Add support for subdir configuration

Author: standage

.gitignore

@@ -3,3 +3,4 @@
 __pycache__
 sandbox/
 dist/
+.vscode/

ezfastq/api.py

@@ -12,12 +12,19 @@
 from pathlib import Path
 
 
-def copy(sample_names, seq_path, pair_mode=PairMode.Unspecified, prefix="", workdir=Path(".")):
+def copy(
+    sample_names,
+    seq_path,
+    pair_mode=PairMode.Unspecified,
+    prefix="",
+    workdir=Path("."),
+    subdir="seq",
+):
     copier = FastqCopier.from_dir(sample_names, seq_path, prefix=prefix, pair_mode=pair_mode)
-    copier.copy_files(workdir / "seq")
+    copier.copy_files(workdir / subdir)
     copier.print_copy_log()
-    nlogs = len(list((workdir / "seq").glob("copy-log-*.toml")))
-    with open(workdir / "seq" / f"copy-log-{nlogs + 1}.toml", "w") as fh:
+    nlogs = len(list((workdir / subdir).glob("copy-log-*.toml")))
+    with open(workdir / subdir / f"copy-log-{nlogs + 1}.toml", "w") as fh:
         print(copier, file=fh)
     added_samples = set(fastq.sample for fastq in copier.copied_files)
     added_samples = sorted(added_samples)

ezfastq/cli.py

@@ -12,6 +12,7 @@
 from argparse import ArgumentParser
 from importlib.metadata import version
 from pathlib import Path
+from rich_argparse import RichHelpFormatter
 
 
 def main(arglist=None):
@@ -22,11 +23,12 @@ def main(arglist=None):
         pair_mode=args.pair_mode,
         prefix=args.prefix,
         workdir=args.workdir,
+        subdir=args.subdir,
     )
 
 
 def parse_args(arglist=None):
-    if arglist:
+    if arglist:  # pragma: no cover
         arglist = map(str, arglist)
     args = get_parser().parse_args(arglist)
     samples_file = Path(args.samples[0])
@@ -38,7 +40,10 @@ def parse_args(arglist=None):
 
 
 def get_parser():
-    parser = ArgumentParser(description="Copy FASTQ files and update sample names")
+    parser = ArgumentParser(
+        description="Copy FASTQ files and use sample names to make filenames consistent",
+        formatter_class=RichHelpFormatter,
+    )
     parser.add_argument(
         "seq_path",
         help="path to directory containing sequences in FASTQ format; subdirectories will be searched recursively",
@@ -57,10 +62,17 @@ def get_parser():
     parser.add_argument(
         "-w",
         "--workdir",
-        metavar="WD",
+        metavar="PATH",
         type=Path,
         default=Path("."),
-        help="directory to which input files will be copied and renamed",
+        help="project directory to which input files will be copied and renamed; current directory is used by default",
+    )
+    parser.add_argument(
+        "-s",
+        "--subdir",
+        metavar="PATH",
+        default="seq",
+        help="subdirectory path under --workdir to which sequence files will be written; PATH=`seq` by default, but can contain nesting (e.g. `seq/study`)",
     )
     parser.add_argument(
         "-p",

ezfastq/tests/test_cli.py

@@ -30,6 +30,15 @@ def test_copy(tmp_path):
     assert "SkippedFiles" not in log_data
 
 
+def test_copy_subdir(tmp_path):
+    seq_path = files("ezfastq") / "tests" / "data" / "flat"
+    arglist = [seq_path, "test1", "test2", "--workdir", tmp_path, "--subdir", "seq/PROJa/RUNb"]
+    cli.main(arglist)
+    rundir = tmp_path / "seq" / "PROJa" / "RUNb"
+    assert rundir.is_dir()
+    assert len(list(rundir.glob("*_R?.fastq.gz"))) == 4
+
+
 def test_copy_sample_names_file(tmp_path):
     sample_names_file = tmp_path / "sample-names.txt"
     sample_names_file.write_text("test1\ntest3\ntest2\n")

pyproject.toml

@@ -6,17 +6,14 @@ readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
     "rich",
+    "rich_argparse",
 ]
 authors = [
     {name = "Daniel Standage", email = "daniel.standage@st.dhs.gov"},
     {name = "Ryan Berger", email = "ryan.berger@st.dhs.gov"},
 ]
 
-[build-system]
-requires = ["setuptools", "setuptools-scm"]
-build-backend = "setuptools.build_meta"
-
-[dependency-groups]
+[project.optional-dependencies]
 dev = [
     "black==25.1",
     "pytest",
@@ -26,5 +23,9 @@ dev = [
 [project.scripts]
 ezfastq = "ezfastq.cli:main"
 
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
 [tool.setuptools]
 packages = ["ezfastq"]