 3879.0 482.8 1393.8 502.9 453.8 700.0 99.6 878.9 632.4 499.5 640.6 516.3 2519.4 1656.0 457.0 265.9 315.5 458.2 5056.4 370.8 4082.1 4039.5 1642.5 373.9 312.7 2354.7 1004.3 1098.0 1837.2 190.0 319.1 2054.4 466.0 1186.9 232.7 1134.1 1702.8 5333.7 518.5 560.5 161.1 1620.7 2448.9 181.4 152.2 633.1 1250.0 1143.6 276.5 873.8 2018.1 2878.3 2151.5 926.1 99.2 142.1 367.3 197.4 314.9 1221.1 371.1 421.3 7580.3 197.4 29.9 307.9 2744.3 2122.4 247.8 174.7 400.2 423.2 186.1 16.9 492.3 813.7 312.5 1101.8 218.7 161.9 248.6 814.6 778.6 13144.2 63.7 106.7 363.8 9074.9 326.4 305.4 319.7 1296.1 205.2 227.4 146.8 515.1 791.6 665.9 2555.5 496.9 8265.1 348.1 2153.7 18.6 2458.3 3648.7 199.2 574.2 847.5 142.2 1965.0 859.4 410.6 12051.4 1072.3 5111.3 324.3 315.4 179.0 5702.1 259.1 1230.7 50.7 7428.3 1221.0 177.2 4953.2 31.4 412.9 915.5 1820.8 1696.3 1508.8 360.1 567.4 7361.0 850.5 145.1 413.6 278.0 771.9 842.5 311.2 155.8 2719.0 261.6 1471.9 4203.6 1373.7 50.7 450.8 145.5 186.5 124.7 387.9 956.6 603.1 174.2 616.0 213.8 494.1 194.5 3336.4 3245.5 2184.4 332.9 267.2 568.4 1538.1 5425.9 598.0 125.9 224.9 246.9 70.6 124.1 470.8 4561.7 837.8 7432.7 2067.4 3654.8 1196.2 1035.1 3997.7 551.4 2424.5 586.2 478.0 1928.7 1005.4 2277.8 4803.5 581.9 1336.8 886.1 277.8 5439.2 812.2 104.0 498.9 642.6 2558.8 513.6 1108.4 299.7 475.4 3333.8 916.1 1969.0 672.4 246.0 442.1 1214.5 638.8 583.1 778.8 1104.2 420.9 22608.5 3367.0 8365.3 723.8 1943.1 902.3 1334.2 91.3 724.5 885.2 1469.7 921.7 923.0 1059.0 1534.0 10791.1 802.9 593.3 1261.2 4575.7 329.3 76.1 447.0 959.5 1399.4 316.0 894.4 234.2 2693.2 260.3 518.3 907.9 470.6 1369.9 294.8 1063.6 735.7 1510.3 568.7 1067.1 307.0 403.4 2565.1 1714.8 296.6 5341.6 736.7 1742.8 301.5 290.5 22552.5 555.4 5317.7 2839.9 484.9 1695.4 436.4 322.3 4740.4 1251.8 8785.6 1981.1 483.9 351.6 568.8 870.3 1017.2 722.1 294.3 497.1 807.0 4134.4 1339.4 830.5 1166.2 491.4 572.9 570.0 288.5 1009.7 6314.0 334.9 325.5 3417.8 595.2 1384.3 319.7 259.8 1389.5 2193.1 993.3 612.7 693.5 535.6 1814.9 847.5 1695.8 1565.6 707.4 4705.8 685.5 304.6 5024.0 746.3 2689.4 265.9 261.0 2866.3 798.3 245.6 548.7 2087.4 9070.0 571.8 8618.9 1090.1 4930.1 14255.8 5534.0 292.0 4389.9 901.9 419.3 364.6 698.8 1832.4 559.8 1483.6 1133.5 388.2 160.4 1921.1 478.6 2634.5 242.0 3066.4 752.1 632.7 1518.2 679.7 1482.5 1307.3 295.1 198.1 9851.4 289.6 532.5 4496.2 1133.1 333.2 597.7 9855.8 7557.5 330.0 512.9 2038.1 698.4 459.8 554.1 775.2 1046.9 613.6 593.4 872.8 1132.4 327.3 681.1 1374.3 957.6 1359.0 819.1 623.0 629.7 1034.1 685.4 3212.9 813.6 413.8 369.4 2145.0 200.4 1214.0 4314.1 441.0 355.2 206.1 145.0 6947.6 1029.1 626.7 180.9 288.1 2708.9 571.3 255.1 291.1 791.3 3516.4 595.1 1892.4 332.2 8486.7 2380.7 354.4 439.1 1881.4 345.1 1850.4 244.4 1030.9 213.4 1049.0 922.3 