Merge branch 'main' into feature/update_pybasecall_client_lib

src/readfish/_cli_args.py

@@ -127,9 +127,10 @@
     (
         "--wait-for-ready",
         dict(
-            help="Timeout for the MinKNOW data folder to appear, and the device to report it is ready to start sequencing. Default 60 seconds.",
+            help="Timeout for the MinKNOW data folder to appear, and the device to report it is ready to start sequencing in seconds. (default: 120s).",
             required=False,
-            default=60,
+            default=120,
+            type=int,
         ),
     ),
 ) + BASE_ARGS

src/readfish/_read_until_client.py

@@ -41,6 +41,8 @@ class RUClient(ReadUntilClient):
     """Subclasses ONTs read_until_api ReadUntilClient adding extra function that logs unblocks read_ids."""
 
     def __init__(self, *args, **kwargs):
+        #  Default to TIMEOUT in the event we are not starting from the CLI.
+        # If started from CLI args.wait-for-ready is used - also defaults to 120s
         self.timeout = kwargs.pop("timeout", TIMEOUT)
         super().__init__(*args, **kwargs)
         # disable the read until client logger
@@ -170,10 +172,10 @@ def set_acquisition_state(self):
             else:
                 raise SystemExit(1)
 
-    def wait_for_minknow_folder(self, timeout: int = TIMEOUT):
+    def wait_for_minknow_folder(self, timeout: int):
         """
         Rather than messing about with permissions wait for MinKNOW to create the run
-        folder. If the folder doesn't appear after TIMEOUT seconds then write to the
+        folder. If the folder doesn't appear after timeout seconds then write to the
         current working directory instead.
         """
         seconds_waited = 0

src/readfish/plugins/_mappy.py

@@ -1,6 +1,7 @@
 """Mapping interface for readfish, using Minimap2 mappy, or mappy-rs as dictated by the experiment TOML
 `mapper_settings.<PLUGIN>` section. See {ref}`plugin configuration <plugins-config>` section.
 """
+
 from __future__ import annotations
 from enum import Enum
 from itertools import chain, repeat
@@ -87,10 +88,7 @@ def validate(self) -> None:
         file_extensions.append(".mmi")
         if all((not Path(index).is_file(), index)):
             raise FileNotFoundError(f"{index} does not exist")
-        if (
-            "".join(map(str.lower, Path(index).suffixes)) not in set(file_extensions)
-            and index
-        ):
+        if not any(index.lower().endswith(suffix) for suffix in file_extensions):
             raise RuntimeError(
                 f"Provided index file appears to be of an incorrect type - should be one of {file_extensions}"
             )

tests/static/mappy_validation_test/fail/004_bad_reference_file_extension.toml

@@ -0,0 +1,13 @@
+[caller_settings.no_op]
+
+[mapper_settings.mappy]
+fn_idx_in = "tests/static/mappy_validation_test/fail/bad_extension.mmi.cabbage"
+
+[[regions]]
+name = "abc"
+no_seq = "proceed"
+no_map = "proceed"
+single_on = "proceed"
+single_off = "proceed"
+multi_on = "proceed"
+multi_off = "proceed"

tests/static/mappy_validation_test/fail/004_bad_reference_file_extension.txt

@@ -0,0 +1 @@
+Provided index file appears to be of an incorrect type - should be one of ['.fasta', '.fna', '.fsa', '.fa', '.fastq', '.fq', '.fasta.gz', '.fna.gz', '.fsa.gz', '.fa.gz', '.fastq.gz', '.fq.gz', '.mmi']

tests/static/mappy_validation_test/pass/006_passing_fna_mmi.toml

@@ -0,0 +1,13 @@
+[caller_settings.no_op]
+
+[mapper_settings.mappy]
+fn_idx_in = "tests/static/mappy_validation_test/pass/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.mmi"
+
+[[regions]]
+name = "abc"
+no_seq = "proceed"
+no_map = "proceed"
+single_on = "proceed"
+single_off = "proceed"
+multi_on = "proceed"
+multi_off = "proceed"

tests/static/mappy_validation_test/pass/006_passing_fna_mmi.txt

@@ -0,0 +1 @@
+Aligner initialised