Merge pull request #210 from fls-bioinformatics-core/IlluminaData-fix…

…-fastq-assignment bcftbx/IlluminaData: fix bug in IlluminaProject assigning undetermined Fastqs
fls-bioinformatics-core · Dec 16, 2022 · 3a0df01 · 3a0df01
2 parents 6f5a6c4 + f9e3427
commit 3a0df01
Show file tree

Hide file tree

Showing 2 changed files with 29 additions and 11 deletions.
diff --git a/bcftbx/IlluminaData.py b/bcftbx/IlluminaData.py
@@ -655,13 +655,15 @@ def __init__(self,dirn):
                                                        leading_dir[0])
                 else:
                     # Handle 'undetermined' data
-                    try:
-                        fqs = [f for f in fastqs
-                               if "lane%d" % IlluminaFastq(f).lane_number
-                               == sample_name]
-                    except TypeError:
-                        # No lane, take all fastqs
-                        fqs = [fq for fq in fastqs]
+                    # Try Fastqs with matching lane
+                    fqs = [fq for fq in fastqs
+                           if IlluminaFastq(fq).lane_number is not None and
+                           "lane%d" % IlluminaFastq(fq).lane_number
+                           == sample_name]
+                    if not fqs:
+                        # No lane, take all fastqs without a lane
+                        fqs = [fq for fq in fastqs
+                               if IlluminaFastq(fq).lane_number is None]
                 self.samples.append(IlluminaSample(sample_dirn,
                                                    fastqs=fqs,
                                                    name=sample_name,

diff --git a/bcftbx/test/test_IlluminaData.py b/bcftbx/test/test_IlluminaData.py
@@ -928,8 +928,10 @@ def makeIlluminaDataDirectoryWithMixedLaneAndNoLaneSplitting(self):
                                                top_dir=self.top_dir)
         mock_illumina_data.add_fastq_batch('AB','AB1','AB1_S1',lanes=(1,2))
         mock_illumina_data.add_fastq_batch('AB','AB2','AB2_S2',lanes=(1,2))
-        mock_illumina_data.add_fastq_batch('CDE','CDE3','CDE3_S3')
-        mock_illumina_data.add_fastq_batch('CDE','CDE4','CDE4_S4')
+        mock_illumina_data.add_fastq_batch('CDE','CDE3','CDE3_S3',
+                                           lanes=(3,4))
+        mock_illumina_data.add_fastq_batch('CDE','CDE4','CDE4_S4',
+                                           lanes=(3,4))
         mock_illumina_data.add_undetermined(lanes=(1,2))
         mock_illumina_data.create()
         # Create second dir with no lane splitting
@@ -938,13 +940,20 @@ def makeIlluminaDataDirectoryWithMixedLaneAndNoLaneSplitting(self):
                                                paired_end=True,
                                                no_lane_splitting=True,
                                                top_dir=self.top_dir)
-        mock_illumina_data2.add_fastq_batch('CDE','CDE3','CDE3_S3')
-        mock_illumina_data2.add_fastq_batch('CDE','CDE4','CDE4_S4')
+        mock_illumina_data2.add_fastq_batch('CDE','CDE3','CDE3_S3',
+                                           lanes=(3,4))
+        mock_illumina_data2.add_fastq_batch('CDE','CDE4','CDE4_S4',
+                                           lanes=(3,4))
+        mock_illumina_data2.add_undetermined(lanes=(3,4))
         mock_illumina_data2.create()
         # Move no lane splitting project into first dir
         shutil.rmtree(os.path.join(mock_illumina_data.unaligned_dir,"CDE"))
         shutil.move(os.path.join(mock_illumina_data2.unaligned_dir,"CDE"),
                     mock_illumina_data.unaligned_dir)
+        for f in ("Undetermined_S0_R1_001.fastq.gz",
+                  "Undetermined_S0_R2_001.fastq.gz"):
+            shutil.move(os.path.join(mock_illumina_data2.unaligned_dir,f),
+                        mock_illumina_data.unaligned_dir)
         # Finish
         self.mock_illumina_data = mock_illumina_data
 
@@ -1033,6 +1042,13 @@ def test_illumina_data_multiple_projects_paired_end_mixed_lane_splitting(self):
                 self.assertEqual(s.name,s_name)
         self.assertEqual(illumina_data.format,'bcl2fastq2')
         self.assertEqual(illumina_data.lanes,[1,2])
+        # Also check undetermined Fastqs are not double counted
+        undetermined_fastqs = []
+        for sample in illumina_data.undetermined.samples:
+            for fq in sample.fastq:
+                self.assertFalse(fq in undetermined_fastqs,
+                                 "%s: Fastq appears multiple times" % fq)
+                undetermined_fastqs.append(fq)
 
 class TestCasavaSampleSheet(unittest.TestCase):