Issue273/README fixes and HTML stats (#283)

* Correcting single image link for testing. * Correcting single image link for testing. * Initial adding of readfish summarise. * Adding images, making minor corrections to text and adding breif readfish stats section. * Adding images, making minor corrections to text and adding breif readfish stats section. * Adding images, making minor corrections to text and adding breif readfish stats section. * Adding images, making minor corrections to text and adding breif readfish stats section. Closes #273 and closes #270 and closes #268 * Updating to a more conventional N50 statistic. * Adding additional 5khz bulkfile and link to close #268 * Add html flag to `stats` command Test HTML table in README.md * Make args optional style and required Rename to --fastq-directory * Bump readfish summarise version requirement * Add default of Non 🇫🇷 to html path * Updating README to html formatted tables driven by readfish_summarise * Update to readfish stats command example. * Move text to correct location * Point image links to main branch * Fix bulk file links and some typos * fix typo --------- Co-authored-by: Adoni5 <roryjmunro1@gmail.com>
LooseLab · Oct 11, 2023 · f058cdd · f058cdd
1 parent d7cf756
commit f058cdd
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Showing 11 changed files with 92 additions and 28 deletions.
diff --git a/README.md b/README.md
diff --git a/docs/_static/images/PlaybackControlRun30Minutes.png b/docs/_static/images/PlaybackControlRun30Minutes.png
diff --git a/docs/_static/images/PlaybackRunTargeted.png b/docs/_static/images/PlaybackRunTargeted.png
diff --git a/docs/_static/images/PlaybackRunTargetedPeak.png b/docs/_static/images/PlaybackRunTargetedPeak.png
diff --git a/docs/_static/images/PlaybackRunTargetedUnblockPeak.png b/docs/_static/images/PlaybackRunTargetedUnblockPeak.png
diff --git a/docs/_static/images/PlaybackUnblockAll30minutes.png b/docs/_static/images/PlaybackUnblockAll30minutes.png
diff --git a/docs/_static/images/PlaybackUnblockAllCloseUp.png b/docs/_static/images/PlaybackUnblockAllCloseUp.png
diff --git a/docs/_static/images/UnblockAllMessages.png b/docs/_static/images/UnblockAllMessages.png
diff --git a/pyproject.toml b/pyproject.toml
@@ -36,7 +36,7 @@ dependencies = [
     "more_itertools",
     'exceptiongroup ; python_version<"3.11"',
     "read_until @ git+https://github.com/nanoporetech/read_until_api@v3.4.1",
-    "readfish_summarise >= 0.2.4",
+    "readfish_summarise >= 0.2.5",
     "readfish[all]",
 ]
 dynamic = ["version"]

diff --git a/src/readfish/entry_points/stats.py b/src/readfish/entry_points/stats.py
@@ -66,6 +66,12 @@
 
     readfish stats --toml tests/static/stats_test/yeast_summary_test.toml --fastq-directory tests/static/stats_test/
 
+To run and output PAF alignments and demutiplexed FASTQ, and output a HTML summary file at summary_adaptive.html
+
+.. code-block:: bash
+
+    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
@@ -84,12 +90,13 @@
 
 _help = "Readfish experiment summary stats"
 _cli = BASE_ARGS + (
-    ("toml", dict(help="TOML file used in the readfish experiment.")),
+    ("--toml", dict(help="TOML file used in the readfish experiment.", required=True)),
     (
-        "fastq_dir",
+        "--fastq-directory",
         dict(
             help="Path to the directory containing the FASTQ files produced by the readfish experiment",
             type=Path,
+            required=True,
         ),
     ),
     (
@@ -116,10 +123,18 @@
     (
         "--prom",
         dict(
-            help="Use this flag if the target platform was a PromethION",
+            help="Use this flag if the target platform was a PromethION. Disabled by default.",
             action="store_true",
         ),
     ),
+    (
+        "--html",
+        dict(
+            help="Filepath to output a HTML file of the summary. Will append .html to given filename/path. Disabled by default.",
+            type=Path,
+            default=None,
+        ),
+    ),
 )
 
 
@@ -152,11 +167,12 @@ def run(_parser, args: argparse.NameSpace, _extras):
     try:
         _fastq(
             args.toml,
-            args.fastq_dir,
+            args.fastq_directory,
             demultiplex=args.no_demultiplex,
             paf_out=args.no_paf_out,
             prom=args.prom,
             csv=args.no_csv,
+            html=args.html,
         )
     except Exception as exc:
         logger.error("Fastq data couldn't be summarised, see below for details:")

diff --git a/tests/stats_test.py b/tests/stats_test.py
@@ -51,7 +51,9 @@ def test_fastq_stats(capfd, toml_file, fastq_directory, expected):
         readfish._cli_base.main(
             [
                 "stats",
+                "--toml",
                 str(toml_file),
+                "--fastq-directory",
                 str(fastq_directory),
                 "--no-paf-out",
                 "--no-demultiplex",