Output TSV file to standard output by default

.github/workflows/rich_codex.yml

@@ -14,6 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       FORCE_COLOR: "true"
+
     steps:
       - name: Check out the repo
         uses: actions/checkout@v3

CHANGELOG.md

@@ -11,6 +11,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - Mash sketch files are now validated using MD5 checksum to ensure integrity
+- Added `--table-path` option to `search-pangenomes` to save TSV output to a file
+- Added `--no-table` flag to disable table output in `search-pangenomes`
+- `list-collections` now automatically detects terminal vs redirected output: displays formatted table in interactive terminals, plain TSV when redirected to files or pipes
+
+### Changed
+
+- `search-pangenomes` table output now defaults to stdout instead of a file (previous default was `pangenomes_information.tsv`)
 
 ## [0.1.1] - 2025-11-09
 

README.md

@@ -107,21 +107,23 @@ pangbank search-pangenomes --help
 pangbank list-collections
 ```
 
-Displays all pangenome collections available in PanGBank, along with their description and the number of pangenomes they contain.
+Displays the list all pangenome collections available in PanGBank, along with their description and the number of pangenomes they contain.
+
+Output is formatted as a rich table in the terminal, or as plain TSV when redirected (e.g., `pangbank list-collections > collections.tsv`).
 
-<!-- RICH-CODEX hide_command: true -->
-![`TERMINAL_WIDTH=110 pangbank list-collections`](docs/img/pangbank-list-collections.svg)
 
 ### Search for pangenomes
 
 ```bash
 pangbank search-pangenomes --taxon "g__Escherichia"
 ```
 
-Searches PanGBank for pangenomes matching the given taxon.
-Results are saved as a **TSV file** named 'pangenomes_information.tsv' by default containing summary metrics for the matching pangenomes.
+![`pangbank search-pangenomes --taxon "g__Escherichia" --no-progress --table-path pangenome_information.tsv`](docs/img/pangbank-search-pangenomes_taxon_Escherichia.svg)
+
+
+This command searches PanGBank for pangenomes matching the given taxon.
+Results are printed to **stdout** as plain TSV by default (suitable for piping or redirection). Use `--table-path <file>` to save directly to a file (e.g., `--table-path pangenomes_information.tsv`), or `--no-table` to disable table output.
 
-![`pangbank search-pangenomes --taxon "g__Escherichia" --no-progress`](docs/img/pangbank-search-pangenomes_taxon_Escherichia.svg)
 
 ### Download pangenomes
 
@@ -132,10 +134,11 @@ pangbank search-pangenomes --taxon "g__Chlamydia" \
     --download
 ```
 
-Searches for **Chlamydia** pangenomes in the `GTDB_refseq` collection, then downloads the corresponding pangenome files into `Chlamydia_pangenomes/`.
-
 ![`pangbank search-pangenomes --taxon "g__Chlamydia" --collection GTDB_refseq --outdir Chlamydia_pangenomes/ --download --no-progress`](docs/img/pangbank-search-pangenomes_taxon_Chlamydia_download.svg)
 
+This command searches for **Chlamydia** pangenomes in the `GTDB_refseq` collection, then downloads the corresponding pangenome files into `Chlamydia_pangenomes/`.
+
+
 ### Match a genome to an existing pangenome
 
 ```bash

pangbank_cli/main.py

@@ -174,7 +174,13 @@ def list_collections(
     logger.info(f"Found {len(collections)} collections in PanGBank.")
 
     df = format_collections_to_dataframe(collections)
-    print_dataframe_as_rich_table(df, title="Available collections of PanGBank:")
+
+    # Use rich formatting if interactive terminal, plain TSV if redirected
+    if sys.stdout.isatty():
+        print_dataframe_as_rich_table(df, title="Available collections of PanGBank:")
+    else:
+        df.to_csv(sys.stdout, index=False, sep="\t")
+
     print_yaml = False
     if print_yaml:
         yaml_collections = format_collections_to_yaml(collections)
@@ -234,17 +240,24 @@ def search_pangenomes(
             rich_help_panel="Output and downloads",
         ),
     ] = False,
+    table: Annotated[
+        bool,
+        typer.Option(
+            help="Output a TSV table summarizing the matching pangenomes to stdout.",
+            rich_help_panel="Output and downloads",
+        ),
+    ] = True,
     table_path: Annotated[
-        Path,
+        Optional[Path],
         typer.Option(
-            "--table",
+            "--table-path",
             help=(
-                "Save a TSV table summarizing the matching pangenomes. "
-                "Use '-' to print the table to stdout."
+                "Save TSV table to a file instead of stdout (e.g., pangenomes_information.tsv). "
+                "Implies --table."
             ),
             rich_help_panel="Output and downloads",
         ),
-    ] = Path("pangenomes_information.tsv"),
+    ] = None,
     # Execution settings
     api_url: HttpUrl = ApiUrlOption,
     verbose: bool = Verbose,
@@ -282,14 +295,18 @@ def search_pangenomes(
 
     df = format_pangenomes_to_dataframe(pangenomes)
 
-    if str(table_path) == "-":
-        logger.info("Printing pangenomes information as TSV table to stdout")
-        output_handle: TextIO | Path = sys.stdout
-    else:
-        logger.info(f"Saving pangenomes information as TSV table to file: {table_path}")
-        output_handle: TextIO | Path = table_path
+    # Output table if enabled
+    if table or table_path is not None:
+        if table_path is not None:
+            logger.info(
+                f"Saving pangenomes information as TSV table to file: {table_path}"
+            )
+            output_handle: TextIO | Path = table_path
+        else:
+            logger.info("Printing pangenomes information as TSV table to stdout")
+            output_handle: TextIO | Path = sys.stdout
 
-    df.to_csv(output_handle, index=False, sep="\t")
+        df.to_csv(output_handle, index=False, sep="\t")
 
     if details:
         display_pangenome_summary_by_collection(pangenomes, True)

pangbank_cli/utils.py

@@ -28,7 +28,7 @@ def print_dataframe_as_rich_table(df: pd.DataFrame, title: Optional[str] = None)
         except ValueError:
             pass  # If not a valid integer, keep None
 
-    console = Console(stderr=True, width=terminal_width)
+    console = Console(width=terminal_width)
     table = Table(
         title=title,
         show_header=True,