From ff03c82e1a5ca4e2cc5452088fee49f0674061e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tom=C3=A1=C5=A1=20Houfek?= Date: Wed, 16 Oct 2024 06:55:47 +0200 Subject: [PATCH] Added nextseq pseudonymization --- pseudonymization/helpers/file_helpers.py | 30 ---------- pseudonymization/process/processor.py | 14 ++++- .../pseudonymizers/nextseq_pseudonymizer.py | 47 +++++++++++++-- .../removers/new_miseq_remover.py | 2 - pseudonymization/removers/nextseq_remover.py | 22 ++++++- tests/next_seq_test_run/CopyComplete.txt | 0 .../Intensities/BaseCalls/L001/0001.bcl.bgzf | 0 .../BaseCalls/L001/0001.bcl.bgzf.bci | 0 .../Intensities/BaseCalls/L001/0002.bcl.bgzf | 0 .../BaseCalls/L001/0002.bcl.bgzf.bci | 0 .../Intensities/BaseCalls/L001/0003.bcl.bgzf | 0 .../BaseCalls/L001/0003.bcl.bgzf.bci | 0 .../Intensities/BaseCalls/L001/0004.bcl.bgzf | 0 .../BaseCalls/L001/0004.bcl.bgzf.bci | 0 .../Intensities/BaseCalls/L001/0005.bcl.bgzf | 0 .../BaseCalls/L001/0005.bcl.bgzf.bci | 0 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a/pseudonymization/helpers/file_helpers.py b/pseudonymization/helpers/file_helpers.py index 0325262..91e652f 100644 --- a/pseudonymization/helpers/file_helpers.py +++ b/pseudonymization/helpers/file_helpers.py @@ -8,33 +8,3 @@ def remove_path_if_exist(file_path): shutil.rmtree(file_path) else: os.remove(file_path) - - -def remove_miseq_run_files(run_path: object) -> object: - remove_path_if_exist(os.path.join(run_path, "Data", "RTALogs")) - remove_path_if_exist(os.path.join(run_path, "Data", "Intensities", "L001")) - remove_path_if_exist(os.path.join(run_path, "Thumbnail_Images")) - remove_path_if_exist(os.path.join(run_path, "Recipe")) - remove_path_if_exist(os.path.join(run_path, "Data", "Intensities", "RTAConfiguration.xml")) - remove_path_if_exist(os.path.join(run_path, "Data", "Intensities", "BaseCalls", "SampleSheet.csv")) - remove_path_if_exist(os.path.join(run_path, "Data", "Intensities", "BaseCalls", "Alignment", "SampleSheetUsed.csv")) - remove_path_if_exist(os.path.join(run_path, "Data", "Intensities", "BaseCalls", "Alignment", "GenerateFASTQRunStatistics.xml")) - remove_path_if_exist(os.path.join(run_path, "Basecalling_Netcopy_complete_Read1.txt")) - remove_path_if_exist(os.path.join(run_path, "Basecalling_Netcopy_complete_Read2.txt")) - remove_path_if_exist(os.path.join(run_path, "Basecalling_Netcopy_complete_Read3.txt")) - remove_path_if_exist(os.path.join(run_path, "Basecalling_Netcopy_complete_Read4.txt")) - remove_path_if_exist(os.path.join(run_path, "ImageAnalysis_Netcopy_complete_Read1.txt")) - remove_path_if_exist(os.path.join(run_path, "ImageAnalysis_Netcopy_complete_Read2.txt")) - remove_path_if_exist(os.path.join(run_path, "ImageAnalysis_Netcopy_complete_Read3.txt")) - remove_path_if_exist(os.path.join(run_path, "ImageAnalysis_Netcopy_complete_Read4.txt")) - remove_path_if_exist(os.path.join(run_path, "QueuedForAnalysis.txt")) - remove_path_if_exist(os.path.join(run_path, "RTAComplete.txt")) - - -def remove_nextseq_run_files(run_path): - pass - -def mv_if_source_not_exist(old_path, new_path): - if not os.path.exists(new_path): - shutil.copytree(old_path, new_path) - shutil.rmtree(old_path) \ No newline at end of file diff --git a/pseudonymization/process/processor.py b/pseudonymization/process/processor.py index 7d7f556..229ca3d 100644 --- a/pseudonymization/process/processor.py +++ b/pseudonymization/process/processor.py @@ -1,6 +1,6 @@ import os import shutil - +import xml.etree.ElementTree as ET from pseudonymization.removers.remover import FileRemover from pseudonymization.pseudonymizers.run_pseudonymizer