diff --git a/bcftbx/IlluminaData.py b/bcftbx/IlluminaData.py index 4da087e..afcb9ce 100644 --- a/bcftbx/IlluminaData.py +++ b/bcftbx/IlluminaData.py @@ -1,5 +1,5 @@ # IlluminaData.py: module for handling data about Illumina sequencer runs -# Copyright (C) University of Manchester 2012-2022 Peter Briggs +# Copyright (C) University of Manchester 2012-2024 Peter Briggs # ######################################################################## # @@ -224,6 +224,26 @@ def cycles(self): return None return ncycles + @property + def complete(self): + """ + Check if run is complete + + Returns: + Boolean: True if run is complete (i.e. all appropriate + sentinel files are present), False if not (i.e. + some sentiel files are missing). + """ + # Acquire run completion files + try: + files = platforms.RUN_COMPLETION_FILES[self.platform] + except KeyError: + # Fallback to default + files = platforms.RUN_COMPLETION_FILES['default'] + # Check if all are present + return all([os.path.exists(os.path.join(self.run_dir,f)) + for f in files]) + class IlluminaRunInfo: """Class for examining Illumina RunInfo.xml file diff --git a/bcftbx/test/test_IlluminaData.py b/bcftbx/test/test_IlluminaData.py index 85a8155..9f5faaa 100644 --- a/bcftbx/test/test_IlluminaData.py +++ b/bcftbx/test/test_IlluminaData.py @@ -72,6 +72,7 @@ def test_illuminarun_miseq(self): self.assertEqual(run.bcl_extension,".bcl") self.assertEqual(run.lanes,[1,]) self.assertEqual(run.cycles,218) + self.assertEqual(run.complete,True) def test_illuminarun_hiseq(self): """ @@ -114,6 +115,7 @@ def test_illuminarun_hiseq(self): self.assertEqual(run.bcl_extension,".bcl.gz") self.assertEqual(run.lanes,[1,2,3,4,5,6,7,8]) self.assertEqual(run.cycles,218) + self.assertEqual(run.complete,True) def test_illuminarun_nextseq(self): """ @@ -153,12 +155,13 @@ def test_illuminarun_nextseq(self): self.assertEqual(run.bcl_extension,".bcl.bgzf") self.assertEqual(run.lanes,[1,2,3,4]) self.assertEqual(run.cycles,158) + self.assertEqual(run.complete,True) def test_illuminarun_novaseq(self): """ IlluminaRun: test for NovaSeq run """ - # Make a mock run directory for NextSeq format + # Make a mock run directory for NovaSeq format self.mock_illumina_run = MockIlluminaRun( '221125_A500968_0038_ABCDE1XX', 'novaseq', @@ -194,6 +197,7 @@ def test_illuminarun_novaseq(self): self.assertEqual(run.bcl_extension,".bcl.bgzf") self.assertEqual(run.lanes,[1,2]) self.assertEqual(run.cycles,158) + self.assertEqual(run.complete,True) def test_illuminarun_unknown_illumina_platform(self): """ @@ -236,6 +240,7 @@ def test_illuminarun_unknown_illumina_platform(self): self.assertEqual(run.bcl_extension,".bcl") self.assertEqual(run.lanes,[1,]) self.assertEqual(run.cycles,218) + self.assertEqual(run.complete,True) def test_illuminarun_unknown_illumina_platform_generic_name(self): """ @@ -281,6 +286,7 @@ def test_illuminarun_unknown_illumina_platform_generic_name(self): self.assertEqual(run.bcl_extension,".bcl") self.assertEqual(run.lanes,[1,]) self.assertEqual(run.cycles,218) + self.assertEqual(run.complete,True) def test_illuminarun_miseq_specify_platform(self): """ @@ -323,6 +329,24 @@ def test_illuminarun_miseq_specify_platform(self): self.assertEqual(run.bcl_extension,".bcl") self.assertEqual(run.lanes,[1,]) self.assertEqual(run.cycles,218) + self.assertEqual(run.complete,True) + + def test_illuminarun_incomplete(self): + """ + IlluminaRun: test 'complete' property when completion files missing + """ + # Make a mock run directory for NovaSeq format + self.mock_illumina_run = MockIlluminaRun( + '221125_A500968_0038_ABCDE1XX', + 'novaseq', + complete=False, + top_dir=self.top_dir) + self.mock_illumina_run.create() + # Load into an IlluminaRun object + run = IlluminaRun(self.mock_illumina_run.dirn, + platform="novaseq") + # Check that run is not complete + self.assertEqual(run.complete,False) def test_illuminarun_miseq_missing_directory(self): """