--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scimap_phenotyping.py	Tue Jul 19 20:29:22 2022 +0000
@@ -0,0 +1,73 @@
+import argparse
+import warnings
+
+import pandas as pd
+import scimap as sm
+from anndata import read_h5ad
+
+
+def main(
+    adata,
+    output,
+    gating_workflow,
+    gating_workflow_ext,
+    manual_gates=None,
+    manual_gates_ext=None,
+    rescale_plots=False
+):
+    """
+    Parameter
+    ---------
+    adata : str
+        File path to the input AnnData.
+    output : str
+        File path to the output AnnData.
+    gating_workflow : str
+        File path to the gating workflow.
+    gating_workflow_ext : str
+        Datatype for gating workflow, either 'csv' or 'tabular'.
+    manual_gates : str
+        File path to the munual gating.
+    manual_gates_ext : str
+        Datatype for munual gate, either 'csv' or 'tabular'.
+    rescale_plots : boolean
+        Save plots from rescaling.
+    """
+    warnings.simplefilter('ignore')
+
+    adata = read_h5ad(adata)
+    # Rescale data
+    if manual_gates:
+        sep = ',' if manual_gates_ext == 'csv' else '\t'
+        manual_gates = pd.read_csv(manual_gates, sep=sep)
+
+    adata = sm.pp.rescale(adata, gate=manual_gates, save_fig=rescale_plots)
+
+    # Phenotype cells
+    # Load the gating workflow
+    sep = ',' if gating_workflow_ext == 'csv' else '\t'
+    phenotype = pd.read_csv(gating_workflow, sep=sep)
+    adata = sm.tl.phenotype_cells(adata, phenotype=phenotype, label="phenotype")
+
+    # Summary of the phenotyping
+    print(adata.obs['phenotype'].value_counts())
+
+    adata.write(output)
+
+
+if __name__ == '__main__':
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument("-a", "--adata", dest="adata", required=True)
+    aparser.add_argument("-o", "--output", dest="output", required=True)
+    aparser.add_argument("-g", "--gating_workflow", dest="gating_workflow", required=True)
+    aparser.add_argument("-s", "--gating_workflow_ext", dest="gating_workflow_ext", required=True)
+    aparser.add_argument("-m", "--manual_gates", dest="manual_gates", required=False)
+    aparser.add_argument("-S", "--manual_gates_ext", dest="manual_gates_ext", required=False)
+    aparser.add_argument("-p", "--rescale_plots", dest="rescale_plots", action="store_true",
+                         default=False, required=False)
+
+    args = aparser.parse_args()
+
+    main(args.adata, args.output, args.gating_workflow,
+         args.gating_workflow_ext, args.manual_gates,
+         args.manual_gates_ext, args.rescale_plots)