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SlideId Subarray SampleId SampleType PercentDilution SampleMatrix Barcode Barcode2d SampleName SampleNotes AliquotingNotes SampleDescription AssayNotes TimePoint ExtIdentifier SsfExtId SampleGroup SiteId TubeUniqueID CLI HybControlNormScale RowCheck NormScale_20 NormScale_0_005 NormScale_0_5 ANMLFractionUsed_20 ANMLFractionUsed_0_005 ANMLFractionUsed_0_5 P0024405 2019-12-08 SG17164580 H8 258495839385 8 170261 Calibrator 20 J284771 0334409388 Pooled Plasma Tube Calibrator Pooled Plasma Calibrator - commercially supplied - 80 individuals EXID40000003624423 EID303533 0.99446784 PASS 0.98027112 1.00000000 0.98795553 704.6 223.7 148.0 627.3 585.0 2835.3 1645.5 499.6 883.8 443.3 936.4 205.2 489.2 851.9 193.1 3555.6 569.7 3029.0 204.2 476.3 34649.9 745.5 452.3 868.8 581.3 942.9 487.5 1525.1 479.8 1167.1 347.0 745.1 8880.1 447.4 1391.1 481.7 491.0 748.7 103.7 980.3 608.3 707.5 566.5 742.0 1396.3 1906.3 374.5 277.6 448.9 734.2 6681.0 393.5 4079.9 3999.7 1613.5 381.5 561.7 2568.8 1294.3 862.5 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56.2 82.7 52.1 90.1 45.0 34.6 275.2 108.7 81.9 32.8 77.0 43.4 104.2 99.7 43.5 39.9 159.8 89.0 191.0 85.4 99.4 71.1 96.5 97.5 87.2 134.2 147.7 87.1 158.5 68.7 80.2 462.2 54.2 387.6 76.8 47.5 93.0 97.5 61.8 142.3 64.4 76.9 76.5 29.1 88.9 83.5 27.4 65.9 58.3 67.0 56.7 49.0 37.0 43.6 53.2 92.5 102.9 41.1 96.1 42.8 31.2 26.0 58.8 130.8 134.1 99.8 42.3 71.3 46.2 80.4 82.8 31.9 70.9 58.7 92.9 29.0 74.3 62.1 73.9 122.1 51.3 135.7 66.8 17.9 46.7 22.7 100.5 69.6 137.3 13.5 78.8 61.2 42.1 111.9 48.1 43.2 51.5 45.2 49.9 57.8 60.8 127.4 50.3 76.7 68.7 67.2 101.8 66.6 123.7 40.7 47.0 51.3 102.4 85.7 73.5 76.0 183.9 99.1 67.9 37.2 57.5 36.3 33.2 47.1 57.2 65.8 53.1 85.7 93.3 77.1 68.9 54.8 44.6 48.1 67.2 91.6 86.2 65.1 65.0 47.9 37.1 96.9 62.2 219.0 49.4 73.3 64.1 68.4 58.1 85.6 167.2 102.4 48.9 79.4 111.8 23.6 68.9 54.7 21.7 119.5 67.3 28.4 135.7 67.2 41.4 34.2 86.4 89.9 54.5 22.3 35.3 40.4 35.5 117.4 98.4 71.0 39.3 90.6 66.0 139.2 124.3 74.8 56.8 18.3 76.2 76.2 58.2 70.6 70.4 32.3 25.7 84.9 51.8 50.2 26.5 21.8 40.2 38.5 62.4 21.4 91.2 84.2 27.8 133.2 70.8 44.3 32.7 24.6 37.5 53.2 47.4 42.1 46.1 59.6 57.7 48.4 59.1 85.5 93.9 114.4 105.2 97.8 140.4 133.2 17.7 42.8 52.5 170.5 27.6 118.5 31.0 173.0 78.0 63.2 112.5 187.9 34.9 27.0 96.8 64.7 84.9 155.5 271.1 116.0 68.8 33.9 104.4 121.4 68.5 54.4 51.2 35.0 46.8 66.0 50.7 208.1 74.0 95.8 83.0 46.5 41.6 75.6 123.6 87.6 109.8 76.8 170.0 53.6 28.0 501.7 73.6 134.0 40.8 135.7 5.8 90.6 42.8 60.8 50.0 135.6 133.0 68.6 84.5 49.2 34.8 94.2 81.0 65.6 50.1 68.0 28.3 58.2 92.6 126.3 98.4 65.0 9.8 96.2 45.5 79.9 41.4 58.4 165.5 47.1 112.3 83.8 83.2 109.4 53.5 66.1 53.5 71.2 12.6 119.8 36.7 146.1 72.5 17.5 80.9 133.8 23.2 95.7 64.5 141.9 58.4 98.5 64.0 83.6 105.7 97.0 53.6 100.4 26.8 62.3 67.2 75.9 126.7 51.2 104.1 93.3 239.6 32.6 160.1 83.6 85.7 237.0 51.5 157.1 20.7 203.6 63.2 43.9 105.1 98.8 91.2 165.8 98.1 120.7 56.9 115.5 41.7 91.9 89.0 114.1 80.5 41.4 156.0 48.6 133.9 71.7 49.8 124.9 45.5 142.8 120.7 235.4 179.9 52.0 83.4 P0024405 2019-12-08 SG17164580 G7 258495839384 7 170255 QC 20 J278170 0311197582 QC Plasma Sample Plasma QC 1 EXID40000003624669 EID303524 1.01057233 PASS 1.30364325 1.16277698 1.19566476 0.817 0.938 0.836 498.0 227.7 118.5 643.9 598.8 2515.0 1173.0 409.6 1164.8 445.3 741.9 200.6 425.2 689.2 199.7 2450.7 546.6 2822.7 162.2 1119.6 44437.2 727.8 514.2 798.4 455.4 749.6 7861.0 1444.0 475.0 1854.7 372.1 743.9 3999.3 432.7 1483.0 583.0 584.0 785.1 113.5 868.2 573.3 447.9 448.7 744.8 1690.3 2173.8 1707.5 327.2 432.2 695.0 9041.9 321.1 3086.0 4779.7 1445.2 388.6 345.5 2607.7 1002.8 946.3 1819.6 206.8 403.5 2415.1 382.9 963.2 282.5 816.9 1856.0 7271.3 453.7 567.5 119.2 1100.4 1941.5 140.0 124.4 725.0 1170.2 1307.7 269.7 783.8 2693.3 1643.6 2559.2 534.6 97.8 143.4 357.7 177.4 338.4 1341.2 338.4 403.6 9310.2 1990.0 95.6 110.9 4082.0 1176.4 214.2 154.7 617.4 288.6 265.8 41.7 369.1 606.8 198.0 1052.2 178.9 158.3 755.3 260.3 566.3 14471.4 61.0 90.9 442.3 3913.4 218.2 251.6 295.5 2070.3 152.1 216.9 99.5 410.4 513.1 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492.6 11473.1 6558.0 740.2 369.2 1471.4 288.2 274.8 290.2 3305.1 332.6 731.0 2439.0 1583.7 574.0 1044.5 172.0 1936.0 1487.6 519.8 585.1 1397.4 1389.0 382.2 500.9 9269.6 712.8 1636.0 342.9 521.7 1705.9 1142.1 3378.8 1449.0 512.6 3166.2 3022.5 2835.9 814.5 556.1 535.5 1058.8 570.3 590.7 1420.7 6267.8 305.4 389.0 9682.0 533.2 1660.8 3480.1 228.9 1082.4 285.0 2146.6 181.6 555.2 3814.3 6242.0 673.2 765.9 1172.8 682.3 5039.8 874.3 4239.1 1495.8 89.7 2384.0 374.8 2385.8 204.9 121.4 884.1 2897.6 123.7 543.9 2177.7 674.5 2144.9 1221.9 275.1 1621.3 441.2 1026.5 1458.7 630.1 2828.1 608.4 1646.9 329.4 381.7 4662.3 1020.0 2805.8 1401.3 385.2 1717.3 451.5 1310.6 2109.3 296.8 582.3 476.1 1308.5 1049.4 334.6 2462.1 732.4 1878.2 1450.4 391.7 690.7 496.0 3344.4 509.5 1142.0 1311.2 2013.5 7431.1 665.1 5126.2 1248.6 3435.2 690.1 419.5 571.0 2886.9 466.3 867.1 1686.4 988.9 5448.8 1079.8 diff --git a/tests/test_adat_reading.py b/tests/test_adat_reading.py index cc30e05..e96db66 100644 --- a/tests/test_adat_reading.py +++ b/tests/test_adat_reading.py @@ -55,7 +55,7 @@ def test_column_metadata_names(self): ]) def test_header_metadata_size(self): - self.assertEqual(len(self.adat.header_metadata.keys()), 40) + self.assertEqual(len(self.adat.header_metadata.keys()), 38) def test_header_metadata_spot_check(self): self.assertEqual(self.adat.header_metadata['HybNormReference'], 'intraplate') diff --git a/tests/test_adat_writing.py