Dorado plugin

README.md

@@ -554,9 +554,11 @@ And for our Awesome Logo please checkout out [@tim_bassford](https://twitter.com
 <!-- start-changelog -->
 # Changelog
 ## Unreleased changes
-1. Change the default `unblock_duration` on the `Analysis` class to use `DEFAULT_UNBLOCK` value defined in `_cli_args.py`. Change type on the Argparser for `--unblock-duration` to float. (#313)
+1. Change the default `unblock_duration` on the `Analysis` class to use `DEFAULT_UNBLOCK` value defined in `_cli_args.py`. Change type on the Argparser for `--unblock-duration` to float. [(#313)](/~https://github.com/LooseLab/readfish/pull/313)
+1. Fix to handling minimap2 indexes with multiple "." in the filename [(#330)](/~https://github.com/LooseLab/readfish/pull/330/)
+1. Add a dorado base-caller which addressed issue [#347](/~https://github.com/LooseLab/readfish/issues/347) - chiefly in Dorado 7.3.9 ONT have moved to `ont-pybasecall-client-lib`, and connections from `ont_pyguppy_client_lib` raise `Connection error. ...  LOAD_CONFIG. Reply: INVALID_PROTOCOL` [(#343)](/~https://github.com/LooseLab/readfish/pull/344)
 ## 2023.1.1
 1. Fix Readme Logo link 🥳 (#296)
-1. Fix bug where we had accidentally started requiring barcoded TOMLs to specify a region. Thanks to @jamesemery for catching this. (#299)
-1. Correctly handle overriding a decision in internal statistics tracking. (#299)
+2. Fix bug where we had accidentally started requiring barcoded TOMLs to specify a region. Thanks to @jamesemery for catching this. (#299)
+3. Correctly handle overriding a decision in internal statistics tracking. (#299)
 <!-- end-changelog -->

docs/developers-guide.md

@@ -67,7 +67,7 @@ conda env create -f docs/development.yml
 
 ## Readfish versioning
 Readfish uses [calver](https://calver.org/) for versioning. Specifically the format should be
-`YYYY.MINOR.MICRO.Modifier`, where `MINOR` is the feature addiiton, `MICRO` is any hotfix/bugfix, and `Modifier` is the modifier (e.g. `rc` for release candidate, `dev` for development, empty for stable).
+`YYYY.MINOR.MICRO.Modifier`, where `MINOR` is the feature addition, `MICRO` is any hotfix/bugfix, and `Modifier` is the modifier (e.g. `rc` for release candidate, `dev` for development, empty for stable).
 
 ## Changelog
 

pyproject.toml

@@ -54,7 +54,8 @@ dev = ["readfish[all,docs,tests]", "pre-commit"]
 mappy = ["mappy"]
 mappy-rs = ["mappy-rs >= 0.0.6"]
 guppy = ["ont_pyguppy_client_lib"]
-all = ["readfish[mappy,mappy-rs,guppy]"]
+dorado = ["ont-pybasecall-client-lib"]
+all = ["readfish[mappy,mappy-rs,guppy,dorado]"]
 
 [project.urls]
 Documentation = "https://looselab.github.io/readfish"
@@ -83,3 +84,10 @@ markers = [
     "alignment: marks tests which rely on loading or using Mappy or Mappy-rs aligners, used to test with both. (deselect with '-m \"not slow\", select with '-k alignment')",
 ]
 addopts = ["-ra", "--doctest-modules", "--ignore=src/readfish/read_until/base.py"]
+
+[tool.coverage.report]
+omit = [
+    "src/readfish/plugins/dorado.py",
+    "src/readfish/_read_until_client.py",
+    "src/readfish/plugins/guppy.py",
+]

src/readfish/__about__.py

@@ -1,4 +1,5 @@
 """__about__.py
 Version of the read until software
 """
-__version__ = "2023.1.1"
+
+__version__ = "2024.0.0"

src/readfish/_config.py

@@ -171,6 +171,7 @@ def load_module(self, override=False):
         """
         builtins = {
             "guppy": "guppy",
+            "dorado": "dorado",
             "mappy": "mappy",
             "mappy_rs": "mappy_rs",
             "no_op": "_no_op",

src/readfish/entry_points/stats.py

@@ -73,6 +73,7 @@
     readfish stats --toml tests/static/stats_test/yeast_summary_test.toml --fastq-directory tests/static/stats_test/ --html summary_adaptive
 
