Revert "Readability improvements"

Author: kedhammar

.devcontainer/devcontainer.json

@@ -18,7 +18,7 @@
         "esbenp.prettier-vscode",
         "wholroyd.jinja",
         "ms-python.python",
-        "charliermarsh.ruff",
+        "charliermarsh.ruff@2024.2.0",
         "ms-azuretools.vscode-docker",
       ],
     },

.gitignore

@@ -6,4 +6,3 @@
 .*_cache
 node_modules
 .vscode
-build

anglerfish/anglerfish.py

@@ -28,19 +28,6 @@
 
 MAX_PROCESSES = 64  # Ought to be enough for anybody
 
-anglerfish_logo = r"""
-     ___
-   ( )  \ -..__
-      _.|~”~~~”…_
-    ^´           `>.
-(+ (+ )             “<..<^(
-  `´  ``´      ___       (
-   \__..~      __(   _…_(
-   \                /
-    “--…_     _..~%´
-         ```´´
-"""
-
 
 def run_demux(args):
     multiprocessing.set_start_method("spawn")
@@ -51,54 +38,44 @@ def run_demux(args):
     ss = SampleSheet(args.samplesheet, args.ont_barcodes)
     version = pkg_resources.get_distribution("bio-anglerfish").version
     report = Report(args.run_name, run_uuid, version)
-    sys.stderr.write(anglerfish_logo)
+    sys.stderr.write("""
+     ___
+   ( )  \ -..__
+      _.|~”~~~”…_
+    ^´           `>.
+(+ (+ )             “<..<^(
+  `´  ``´      ___       (
+   \__..~      __(   _…_(
+   \                /
+    “--…_     _..~%´
+         ```´´
+""")
     log.info(f" version {version}")
     log.info(f" arguments {vars(args)}")
     log.info(f" run uuid {run_uuid}")
-    min_distance = ss.minimum_bc_distance()
+    bc_dist = ss.minimum_bc_distance()
     if args.max_distance is None:
-        # Default: Set the maximum distance for barcode matching to 0, 1 or 2
-        # depending on the smallest detected edit distance between indices in the samplesheet
-        args.max_distance = min(min_distance - 1, 2)
+        if bc_dist > 1:
+            args.max_distance = 2
+        else:
+            args.max_distance = 1
         log.info(f"Using maximum edit distance of {args.max_distance}")
-    if args.max_distance >= min_distance:
+    if args.max_distance >= bc_dist:
         log.error(
-            f" The maximum allowed edit distance for barcode matching (={args.max_distance})"
-            + f"is greater than the smallest detected edit distance between indices in samplesheet (={min_distance})"
-            + ", which will result in ambiguous matches."
+            f" Edit distance of barcodes in samplesheet are less than the minimum specified {args.max_distance}>={bc_dist}"
         )
         exit()
-    log.debug(f"Samplesheet bc_dist == {min_distance}")
+    log.debug(f"Samplesheet bc_dist == {bc_dist}")
     if args.threads > MAX_PROCESSES:
         log.warning(
             f" Setting threads to {MAX_PROCESSES} as the maximum number of processes is {MAX_PROCESSES}"
         )
         args.threads = MAX_PROCESSES
 
-    ## Sort the adaptors by type and size
-
-    # Get a list of tuples with the adaptor name and ONT barcode
-    adaptor_tuples: list[tuple[str, str]] = [
-        (entry.adaptor.name, entry.ont_barcode) for entry in ss
-    ]
-
-    # Convert to set to enforce uniqueness
-    adaptor_set: set[tuple[str, str]] = set(adaptor_tuples)
-
-    # Create a dictionary with the adaptors as keys and an empty list as value
-    adaptors_sorted: dict[tuple[str, str], list] = dict([(i, []) for i in adaptor_set])
-
-    # Populate the dictionary values with sample-specific information
-    """
-        adaptors_sorted = {
-            ( adaptor_name, ont_barcode ) : [
-                (sample_name, adaptor, fastq),
-                (sample_name, adaptor, fastq),
-                ...
-            ],
-            ...
-        } 
-    """
+    # Sort the adaptors by type and size
+    adaptors_t = [(entry.adaptor.name, entry.ont_barcode) for entry in ss]
+    adaptor_set = set(adaptors_t)
+    adaptors_sorted = dict([(i, []) for i in adaptor_set])
     for entry in ss:
         adaptors_sorted[(entry.adaptor.name, entry.ont_barcode)].append(
             (entry.sample_name, entry.adaptor, os.path.abspath(entry.fastq))
@@ -114,19 +91,18 @@ def run_demux(args):
         adaptor_name, ont_barcode = key
         fastq_path = sample[0][2]
         # If there are multiple ONT barcodes, we need to add the ONT barcode to the adaptor name
+        adaptor_bc_name = adaptor_name
         if ont_barcode:
-            adaptor_bc_name = f"{adaptor_name}_{ont_barcode}"
-        else:
-            adaptor_bc_name = adaptor_name
+            adaptor_bc_name = adaptor_name + "_" + ont_barcode
         fastq_files = glob.glob(fastq_path)
 
         # Align
-        align_path = os.path.join(args.out_fastq, f"{adaptor_bc_name}.paf")
+        aln_path = os.path.join(args.out_fastq, f"{adaptor_bc_name}.paf")
         adaptor_path = os.path.join(args.out_fastq, f"{adaptor_name}.fasta")
         with open(adaptor_path, "w") as f:
             f.write(ss.get_fastastring(adaptor_name))
         for fq in fastq_files:
-            run_minimap2(fq, adaptor_path, align_path, args.threads)
+            run_minimap2(fq, adaptor_path, aln_path, args.threads)
 
         # Easy line count in input fastq files
         num_fq = 0
@@ -135,7 +111,7 @@ def run_demux(args):
                 for i in f:
                     num_fq += 1
         num_fq = int(num_fq / 4)
-        paf_entries = parse_paf_lines(align_path)
+        paf_entries = parse_paf_lines(aln_path)
 
         # Make stats
         log.info(f" Searching for adaptor hits in {adaptor_bc_name}")
@@ -277,8 +253,7 @@ def run_demux(args):
             sample_dists = [
                 (
                     lev.distance(
-                        i[0],
-                        f"{x.adaptor.i7.index_seq}+{x.adaptor.i5.index_seq}".lower(),
+                        i[0], f"{x.adaptor.i7_index}+{x.adaptor.i5_index}".lower()
                     ),
                     x.sample_name,
                 )

anglerfish/cli.py

@@ -193,9 +193,7 @@ def run(
         typer.Option(
             "--max-distance",
             "-m",
-            help="Manually set maximum allowed edit distance for index matching,"
-            + "by default this is set to 0, 1 or 2 based on the minimum detected"
-            + "index distance in the samplesheet.",
+            help="Manually set maximum edit distance for BC matching, automatically set this is set to either 1 or 2",
         ),
     ] = 2,
     max_unknowns: Annotated[