mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-27 01:08:11 +08:00
Apply yapf to python files
This commit is contained in:
Matt Weiden
+90
-47
@@ -8,9 +8,11 @@ from server.utils.utils import sort_options
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@sort_options
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@click.command(short_help="Preprocess data for use with cellxgene. "
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"Run `cellxgene prepare --help` for more information.",
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options_metavar="<options>",)
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@click.command(
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short_help="Preprocess data for use with cellxgene. "
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"Run `cellxgene prepare --help` for more information.",
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options_metavar="<options>",
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)
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@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
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@click.option(
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"--embedding",
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@@ -29,43 +31,66 @@ from server.utils.utils import sort_options
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help="Preprocessing to run.",
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show_default=True,
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)
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@click.option("--output", "-o", default="", help="Save a new file to filename.", metavar="<filename>")
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@click.option("--plotting", "-p", default=False, is_flag=True, help="Generate plots.", show_default=True)
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@click.option("--sparse", default=False, is_flag=True, help="Force sparsity.", show_default=True)
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@click.option("--overwrite", default=False, is_flag=True, help="Allow file overwriting.", show_default=True)
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@click.option("--set-obs-names", default="", help="Named field to set as index for obs.", metavar="<name>")
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@click.option("--set-var-names", default="", help="Named field to set as index for var.", metavar="<name>")
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@click.option("--skip-qc", default=False, is_flag=True,
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help="Do not run quality control metrics. By default cellxgene runs them "
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"(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details).")
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@click.option("--output",
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"-o",
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default="",
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help="Save a new file to filename.",
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metavar="<filename>")
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@click.option("--plotting",
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"-p",
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default=False,
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is_flag=True,
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help="Generate plots.",
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show_default=True)
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@click.option("--sparse",
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default=False,
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is_flag=True,
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help="Force sparsity.",
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show_default=True)
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@click.option("--overwrite",
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default=False,
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is_flag=True,
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help="Allow file overwriting.",
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show_default=True)
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@click.option("--set-obs-names",
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default="",
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help="Named field to set as index for obs.",
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metavar="<name>")
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@click.option("--set-var-names",
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default="",
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help="Named field to set as index for var.",
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metavar="<name>")
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@click.option(
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"--make-obs-names-unique",
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default=True,
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"--skip-qc",
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default=False,
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is_flag=True,
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help="Ensure obs index is unique.",
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show_default=True
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)
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@click.option(
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"--make-var-names-unique",
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default=True,
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is_flag=True,
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help="Ensure var index is unique.",
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show_default=True
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help="Do not run quality control metrics. By default cellxgene runs them "
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"(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details)."
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)
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@click.option("--make-obs-names-unique",
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default=True,
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is_flag=True,
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help="Ensure obs index is unique.",
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show_default=True)
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@click.option("--make-var-names-unique",
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default=True,
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is_flag=True,
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help="Ensure var index is unique.",
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show_default=True)
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@click.help_option("--help", "-h", help="Show this message and exit.")
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def prepare(
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data,
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embedding,
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recipe,
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output,
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plotting,
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sparse,
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overwrite,
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set_obs_names,
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set_var_names,
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skip_qc,
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make_obs_names_unique,
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make_var_names_unique,
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data,
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embedding,
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recipe,
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output,
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plotting,
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sparse,
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overwrite,
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set_obs_names,
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set_var_names,
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skip_qc,
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make_obs_names_unique,
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make_var_names_unique,
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):
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"""
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Preprocess data for use with cellxgene.
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@@ -86,8 +111,7 @@ def prepare(
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except ImportError:
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raise click.ClickException(
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"[cellxgene] cellxgene prepare has not been installed. Please run `pip install cellxgene[prepare]` "
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"to install the necessary requirements."
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)
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"to install the necessary requirements.")
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# scanpy settings
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sc.settings.verbosity = 0
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@@ -102,10 +126,11 @@ def prepare(
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if not output:
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click.echo(
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"Warning: No file will be saved, to save the results of cellxgene prepare include "
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"--output <filename> to save output to a new file"
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)
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"--output <filename> to save output to a new file")
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if isfile(output) and not overwrite:
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raise click.UsageError(f"Cannot overwrite existing file {output}, try using the flag --overwrite")
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raise click.UsageError(
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f"Cannot overwrite existing file {output}, try using the flag --overwrite"
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)
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def load_data(data):
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if isfile(data):
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@@ -115,7 +140,9 @@ def prepare(
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elif extension == ".loom":
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adata = sc.read_loom(data)
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else:
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raise click.FileError(data, hint="does not have a valid extension [.h5ad | .loom]")
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raise click.FileError(
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data,
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hint="does not have a valid extension [.h5ad | .loom]")
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elif isdir(data):
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if not data.endswith(sep):
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data += sep
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@@ -125,11 +152,15 @@ def prepare(
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if not set_obs_names == "":
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if set_obs_names not in adata.obs_keys():
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raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
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raise click.UsageError(
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f"obs {set_obs_names} not found, options are: {adata.obs_keys()}"
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)
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adata.obs_names = adata.obs[set_obs_names]
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if not set_var_names == "":
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if set_var_names not in adata.var_keys():
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raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
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raise click.UsageError(
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f"var {set_var_names} not found, options are: {adata.var_keys()}"
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)
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adata.var_names = adata.var[set_var_names]
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if make_obs_names_unique:
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adata.obs_names_make_unique()
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@@ -184,12 +215,18 @@ def prepare(
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if "umap" in embedding:
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sc.tl.umap(adata)
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if plotting:
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sc.pl.umap(adata, color="louvain", palette=palette, save="_louvain")
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sc.pl.umap(adata,
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color="louvain",
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palette=palette,
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save="_louvain")
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if "tsne" in embedding:
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sc.tl.tsne(adata)
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if plotting:
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sc.pl.tsne(adata, color="louvain", palette=palette, save="_louvain")
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sc.pl.tsne(adata,
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color="louvain",
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palette=palette,
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save="_louvain")
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def show_step(item):
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if not skip_qc:
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@@ -208,13 +245,19 @@ def prepare(
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if item is not None:
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return names[item.__name__]
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steps = [calculate_qc_metrics, make_sparse, run_recipe, run_pca, run_neighbors, run_louvain, run_embedding]
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steps = [
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calculate_qc_metrics, make_sparse, run_recipe, run_pca, run_neighbors,
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run_louvain, run_embedding
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]
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click.echo(f"[cellxgene] Loading data from {data}, please wait...")
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adata = load_data(data)
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click.echo("[cellxgene] Beginning preprocessing...")
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with click.progressbar(steps, label="[cellxgene] Progress", show_eta=False, item_show_func=show_step) as bar:
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with click.progressbar(steps,
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label="[cellxgene] Progress",
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show_eta=False,
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item_show_func=show_step) as bar:
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for step in bar:
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step(adata)
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