Increase coverage

pytximport/core/_tximport.py

@@ -46,6 +46,7 @@ def tximport(
  output_type: Literal["xarray", "anndata"] = "anndata",
  output_format: Literal["csv", "h5ad"] = "csv",
  save_path: Optional[Union[str, Path]] = None,
+ save_path_override: bool = False,
  return_data: bool = True,
  biotype_filter: Optional[List[str]] = None,
 ) -> Union[xr.Dataset, ad.AnnData, None]:
@@ -93,6 +94,7 @@ def tximport(
  output_type (Literal["xarray", "anndata"], optional): The type of output. Defaults to "anndata".
  output_format (Literal["csv", "h5ad"], optional): The type of output file. Defaults to "csv".
  save_path (Optional[Union[str, Path]], optional): The path to save the gene-level expression. Defaults to None.
+ save_path_override (bool, optional): Whether to override the save path if it already exists. Defaults to False.
  return_data (bool, optional): Whether to return the gene-level expression. Defaults to True.
  biotype_filter (List[str], optional): Filter the transcripts by biotype, including only those provided.
  Defaults to None.
@@ -215,7 +217,6 @@ def tximport(
 
  transcript_data: Optional[xr.Dataset] = None
  file_paths_missing_idx: List[int] = []
- inferential_replicates_data: Optional[xr.DataArray] = None
 
  # iterate through the files
  for file_idx, file_path in tqdm(enumerate(file_paths), desc="Reading quantification files"):
@@ -370,6 +371,17 @@ def tximport(
  )
  result_index = "gene_id"
 
+ if save_path is not None:
+ if not isinstance(save_path, Path):
+ save_path = Path(save_path)
+
+ if save_path.suffix == ".csv" and output_format == "h5ad":
+ warning(
+ "The file extension of the `save_path` is `.csv` but the output format is `.h5ad`. "
+ "Changing the output format to `.csv`."
+ )
+ output_format = "csv"
+
  if output_format == "h5ad" and output_type != "anndata":
  warning("The output format is h5ad but the output type is not anndata. Changing the output type to anndata.")
  output_type = "anndata"
@@ -396,8 +408,13 @@ def tximport(
  )
 
  if save_path is not None:
- if not isinstance(save_path, Path):
- save_path = Path(save_path)
+ if save_path.exists() and not save_path_override:
+ raise FileExistsError(
+ f"The file already exists: {save_path}. Set `save_path_override` to True to override."
+ )
+
+ if not save_path.parent.exists():
+ save_path.parent.mkdir(parents=True)
 
  log(25, f"Saving the gene-level expression to: {save_path}.")
 
@@ -425,8 +442,8 @@ def tximport(
 
  df_gene_data = pd.DataFrame(
  data=count_data,
- index=result[result_index],
- columns=result.coords["file_path"].values,
+ index=(result[result_index] if output_type != "anndata" else result.var.index),
+ columns=(result.coords["file_path"].values if output_type != "anndata" else result.obs.index),
  )
  df_gene_data.sort_index(inplace=True)
  df_gene_data.to_csv(save_path, index=True, header=True, quoting=2)

test/test_export.py

@@ -0,0 +1,49 @@
+"""Test the cli function."""
+
+import os
+from pathlib import Path
+from time import time
+from typing import List
+
+from pytximport import tximport
+
+
+def test_export(
+ salmon_multiple_files: List[Path],
+ transcript_gene_mapping_path_mouse: Path,
+) -> None:
+ """Test saving the output of the tximport function as a csv and h5ad file."""
+ if not os.access(os.getcwd(), os.W_OK):
+ raise PermissionError("The current directory cannot be written to.")
+
+ current_time = int(time())
+
+ _ = tximport(
+ salmon_multiple_files,
+ "salmon",
+ transcript_gene_mapping_path_mouse,
+ output_format="csv",
+ save_path=f"./pytximport_cli_test_{int(time())}.csv",
+ )
+
+ # check that the output file was created
+ assert os.path.exists(f"./pytximport_cli_test_{current_time}.csv"), "Output file was not created."
+
+ # remove the temporary file
+ os.system(f"rm ./pytximport_cli_test_{current_time}.csv") # nosec
+
+ # test saving as h5ad
+ _ = tximport(
+ salmon_multiple_files,
+ "salmon",
+ transcript_gene_mapping_path_mouse,
+ output_type="anndata",
+ output_format="h5ad",
+ save_path=f"./pytximport_cli_test_{current_time}.h5ad",
+ )
+
+ # check that the output file was created
+ assert os.path.exists(f"./pytximport_cli_test_{current_time}.h5ad"), "AnnData output file was not created."
+
+ # remove the temporary file
+ os.system(f"rm ./pytximport_cli_test_{current_time}.h5ad") # nosec