import RunPseudonymizer from pseudonymization.pseudonymizers.old_miseq_pseudonymizer import OldMiseqPseudonymizer @@ -36,9 +36,17 @@ def _copy_pseudonymizer_run_to_sc(self, run_name): def _initialize_based_on_record_type(self, full_run_path) -> (FileRemover, RunPseudonymizer): if "SoftwareVersionsFile.csv" in os.listdir(full_run_path) or "Alignment_1" in os.listdir(full_run_path): pseudonymizer = NewMiseqPseudonymizer(full_run_path, self.pseudonymization_tables_folder) - elif "Something NextSeqSpecific" in os.listdir(full_run_path): - pseudonymizer = NextSeqPseudonymizer() + elif self._is_next_seq_based_on_run_parameters(full_run_path): + pseudonymizer = NextSeqPseudonymizer(full_run_path, self.pseudonymization_tables_folder) else: pseudonymizer = OldMiseqPseudonymizer(full_run_path, self.pseudonymization_tables_folder) return pseudonymizer + + def _is_next_seq_based_on_run_parameters(self, full_run_path): + run_parameters = os.path.join(full_run_path, "RunParameters.xml") + tree = ET.parse(run_parameters) + root = tree.getroot() + for child in root: + if child.tag == "RunParametersVersion": + return "nextseq" in child.text.lower() diff --git a/pseudonymization/pseudonymizers/nextseq_pseudonymizer.py b/pseudonymization/pseudonymizers/nextseq_pseudonymizer.py index c1c17c7..11a98cd 100644 --- a/pseudonymization/pseudonymizers/nextseq_pseudonymizer.py +++ b/pseudonymization/pseudonymizers/nextseq_pseudonymizer.py @@ -1,10 +1,49 @@ -from .run_pseudonymizer import RunPseudonymizer +import os +import pandas as pd +from .run_pseudonymizer import RunPseudonymizer +from pseudonymization.pseudonimization_api.pseudonimize_predictive import PseudonymizePredictive +from pseudonymization.removers.nextseq_remover import NextSeqRemover class NextSeqPseudonymizer(RunPseudonymizer): - def __init__(self): - pass + def __init__(self, run_path, pseudo_tables_folder_path): + self.patient_pseudo_table = os.path.join(pseudo_tables_folder_path, "patients.json") + self.predictive_pseudo_table = os.path.join(pseudo_tables_folder_path, "predictive.json") + self.sample_pseudo_table = os.path.join(pseudo_tables_folder_path, "samples.json") + self.run_path = run_path def pseudonymize(self): - pass + # NextSeqRemover(self.run_path).remove_files() + pred_pseudo_tuples = self._get_all_predictive_numbers_pseudonymize_sample_sheet() + return pred_pseudo_tuples + + + def _get_all_predictive_numbers_pseudonymize_sample_sheet(self): + sample_sheet_path = os.path.join(self.run_path, "SampleSheet.csv") + df = pd.read_csv(sample_sheet_path, + delimiter=",", + names=["[Header]", "Unnamed: 1", "Unnamed: 2", "Unnamed: 3", "Unnamed: 4", + "Unnamed: 5", "Unnamed: 6", "Unnamed: 7", "Unnamed: 8"]) + + sample_list_header = df["[Header]"].to_list() + sample_list_last = df["Unnamed: 8"].to_list() + sample_ids_start = sample_list_header.index("Sample_ID") + 1 + + predictive_numbers = sample_list_header[sample_ids_start:] + predictive_pseudonimizer = PseudonymizePredictive(self.predictive_pseudo_table) + pseudo_numbers = [predictive_pseudonimizer.pseudonymize(pred_number) for pred_number in predictive_numbers] + + new_column_header = sample_list_header[:sample_ids_start] + pseudo_numbers + new_column_last = sample_list_last[:sample_ids_start] + pseudo_numbers + + df.drop(["[Header]", "Unnamed: 8"], axis=1, inplace=True) + df.insert(loc=0, column="[Header]", value=new_column_header) + df["Unnamed: 8"] = new_column_last + df.columns = ["[Header]"] + ["" for _ in range(len(df.columns) - 1)] + df.fillna("", inplace=True) + df.to_csv(sample_sheet_path, header=False, index=False) + + predictive_pseudo_tuples = [(predictive_numbers[i], pseudo_numbers[i]) for i in range(len(predictive_numbers))] + + return predictive_pseudo_tuples \ No newline at end of file diff --git a/pseudonymization/removers/new_miseq_remover.py b/pseudonymization/removers/new_miseq_remover.py index 58688fb..bf1fb9f 100644 --- a/pseudonymization/removers/new_miseq_remover.py +++ b/pseudonymization/removers/new_miseq_remover.py @@ -1,6 +1,4 @@ import os.path -from typing import Optional - from .remover import FileRemover from pseudonymization.helpers.file_helpers import remove_path_if_exist diff --git a/pseudonymization/removers/nextseq_remover.py b/pseudonymization/removers/nextseq_remover.py index 0582008..ebb0153 100644 --- a/pseudonymization/removers/nextseq_remover.py +++ b/pseudonymization/removers/nextseq_remover.py @@ -1,4 +1,7 @@ +import os.path + from .remover import FileRemover +from pseudonymization.helpers.file_helpers import remove_path_if_exist class NextSeqRemover(FileRemover): @@ -7,4 +10,21 @@ def __init__(self, sequencing_folder_path): self.folder_path = sequencing_folder_path def remove_files(self) -> None: - pass + paths_to_remove = [ + "Config", + "Recipe", + "Images", + "Logs", + "InstrumentAnalyticsLogs", + "InterOp", + "RTALogs", + "CopyComplete.txt", + "RTAComplete.txt", + "RTARead1Complete.txt", + "RTARead2Complete.txt", + "RTARead3Complete.txt", + "RTARead4Complete.txt", + ] + + for path in paths_to_remove: + remove_path_if_exist(os.path.join(self.folder_path, path)) diff --git a/tests/next_seq_test_run/CopyComplete.txt b/tests/next_seq_test_run/CopyComplete.txt new file mode 100644 index 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0000000..e69de29 diff --git a/tests/next_seq_test_run/RTAComplete.txt b/tests/next_seq_test_run/RTAComplete.txt new file mode 100644 index 0000000..e69de29 diff --git a/tests/next_seq_test_run/RTAConfiguration.xml b/tests/next_seq_test_run/RTAConfiguration.xml new file mode 100644 index 0000000..e69de29 diff --git a/tests/next_seq_test_run/RTARead1Complete.txt b/tests/next_seq_test_run/RTARead1Complete.txt new file mode 100644 index 0000000..e69de29 diff --git a/tests/next_seq_test_run/RTARead2Complete.txt b/tests/next_seq_test_run/RTARead2Complete.txt new file mode 100644 index 0000000..e69de29 diff --git a/tests/next_seq_test_run/RTARead3Complete.txt b/tests/next_seq_test_run/RTARead3Complete.txt new file mode 100644 index 0000000..23b097a --- /dev/null +++ b/tests/next_seq_test_run/RTARead3Complete.txt @@ -0,0 +1 @@ +RTARead1Complete.txt \ No newline at end of file diff --git a/tests/next_seq_test_run/RTARead4Complete.txt b/tests/next_seq_test_run/RTARead4Complete.txt new file mode 100644 index 0000000..e69de29 diff --git a/tests/next_seq_test_run/RunCompletionStatus.xml b/tests/next_seq_test_run/RunCompletionStatus.xml new file mode 100644 index 0000000..e69de29 diff --git a/tests/next_seq_test_run/RunInfo.xml b/tests/next_seq_test_run/RunInfo.xml new file mode 100644 index 0000000..e69de29 diff --git a/tests/next_seq_test_run/RunParameters.xml b/tests/next_seq_test_run/RunParameters.xml new file mode 100644 index 0000000..e69de29 diff --git a/tests/next_seq_test_run/SampleSheet.csv b/tests/next_seq_test_run/SampleSheet.csv new file mode 100755 index 0000000..b620a54 --- /dev/null +++ b/tests/next_seq_test_run/SampleSheet.csv @@ -0,0 +1,41 @@ +[Header],,,,,,,, +IEMFileVersion,4,,,,,,, +Investigator Name,OHO,,,,,,, +Experiment Name,TSO500_Run2000_00,,,,,,, +Date,1.1.2000,,,,,,, +Workflow,GenerateFASTQ,,,,,,, +Application,NextSeq FASTQ Only,,,,,,, +Assay,,,,,,,, +Description,,,,,,,, +Chemistry,Default,,,,,,, +,,,,,,,, +[Reads],,,,,,,, +101,,,,,,,, +101,,,,,,,, +,,,,,,,, +[Settings],,,,,,,, +AdapterRead1,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,, +AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,, +AdapterBehavior,trim,,,,,,, +MinimumTrimmedReadLength,35,,,,,,, +MaskShortReads,35,,,,,,, +OverrideCycles,U7N1Y93,,,,,,, +,,,,,,,, +[Data],,,,,,,, +Sample_ID,Sample_Name,Sample_Plate,Sample_Well,Index_ID,index,index2,Sample_Type,Pair_ID +2000_0000_DNA,,,,UP01,TCCGGAGA,AGGATAGG,DNA,2000_0000 +2000_0001_DNA,,,,UP02,CTGAAGCT,TCAGAGCC,DNA,2000_0001 +2000_0002_DNA,,,,UP03,CGTAGCTC,CATCCGAA,DNA,2000_0002 +2000_0003_DNA,,,,UP04,GAATTCGT,TTATGAGT,DNA,2000_0003 +2000_0004_DNA,,,,UP05,AGCGATAG,ACGAATAA,DNA,2000_0004 +2000_0005_DNA,,,,UP06,GCGATTAA,GATCTGCT,DNA,2000_0005 +2000_0006_DNA,,,,UP07,ATTCAGAA,AGGCTATA,DNA,2000_0006 +ST20-00_DNA,,,,UP08,GAATAATC,GCCTCTAT,DNA,ST20-00 +2000_0007_RNA,,,,UP09,TTAATCAG,CTTCGCCT,RNA,2000_0007 +2000_0008_RNA,,,,UP10,CGCTCATT,TAAGATTA,RNA,2000_0008 +2000_0009_RNA,,,,UP11,TCCGCGAA,AGTAAGTA,RNA,2000_0009 +2000_0010_RNA,,,,UP12,ATTACTCG,GACTTCCT,RNA,2000_0010 +2000_0011_RNA,,,,UP13,ACTGCTTA,AGAGGCGC,RNA,2000_0011 +2000_0012_RNA,,,,UP14,ATGCGGCT,TAGCCGCG,RNA,2000_0012 +2000_0013_RNA,,,,UP15,GCCTCTCT,TTCGTAGG,RNA,2000_0013 +ST20-01_DNA,,,,UP16,GCCGTAGG,CGCTCCGC,DNA,ST20-01 \ No newline at end of file diff --git a/tests/tests_run_psedonymization/test_next_seq_pseudonymization.py b/tests/tests_run_psedonymization/test_next_seq_pseudonymization.py new file mode 100644 index 0000000..51fff0d --- /dev/null +++ b/tests/tests_run_psedonymization/test_next_seq_pseudonymization.py @@ -0,0 +1,57 @@ +import os +import shutil +import pytest +from pseudonymization.pseudonymizers.nextseq_pseudonymizer import NextSeqPseudonymizer + +tests_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..") + +FAKE_RUN_FOLDER_FOR_COPY = os.path.join(tests_dir, "next_seq_test_run") +FAKE_RUN_FOR_TESTING = os.path.join(tests_dir, "FAKE_RUN") + +PSEUDONYMIZATION_FILES_FOLDER = os.path.join(tests_dir, "pseudonymization_files") +PSEUDONYMIZATION_PATIENTS_FILE = os.path.join(PSEUDONYMIZATION_FILES_FOLDER, "patients.json") +PSEUDONYMIZATION_SAMPLES_FILE = os.path.join(PSEUDONYMIZATION_FILES_FOLDER, "samples.json") +PSEUDONYMIZATION_PREDICTIVE_FILE = os.path.join(PSEUDONYMIZATION_FILES_FOLDER, "predictive.json") + + +def test_sample_sheet_pseudonymized(mock_pseudonymize_predictive): + values = NextSeqPseudonymizer(FAKE_RUN_FOR_TESTING, PSEUDONYMIZATION_FILES_FOLDER).pseudonymize() + + assert values == [] + + +def _setup_pseudonymization_files(): + os.mkdir(PSEUDONYMIZATION_FILES_FOLDER) + + +def _copy_fake_run(): + shutil.copytree(FAKE_RUN_FOLDER_FOR_COPY, FAKE_RUN_FOR_TESTING) + + +def _teardown_pseudonymization_files(): + shutil.rmtree(PSEUDONYMIZATION_FILES_FOLDER) + + +def _remove_coppied_fake_run(): + shutil.rmtree(FAKE_RUN_FOR_TESTING) + + +@pytest.fixture(autouse=True) +def setup_and_teardown_pseodonymization_files(request): + _setup_pseudonymization_files() + _copy_fake_run() + + request.addfinalizer(_teardown_pseudonymization_files) + request.addfinalizer(_remove_coppied_fake_run) + + +@pytest.fixture +def uuid_generated_values(): + return ["mmci_predictive_12345678-1234-5678-1234-5678123456" + "{:02d}".format(number) + for number in range(0, 19)] + + +@pytest.fixture +def mock_pseudonymize_predictive(mocker, uuid_generated_values): + mocker.patch("pseudonymization.pseudonymizers.nextseq_pseudonymizer.PseudonymizePredictive.pseudonymize", + side_effect=uuid_generated_values)