 """
+
 from __future__ import annotations
 import argparse
 from pathlib import Path

src/readfish/entry_points/targets.py

@@ -66,6 +66,7 @@
 
 
 """
+
 # Core imports
 from __future__ import annotations
 import argparse
@@ -171,16 +172,18 @@ def __init__(
         self.break_reads_after_seconds = (
             self.client.connection.analysis_configuration.get_analysis_configuration().read_detection.break_reads_after_seconds.value
         )
+        self.sample_rate = self.client.connection.device.get_sample_rate().sample_rate
         self.logger.info("Run Configuration Received")
         self.logger.info(f"run_id={self.run_information.run_id}")
         self.logger.info(f"break_reads_after_seconds={self.break_reads_after_seconds}")
+        self.logger.info(f"sample_rate={self.sample_rate}")
         # Create our statistics tracker
         self.loop_statistics = ReadfishStatistics(
             read_log_name, self.break_reads_after_seconds
         )
         logger.info("Initialising Caller")
         self.caller: CallerABC = self.conf.caller_settings.load_object(
-            "Caller", run_information=self.run_information
+            "Caller", run_information=self.run_information, sample_rate=self.sample_rate
         )
         logger.info("Caller initialised")
         caller_description = self.caller.describe()

src/readfish/entry_points/unblock_all.py

@@ -12,6 +12,7 @@
 
    readfish unblock-all --device X3 --experiment-name "test unblock all"
 """
+
 from tempfile import NamedTemporaryFile
 
 from readfish._cli_args import DEVICE_BASE_ARGS

src/readfish/plugins/guppy.py

@@ -2,6 +2,7 @@
 
 Extension of pyguppy Caller that maintains a connection to the basecaller
 """
+
 from __future__ import annotations
 import logging
 import os
@@ -13,8 +14,12 @@
 import numpy as np
 import numpy.typing as npt
 from minknow_api.protocol_pb2 import ProtocolRunInfo
-from pyguppy_client_lib.helper_functions import package_read
-from pyguppy_client_lib.pyclient import PyGuppyClient
+
+try:
+    from pyguppy_client_lib.helper_functions import package_read
+    from pyguppy_client_lib.pyclient import PyGuppyClient
+except ImportError:
+    pass
 
 from readfish._loggers import setup_logger
 from readfish.plugins.abc import CallerABC

tests/static/guppy_validation_test/fail/001_no_write_socket.toml

@@ -1,4 +1,4 @@
-[caller_settings.guppy]
+[caller_settings.dorado]
 address = "ipc://tests/static/guppy_validation_test/fail/5555_fail_nw"
 config = "dna_r10.4.1_e8.2_400bps_hac"
 

tests/static/guppy_validation_test/fail/001_no_write_socket.txt

@@ -1 +1 @@
-The user account running readfish doesn't appear to have permissions to write to the guppy base-caller socket. Please check permissions on ipc://tests/static/guppy_validation_test/fail/5555_fail_nw. See /~https://github.com/LooseLab/readfish/issues/221#issuecomment-1375673490 for more information.
+The user account running readfish doesn't appear to have permissions to write to the dorado base-caller socket. Please check permissions on ipc://tests/static/guppy_validation_test/fail/5555_fail_nw. See /~https://github.com/LooseLab/readfish/issues/221#issuecomment-1375673490 for more information.

tests/static/guppy_validation_test/fail/002_missing_socket.toml

@@ -1,4 +1,4 @@
-[caller_settings.guppy]
+[caller_settings.dorado]
 address = "ipc://tests/static/guppy_validation_test/fail/5555_not_there"
 config = "dna_r10.4.1_e8.2_400bps_hac"
 

tests/static/guppy_validation_test/fail/002_missing_socket.txt

@@ -1 +1 @@
-The provided guppy base-caller socket address doesn't appear to exist. Please check your Guppy Settings. ipc://tests/static/guppy_validation_test/fail/5555_not_there
+The provided dorado base-caller socket address doesn't appear to exist. Please check your dorado Settings. ipc://tests/static/guppy_validation_test/fail/5555_not_there

tests/static/guppy_validation_test/fail/003_no_read_socket.toml

@@ -1,4 +1,4 @@
-[caller_settings.guppy]
+[caller_settings.dorado]
 address = "ipc://tests/static/guppy_validation_test/fail/5555_fail_nr"
 config = "dna_r10.4.1_e8.2_400bps_hac"
 

tests/static/guppy_validation_test/fail/003_no_read_socket.txt

@@ -1 +1 @@
-The user account running readfish doesn't appear to have permissions to read the guppy base-caller socket. Please check permissions on ipc://tests/static/guppy_validation_test/fail/5555_fail_nr. See /~https://github.com/LooseLab/readfish/issues/221#issuecomment-1375673490 for more information.
+The user account running readfish doesn't appear to have permissions to read the dorado base-caller socket. Please check permissions on ipc://tests/static/guppy_validation_test/fail/5555_fail_nr. See /~https://github.com/LooseLab/readfish/issues/221#issuecomment-1375673490 for more information.

tests/static/toml_validation_test/fail/001_missing_keys.toml

@@ -1,4 +1,4 @@
-[caller_settings.guppy]
+[caller_settings.dorado]
 host = "127.0.0.1"
 
 [mapper_settings.mappy]