b/tests/test_adat_writing.py index 7afa4d0..f35410b 100644 --- a/tests/test_adat_writing.py +++ b/tests/test_adat_writing.py @@ -7,7 +7,7 @@ def require_side_effect(*args, **kwargs): class Version(): - version = '0.0.1' + version = '0.2.1' return [Version()] @@ -16,8 +16,12 @@ class AdatWritingTest(TestCase): """ filename = './tests/data/control_data_written.adat' + source_filename = './tests/data/control_data.adat' def setUp(self): + self.source_md5 = hashlib.md5() + with open(self.source_filename, 'rb') as f: + self.source_md5.update(f.read()) self.adat = canopy.read_adat('./tests/data/control_data.adat') def tearDown(self): @@ -34,7 +38,7 @@ def test_adat_md5(self): hash_md5 = hashlib.md5() with open(self.filename, 'rb') as f: hash_md5.update(f.read()) - self.assertEqual(hash_md5.hexdigest(), '58d675e7e43cc4e142ff94ac6efdfd94') + self.assertEqual(hash_md5.hexdigest(), 'e288d94404e1e30a2138b188daa9a7e9') def require_side_effect_0_2(*args, **kwargs): diff --git a/tests/test_annotation_lifting.py b/tests/test_annotation_lifting.py new file mode 100644 index 0000000..0b6ad4e --- /dev/null +++ b/tests/test_annotation_lifting.py @@ -0,0 +1,98 @@ +from unittest import TestCase +from canopy import Annotations, Adat +from canopy.errors import AnnotationsLiftingError +from io import StringIO +import pandas as pd + + +def build_annotation_example(): + s = StringIO('SeqId,SomaId,Plasma Scalar v4.0 to v4.1\n54321-21,SL054321,0.8\n12345-12,SL012345,1.1\n') + df = pd.read_csv(s, index_col=[0]) + return Annotations(data=df.values, index=df.index, columns=df.columns) + + +def build_good_example_adat(): + rfu_data = [[1, 2], [4, 5]] + col_metadata = {'SeqId': ['12345-12', '54321-21'], 'SeqIdVersion': ['1', '2'], 'ColCheck': ['PASS', 'FLAG']} + row_metadata = {'PlateId': ['A12', 'A12'], 'Barcode': ['SL1234', 'SL1235']} + header_metadata = { + 'AdatId': '1a2b3c', + '!ProcessSteps': 'Raw RFU, Hyb Normalization, medNormInt (SampleId), plateScale, Calibration, anmlQC, qcCheck, anmlSMP', + 'StudyMatrix': 'EDTA Plasma', + '!AssayVersion': 'v4.0', + } + return Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata) + + +def build_example_adat_with_extra_somamers(): + rfu_data = [[1, 2, 3], [4, 5, 6]] + col_metadata = {'SeqId': ['12345-12', '54321-21', '23456-78'], 'SeqIdVersion': ['1', '2', '3'], 'ColCheck': ['PASS', 'FLAG', 'FLAG']} + row_metadata = {'PlateId': ['A12', 'A12'], 'Barcode': ['SL1234', 'SL1235']} + header_metadata = { + 'AdatId': '1a2b3c', + '!ProcessSteps': 'Raw RFU, Hyb Normalization, medNormInt (SampleId), plateScale, Calibration, anmlQC, qcCheck, anmlSMP', + 'StudyMatrix': 'EDTA Plasma', + '!AssayVersion': 'v4.0', + } + return Adat.from_features(rfu_data, row_metadata, col_metadata, header_metadata) + + +class