Change order of primer trimming steps for #530.

cfe-lab · Jun 2, 2020 · 2c51f0f · 2c51f0f
1 parent bacac0c
commit 2c51f0f
Show file tree

Hide file tree

Showing 2 changed files with 19 additions and 7 deletions.
diff --git a/micall/core/trim_fastqs.py b/micall/core/trim_fastqs.py
@@ -108,7 +108,7 @@ def cut_all(censored_fastq1: Path,
                           for filename in (censored_fastq1, censored_fastq2)]
     ltrimmed_filenames = [Path(str(filename) + '.ltrimmed.fastq')
                           for filename in (censored_fastq1, censored_fastq2)]
-    rtrimmed_filenames = [Path(str(filename) + '.rtrimmed.fastq')
+    dtrimmed_filenames = [Path(str(filename) + '.dtrimmed.fastq')
                           for filename in (censored_fastq1, censored_fastq2)]
     if TrimSteps.adapters in skip:
         dedapted_filenames[0].symlink_to(censored_fastq1)
@@ -126,17 +126,17 @@ def cut_all(censored_fastq1: Path,
                          dedapted_filenames[1],
                          ltrimmed_filenames[0],
                          ltrimmed_filenames[1])
-        cut_right_primers(ltrimmed_filenames[0],
+        cut_primer_dimers(ltrimmed_filenames[0],
                           ltrimmed_filenames[1],
-                          rtrimmed_filenames[0],
-                          rtrimmed_filenames[1])
-        cut_primer_dimers(rtrimmed_filenames[0],
-                          rtrimmed_filenames[1],
+                          dtrimmed_filenames[0],
+                          dtrimmed_filenames[1])
+        cut_right_primers(dtrimmed_filenames[0],
+                          dtrimmed_filenames[1],
                           Path(trimmed_fastq1),
                           Path(trimmed_fastq2))
     purge_temp_files(dedapted_filenames)
     purge_temp_files(ltrimmed_filenames)
-    purge_temp_files(rtrimmed_filenames)
+    purge_temp_files(dtrimmed_filenames)
 
 
 def purge_temp_files(filenames):

diff --git a/micall/tests/test_trim_fastqs.py b/micall/tests/test_trim_fastqs.py
@@ -403,6 +403,18 @@ def test_trim(tmpdir):
       # Trimmed to nothing
       '',
       # Trimmed to nothing
+      ),
+     ('primer dimer with partial right match',
+      'TGGCTATTGATTATAAACACTACACACCCTGCACAAGAAAAGAACTTCACCTGTCTCTTATACACATCTCCGAGCCCACGAGACACTACCTGGAA',
+      #  nCoV-2019_21_LEFT         ]                     [ rev(ADAPTER2)                  ][ garbage ]
+      #                          [ rev(..._81_RIGHT)    ] last 5 of 81_RIGHT match start of HCV_Pr3
+      'GTGAAGTTCTTTTCTTGTGCAGGGTGTGTAGTGTTTATAATCAATAGCCACTGTCTCTTATACACATCTGACGCTGCCGACGAAGGTTCTCAGGA',
+      # nCoV-2019_81_RIGHT    ]                          [ rev(ADAPTER1)                 ][ garbage
+      #                     [ rev(nCoV-2019_21_LEFT)    ]
+      '',
+      # Trimmed to nothing
+      '',
+      # Trimmed to nothing
       )
      ])
 def test_cut_adapters(tmpdir: str,