Added explore as a command

anglerfish/cli.py

@@ -1,12 +1,15 @@
 import argparse
+import datetime as dt
 import os
-from datetime import datetime as dt
 from enum import Enum
 
+import pkg_resources
 import typer
 from typing_extensions import Annotated
+from typing import Optional
 
 from .anglerfish import run_demux
+from .explore.explore import run_explore
 
 app = typer.Typer(pretty_exceptions_show_locals=False)
 
@@ -15,7 +18,155 @@ class IndexOrientations(str, Enum):
     i7 = "i7"
     i5 = "i5"
     i7i5 = "i7+i5"
-    default = "default"
+
+
+def version_callback(value: bool):
+    if value:
+        print(f'anglerfish {pkg_resources.get_distribution("bio-anglerfish").version}')
+        raise typer.Exit()
+
+
+def deprecated_callback(value: bool):
+    if value:
+        raise typer.BadParameter(
+            "Please use the 'anglerfish run -s' command to run anglerfish with a samplesheet. Running only 'anglerfish -s' is not supported as of version 0.7.0"
+        )
+
+
+@app.callback()
+def main(
+    version: Annotated[
+        Optional[bool],
+        typer.Option(
+            "--version",
+            "-v",
+            help="Print version and quit",
+            is_eager=True,
+            callback=version_callback,
+        ),
+    ] = False,
+    samplesheet: Annotated[
+        Optional[str],
+        typer.Option(
+            "--samplesheet",
+            "-s",
+            hidden=True,
+            is_eager=True,
+            callback=deprecated_callback,
+        ),
+    ] = "",
+):
+    """
+    Anglerfish is a tool designed to demultiplex Illumina libraries sequenced on Oxford Nanopore flowcells.
+    The primary purpose for this would be to do QC, i.e. to check pool balancing, assess contamination, library insert sizes and so on.
+    """
+    if samplesheet:
+        raise typer.BadParameter(
+            "Please use the 'run' command to run anglerfish with a samplesheet. Running only 'anglerfish' is not supported as of version 0.7.0"
+        )
+
+
+@app.command()
+def explore(
+    fastq: Annotated[str, typer.Option("--fastq", "-f", help="Fastq file to align")],
+    outdir: Annotated[str, typer.Option("--outdir", "-o", help="Output directory")],
+    threads: Annotated[
+        int,
+        typer.Option(
+            "--threads",
+            "-t",
+            help="Number of threads specified to minimap2",
+        ),
+    ] = 4,
+    use_existing: Annotated[
+        bool,
+        typer.Option(
+            "--use-existing",
+            "-e",
+            help="Use existing alignments if found in the specified output directory.",
+        ),
+    ] = False,
+    good_hit_threshold: Annotated[
+        float,
+        typer.Option(
+            "--good_hit_threshold",
+            "-g",
+            help="Fraction of adaptor bases immediately before and immediately after index insert required to match perfectly for a hit to be considered a good hit",
+        ),
+    ] = 0.9,
+    insert_thres_low: Annotated[
+        int,
+        typer.Option(
+            "--insert_thres_low",
+            "-i",
+            help="Lower threshold for index(+UMI) insert length, with value included.",
+        ),
+    ] = 4,
+    insert_thres_high: Annotated[
+        int,
+        typer.Option(
+            "--insert_thres_high",
+            "-j",
+            help="Upper threshold for index(+UMI) insert length, with value included.",
+        ),
+    ] = 30,
+    minimap_b: Annotated[
+        int,
+        typer.Option(
+            "--minimap_b",
+            "-B",
+            help="Minimap2 -B parameter, mismatch penalty.",
+        ),
+    ] = 4,
+    min_hits_per_adaptor: Annotated[
+        int,
+        typer.Option(
+            "--min_hits_per_adaptor",
+            "-m",
+            help="Minimum number of good hits for an adaptor to be included in the analysis.",
+        ),
+    ] = 50,
+    umi_threshold: Annotated[
+        float,
+        typer.Option(
+            "--umi_threshold",
+            "-u",
+            help="Minimum number of bases in insert to perform entropy calculation.",
+        ),
+    ] = 11,
+    kmer_length: Annotated[
+        int,
+        typer.Option(
+            "--kmer_length",
+            "-k",
+            help="Kmer length for entropy calculation.",
+        ),
+    ] = 2,
+    version: Annotated[
+        Optional[bool],
+        typer.Option(
+            "--version",
+            "-v",
+            help="Print version and quit",
+            is_eager=True,
+            callback=version_callback,
+        ),
+    ] = False,
+):
+    """This is an advanced samplesheet-free version of anglerfish."""
+    run_explore(
+        fastq,
+        outdir,
+        threads,
+        use_existing,
+        good_hit_threshold,
+        insert_thres_low,
+        insert_thres_high,
+        minimap_b,
+        min_hits_per_adaptor,
+        umi_threshold,
+        kmer_length,
+    )
 
 
 @app.command()
@@ -70,15 +221,15 @@ def run(
             "-x",
             help="If lenient is set, this is the minimum factor of additional matches required to reverse complement the index",
         ),
-    ] = 2,
+    ] = 4.0,
     force_rc: Annotated[
         IndexOrientations,
         typer.Option(
             "--force_rc",
             "-p",
-            help="Force reverse complementing the I5 and/or I7 indices. This will disregard lenient mode.",
+            help="Force reverse complementing the I5 and/or I7 indices. If set to anything other than 'original' this will disregard lenient mode.",
         ),
-    ] = IndexOrientations.default,
+    ] = None,
     ont_barcodes: Annotated[
         bool,
         typer.Option(
@@ -89,10 +240,17 @@ def run(
     ] = False,
     debug: Annotated[bool, typer.Option("--debug", "-d", help="Debug mode")] = False,
     version: Annotated[
-        bool, typer.Option("--version", "-v", help="Print version and quit")
+        Optional[bool],
+        typer.Option(
+            "--version",
+            "-v",
+            help="Print version and quit",
+            is_eager=True,
+            callback=version_callback,
+        ),
     ] = False,
 ):
-    """Run anglerfish demux. Now with emojis 💩✨"""
+    """Run anglerfish. This is the main command for anglerfish"""
     args = argparse.Namespace(
         samplesheet=samplesheet,
         out_fastq=out_fastq,
@@ -108,10 +266,12 @@ def run(
         debug=debug,
         version=version,
     )
-    utcnow = dt.utcnow()
+    utcnow = dt.datetime.now(dt.timezone.utc)
     runname = utcnow.strftime(f"{args.run_name}_%Y_%m_%d_%H%M%S")
-    assert os.path.exists(args.out_fastq)
-    assert os.path.exists(args.samplesheet)
+    assert os.path.exists(args.out_fastq), f"Output folder '{args.out_fastq}' not found"
+    assert os.path.exists(
+        args.samplesheet
+    ), f"Samplesheet file '{args.samplesheet}' not found, please provide a valid path when using the --samplesheet option."
     args.out_fastq = os.path.join(os.path.abspath(args.out_fastq), runname)
     args.samplesheet = os.path.abspath(args.samplesheet)
     args.run_name = runname