AdatLiftingTestCase(TestCase): + def setUp(self): + self.an = build_annotation_example() + self.adat = build_good_example_adat() + + def test_lifting_correct(self): + lifted_adat = self.an.lift_adat(self.adat) + correct_lifted_values = [[1.1, 1.6], [4.4, 4]] + for correct_row, lifted_row in zip(correct_lifted_values, lifted_adat.values): + for correct_value, lifted_value in zip(correct_row, lifted_row): + self.assertAlmostEqual(correct_value, lifted_value) + + self.assertEqual(lifted_adat.header_metadata['SignalSpace'], 'v4.1') + self.assertTrue(lifted_adat.header_metadata['!ProcessSteps'].endswith(', Annotation Lift (v4.0 to v4.1)')) + + def test_orig_adat_unmodified(self): + self.an.lift_adat(self.adat) + + orig_values = [[1, 2], [4, 5]] + for orig_row, adat_row in zip(orig_values, self.adat.values): + for orig_value, adat_value in zip(orig_row, adat_row): + self.assertAlmostEqual(orig_value, adat_value) + + self.assertNotIn('SignalSpace', self.adat.header_metadata) + self.assertFalse(self.adat.header_metadata['!ProcessSteps'].endswith(', Annotation Lift (v4.0 to v4.1)')) + + def test_lifting_matrix_error(self): + self.adat.header_metadata['StudyMatrix'] = 'NotSupportedMatrix' + with self.assertRaises(AnnotationsLiftingError) as cm: + self.an.lift_adat(self.adat) + e_msg = str(cm.exception) + self.assertEqual(e_msg, 'Unsupported matrix: "NotSupportedMatrix". Supported matrices: Plasma.') + + def test_lifting_assay_version_error(self): + self.adat.header_metadata['!AssayVersion'] = 'NotSupportedVersion' + with self.assertRaises(AnnotationsLiftingError) as cm: + self.an.lift_adat(self.adat) + e_msg = str(cm.exception) + self.assertEqual(e_msg, 'Unsupported lifting from: "NotSupportedVersion". Supported lifting: from "v4.0" to "v4.1".') + + def test_lifting_signal_space_error(self): + self.adat.header_metadata['SignalSpace'] = 'NotSupportedVersion' + with self.assertRaises(AnnotationsLiftingError) as cm: + self.an.lift_adat(self.adat) + e_msg = str(cm.exception) + self.assertEqual(e_msg, 'Unsupported lifting from: "NotSupportedVersion". Supported lifting: from "v4.0" to "v4.1".') + + def test_lifting_to_space_error(self): + with self.assertRaises(AnnotationsLiftingError) as cm: + self.an.lift_adat(self.adat, lift_to_version='NotSupportedVersion') + e_msg = str(cm.exception) + self.assertEqual(e_msg, 'Unsupported lifting from "v4.0" to "NotSupportedVersion". Supported lifting: from "v4.0" to "v4.1".') + + def test_analyte_mismatch(self): + self.adat = build_example_adat_with_extra_somamers() + with self.assertRaises(AnnotationsLiftingError) as cm: + self.an.lift_adat(self.adat) + e_msg = str(cm.exception) + self.assertEqual(e_msg, 'Unable to perform lifting due to analyte mismatch between adat & annotations. Has either file been modified?')