bcftbx/IlluminaData: add 'complete' property to IlluminaRun (check if…

… run is complete).
fls-bioinformatics-core · Feb 16, 2024 · b9b968a · b9b968a
1 parent cbe61e0
commit b9b968a
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Showing 2 changed files with 46 additions and 2 deletions.
diff --git 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
@@ -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):
         """