Merge pull request #81 from remiolsen/typer

Switch CLI over to typer, change command to "anglerfish run"

Author: remiolsen

.github/workflows/anglerfish.yml

@@ -37,4 +37,10 @@ jobs:
       - shell: bash -l {0}
         name: Run anglerfish with test data
         run: |
-          anglerfish -s test/samples.csv
+          anglerfish run -s test/samples.csv
+
+      # Run anglerfish explore
+      - shell: bash -l {0}
+        name: Run anglerfish explore
+        run: |
+          anglerfish explore -f test/BC18_P14351_1001.fastq.gz -o test/explore_output

README.md

@@ -122,7 +122,7 @@ P12345_101,truseq,CAGGACGT,/path/to/*.fastq.gz
 Then run:
 
 ```
-anglerfish -s /path/to/samples.csv
+anglerfish run -s /path/to/samples.csv
 ```
 
 ### Options
@@ -173,10 +173,10 @@ In folder `anglerfish_????_??_??_?????/`
 
 ## Anglerfish Explore (Experimental)
 
-`anglerfish-explore` is a command that aims to explore a sequencing pool without a given samplesheet and give hints on what adapter types are present, which index lenghts are used and whether there are any UMIs within the index sequence. The Anglerfish explore command is still under heavy development but can be triggered by running, e.g. for help text:
+`anglerfish explore` is a command that aims to explore a sequencing pool without a given samplesheet and give hints on what adapter types are present, which index lenghts are used and whether there are any UMIs within the index sequence. The Anglerfish explore command is still under heavy development but can be triggered by running, e.g. for help text:
 
 ```shell
-anglerfish-explore --help
+anglerfish explore --help
 ```
 
 ## Credits

anglerfish/__main__.py

@@ -1,7 +1,7 @@
 import multiprocessing
 
-from .anglerfish import anglerfish
+from .cli import app
 
 if __name__ == "__main__":
     multiprocessing.freeze_support()
-    anglerfish()
+    app()

anglerfish/anglerfish.py

@@ -1,13 +1,12 @@
 #!/usr/bin/env python
-import argparse
 import glob
 import gzip
 import logging
 import multiprocessing
 import os
+import sys
 import uuid
 from collections import Counter
-from datetime import datetime as dt
 from itertools import groupby
 
 import numpy as np
@@ -39,7 +38,18 @@ 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("""
+     ___
+   ( )  \ -..__
+      _.|~”~~~”…_
+    ^´           `>.
+(+ (+ )             “<..<^(
+  `´  ``´      ___       (
+   \__..~      __(   _…_(
+   \                /
+    “--…_     _..~%´
+         ```´´
+""")
     log.info(f" version {version}")
     log.info(f" arguments {vars(args)}")
     log.info(f" run uuid {run_uuid}")
@@ -118,7 +128,7 @@ def run_demux(args):
             "i5": {"i7_reversed": False, "i5_reversed": True},
             "i7+i5": {"i7_reversed": True, "i5_reversed": True},
         }
-        if args.force_rc is not None:
+        if args.force_rc != "original":
             log.info(
                 f" Force reverse complementing {args.force_rc} index for adaptor {adaptor_name}. Lenient mode is disabled"
             )
@@ -245,105 +255,3 @@ def run_demux(args):
     report.write_report(args.out_fastq)
     report.write_json(args.out_fastq)
     report.write_dataframe(args.out_fastq, ss)
-
-    if args.skip_fastqc:
-        log.warning(
-            " As of version 0.4.1, built in support for FastQC + MultiQC is removed. The '-f' flag is redundant."
-        )
-
-
-def anglerfish():
-    parser = argparse.ArgumentParser(
-        description="Tools to demux I7 and I5 barcodes when sequenced by single-molecules"
-    )
-    parser.add_argument(
-        "--samplesheet",
-        "-s",
-        required=True,
-        help="CSV formatted list of samples and barcodes",
-    )
-    parser.add_argument(
-        "--out_fastq",
-        "-o",
-        default=".",
-        help="Analysis output folder (default: Current dir)",
-    )
-    parser.add_argument(
-        "--threads",
-        "-t",
-        default=4,
-        type=int,
-        help="Number of threads to use (default: 4)",
-    )
-    parser.add_argument(
-        "--skip_demux",
-        "-c",
-        action="store_true",
-        help="Only do BC counting and not demuxing",
-    )
-    parser.add_argument(
-        "--skip_fastqc", "-f", action="store_true", help=argparse.SUPPRESS
-    )
-    parser.add_argument(
-        "--max-distance",
-        "-m",
-        type=int,
-        help="Manually set maximum edit distance for BC matching, automatically set this is set to either 1 or 2",
-    )
-    parser.add_argument(
-        "--max-unknowns",
-        "-u",
-        type=int,
-        help="Maximum number of unknown indices to show in the output (default: length of samplesheet + 10)",
-    )
-    parser.add_argument(
-        "--run_name",
-        "-r",
-        default="anglerfish",
-        help="Name of the run (default: anglerfish)",
-    )
-    parser.add_argument(
-        "--lenient",
-        "-l",
-        action="store_true",
-        help="Will try reverse complementing the I5 and/or I7 indices and choose the best match.",
-    )
-    parser.add_argument(
-        "--lenient_factor",
-        "-x",
-        default=4.0,
-        type=float,
-        help="If lenient is set, this is the minimum factor of additional matches required to reverse complement the index (default: 4.0)",
-    )
-    parser.add_argument(
-        "--force_rc",
-        "-p",
-        choices=["i7", "i5", "i7+i5"],
-        help="Force reverse complementing the I5 and/or I7 indices. This will disregard lenient mode.",
-    )
-    parser.add_argument(
-        "--ont_barcodes",
-        "-n",
-        action="store_true",
-        help="Will assume the samplesheet refers to a single ONT run prepped with a barcoding kit. And will treat each barcode separately",
-    )
-    parser.add_argument(
-        "--debug", "-d", action="store_true", help="Extra commandline output"
-    )
-    parser.add_argument(
-        "--version",
-        "-v",
-        action="version",
-        help="Print version and quit",
-        version=f'anglerfish {pkg_resources.get_distribution("bio-anglerfish").version}',
-    )
-    args = parser.parse_args()
-    utcnow = dt.utcnow()
-    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)
-    args.out_fastq = os.path.join(os.path.abspath(args.out_fastq), runname)
-    args.samplesheet = os.path.abspath(args.samplesheet)
-    args.run_name = runname
-    run_demux(args)