Merge pull request #305 from kedhammar/fix-anglerfish-df

Update Anglerfish parsing to handle runs w/o ONT barcodes
SciLifeLab · Jan 31, 2024 · 631c48a · 631c48a
2 parents 8c2657e + 380ab38
commit 631c48a
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Showing 2 changed files with 23 additions and 10 deletions.
diff --git a/VERSIONLOG.md b/VERSIONLOG.md
@@ -1,5 +1,9 @@
 # Scilifelab_epps Version Log
 
+## 20240130.1
+
+Handle Anglerfish result parsing for runs W/O ONT barcodes
+
 ## 20240126.1
 
 Discover latest anglerfish run even if embedded in subdir of run dir

diff --git a/scripts/parse_anglerfish_results.py b/scripts/parse_anglerfish_results.py
@@ -36,7 +36,7 @@ def find_latest_flowcell_run(currentStep: Process) -> str:
 
 def find_latest_anglerfish_run(latest_flowcell_run_path: str) -> str:
     anglerfish_query = f"{latest_flowcell_run_path}/**/anglerfish_run*"
-    anglerfish_glob = glob.glob(anglerfish_query)
+    anglerfish_glob = glob.glob(anglerfish_query, recursive=True)
 
     assert (
         len(anglerfish_glob) != 0
@@ -88,7 +88,9 @@ def parse_data(df_raw: pd.DataFrame):
         # Sample reads divided by sum of all sample reads w. the same barcode
         lambda row: row["num_reads"]
         / df[df["ont_barcode"] == row["ont_barcode"]]["num_reads"].sum()
-        * 100,
+        * 100
+        if not pd.isna(row["ont_barcode"])
+        else None,
         axis=1,
     )
 
@@ -141,17 +143,24 @@ def fill_udfs(currentStep: Process, df: pd.DataFrame):
 
             for illumina_sample in illumina_samples:
                 try:
-                    barcode_name = ont_barcode_well2name(
-                        fetch(illumina_sample, "ONT Barcode Well")
+                    # Get ONT barcode well, if there is one
+                    barcode_well = fetch(
+                        illumina_sample, "ONT Barcode Well", on_fail=None
                     )
 
-                    # Subset df to the current ONT barcode
-                    df_barcode = df[df["ont_barcode"] == barcode_name]
+                    if barcode_well:
+                        barcode_name = ont_barcode_well2name(barcode_well)
 
-                    # Further subset df to the current Illumina sample
-                    df_sample = df_barcode[
-                        df_barcode["sample_name"] == illumina_sample.name
-                    ]
+                        # Subset df to the current ONT barcode
+                        df_barcode = df[df["ont_barcode"] == barcode_name]
+
+                        # Subset df to the current Illumina sample
+                        df_sample = df_barcode[
+                            df_barcode["sample_name"] == illumina_sample.name
+                        ]
+
+                    else:
+                        df_sample = df[df["sample_name"] == illumina_sample.name]
 
                     assert (
                         len(df_sample) == 1