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feat: add new command line options for tree format, usher arguments, threads, matutils overlap, prefix, and plot chunk size #8

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Merged
gp201 merged 4 commits into from
Jun 13, 2025
Merged

feat: add new command line options for tree format, usher arguments, threads, matutils overlap, prefix, and plot chunk size #8

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023b686
feat: add new command line options for tree format, usher arguments, …
gp201 Jun 13, 2025
059138f
fix: update option types for threads and matutils overlap in CLI to e…
gp201 Jun 13, 2025
3175a68
refactor: standardize option names and types in CLI for consistency
gp201 Jun 13, 2025
466e983
fix: standardize CLI option name for tree format to improve consistency
gp201 Jun 13, 2025
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15 changes: 11 additions & 4 deletions barcodeforge/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,39 +34,46 @@ def cli(ctx, debug):
@click.argument("tree", type=click.Path(exists=True, readable=True))
@click.argument("lineages", type=click.Path(exists=True, readable=True))
@click.option(
"--tree_format",
"-t",
"--tree-format",
type=click.Choice(["newick", "nexus"], case_sensitive=False),
help="Specify the format of the tree file (newick or nexus)",
)
@click.option(
"-u",
"--usher-args",
type=str,
default="",
help="Additional arguments to pass to usher (e.g., '-U -l'). Quote multiple arguments.",
)
@click.option(
"-T",
"--threads",
type=int,
type=click.IntRange(min=1),
metavar="INT",
default=8,
show_default=True,
help="Number of CPUs/threads to use.",
)
@click.option(
"-m",
"--matutils-overlap",
type=float,
type=click.FloatRange(min=0.0, max=1.0),
metavar="FLOAT",
default="0",
default=0,
show_default=True,
help="Value for --set-overlap in matUtils annotate.",
)
@click.option(
"-p",
"--prefix",
type=str,
default="",
show_default=True,
help="Prefix to add to lineage names in the barcode file.",
)
@click.option(
"-c",
"--plot-chunk-size",
type=int,
default=100,
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2 changes: 1 addition & 1 deletion barcodeforge/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def resolve_tree_format(
f"[{STYLES['error']}]Error: Unknown tree format for file '{tree_path}'. Extension '{ext}' is not recognized.[/{STYLES['error']}]"
)
console.print(
f"[{STYLES['error']}]Please specify the format using --tree_format ('newick' or 'nexus').[/]"
f"[{STYLES['error']}]Please specify the format using --tree-format ('newick' or 'nexus').[/]"
)
raise click.Abort()

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4 changes: 2 additions & 2 deletions tests/test_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -389,7 +389,7 @@ def test_barcode_command_nexus_tree(runner, temp_files, mocker):
temp_files["alignment"],
temp_files["tree"],
temp_files["lineages"],
"--tree_format",
"--tree-format",
"nexus",
]
result = runner.invoke(cli, args, catch_exceptions=False)
Expand Down Expand Up @@ -446,7 +446,7 @@ def test_barcode_command_newick_tree_reformat(runner, temp_files, mocker):
temp_files["alignment"],
temp_files["tree"],
temp_files["lineages"],
"--tree_format",
"--tree-format",
"newick",
]
result = runner.invoke(cli, args, catch_exceptions=False)
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