diff scimap_phenotyping.py @ 0:199b5f278356 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scimap_phenotyping.py	Mon Jun 10 18:44:49 2024 +0000
@@ -0,0 +1,120 @@
+import argparse
+import warnings
+
+import pandas as pd
+import scimap as sm
+from anndata import read_h5ad
+
+
+def main(
+    adata,
+    output,
+    log,
+    gating_workflow,
+    gating_workflow_ext,
+    manual_gates=None,
+    manual_gates_ext=None,
+    random_state=0
+):
+    """
+    Parameter
+    ---------
+    adata : str
+        File path to the input AnnData.
+    output : str
+        File path to the output AnnData.
+    log: bool
+        Boolean whether to log the input data prior to rescaling
+    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'.
+    random_state: int
+        The seed used by the random number generator for GMM in sm.pp.rescale
+    """
+    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,
+        log=log,
+        random_state=random_state
+    )
+
+    # 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("-l", "--log", dest="log", action="store_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(
+        "--random_state",
+        dest="random_state",
+        type=int,
+        required=False
+    )
+
+    args = aparser.parse_args()
+
+    if args.log:
+        print("\n adata.raw.X will be log1p transformed \n")
+
+    main(
+        adata=args.adata,
+        output=args.output,
+        log=args.log,
+        gating_workflow=args.gating_workflow,
+        gating_workflow_ext=args.gating_workflow_ext,
+        manual_gates=args.manual_gates,
+        manual_gates_ext=args.manual_gates_ext,
+        random_state=args.random_state
+    )