diff decoupler_aucell_score.py @ 3:4fa5f370599f draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/decoupler_aucell_score.py	Thu Nov 09 11:35:57 2023 +0000
@@ -0,0 +1,181 @@
+import argparse
+import os
+import tempfile
+
+import anndata
+import decoupler as dc
+import pandas as pd
+
+
+def read_gmt(gmt_file):
+    """
+    Reads a GMT file into a Pandas DataFrame.
+
+    Parameters
+    ----------
+    gmt_file : str
+        Path to the GMT file.
+
+    Returns
+    -------
+    pd.DataFrame
+        A DataFrame with the gene sets. Each row represents a gene set, and the columns are "gene_set_name", "gene_set_url", and "genes".
+    >>> line = "HALLMARK_NOTCH_SIGNALING\\thttp://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HALLMARK_NOTCH_SIGNALING\\tJAG1\\tNOTCH3\\tNOTCH2\\tAPH1A\\tHES1\\tCCND1\\tFZD1\\tPSEN2\\tFZD7\\tDTX1\\tDLL1\\tFZD5\\tMAML2\\tNOTCH1\\tPSENEN\\tWNT5A\\tCUL1\\tWNT2\\tDTX4\\tSAP30\\tPPARD\\tKAT2A\\tHEYL\\tSKP1\\tRBX1\\tTCF7L2\\tARRB1\\tLFNG\\tPRKCA\\tDTX2\\tST3GAL6\\tFBXW11\\n"
+    >>> line2 = "HALLMARK_APICAL_SURFACE\\thttp://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HALLMARK_APICAL_SURFACE\\tB4GALT1\\tRHCG\\tMAL\\tLYPD3\\tPKHD1\\tATP6V0A4\\tCRYBG1\\tSHROOM2\\tSRPX\\tMDGA1\\tTMEM8B\\tTHY1\\tPCSK9\\tEPHB4\\tDCBLD2\\tGHRL\\tLYN\\tGAS1\\tFLOT2\\tPLAUR\\tAKAP7\\tATP8B1\\tEFNA5\\tSLC34A3\\tAPP\\tGSTM3\\tHSPB1\\tSLC2A4\\tIL2RB\\tRTN4RL1\\tNCOA6\\tSULF2\\tADAM10\\tBRCA1\\tGATA3\\tAFAP1L2\\tIL2RG\\tCD160\\tADIPOR2\\tSLC22A12\\tNTNG1\\tSCUBE1\\tCX3CL1\\tCROCC\\n"
+    >>> temp_dir = tempfile.gettempdir()
+    >>> temp_gmt = os.path.join(temp_dir, "temp_file.gmt")
+    >>> with open(temp_gmt, "w") as f:
+    ...   f.write(line)
+    ...   f.write(line2)
+    288
+    380
+    >>> df = read_gmt(temp_gmt)
+    >>> df.shape[0]
+    2
+    >>> df.columns == ["gene_set_name", "genes"]
+    array([ True,  True])
+    >>> df.loc[df["gene_set_name"] == "HALLMARK_APICAL_SURFACE"].genes.tolist()[0].startswith("B4GALT1")
+    True
+    """
+    # Read the GMT file into a list of lines
+    with open(gmt_file, "r") as f:
+        lines = f.readlines()
+
+    # Create a list of dictionaries, where each dictionary represents a gene set
+    gene_sets = []
+    for line in lines:
+        fields = line.strip().split("\t")
+        gene_set = {"gene_set_name": fields[0], "genes": ",".join(fields[2:])}
+        gene_sets.append(gene_set)
+
+    # Convert the list of dictionaries to a DataFrame
+    return pd.DataFrame(gene_sets)
+
+
+def score_genes_aucell(
+    adata: anndata.AnnData, gene_list: list, score_name: str, use_raw=False
+):
+    """Score genes using Aucell.
+
+    Parameters
+    ----------
+    adata : anndata.AnnData
+    gene_list : list
+    score_names : str
+    use_raw : bool, optional
+
+    >>> import scanpy as sc
+    >>> import decoupler as dc
+    >>> adata = sc.datasets.pbmc68k_reduced()
+    >>> gene_list = adata.var[adata.var.index.str.startswith("RP")].index.tolist()
+    >>> score_genes_aucell(adata, gene_list, "ribosomal_aucell", use_raw=False)
+    >>> "ribosomal_aucell" in adata.obs.columns
+    True
+    """
+    # make a data.frame with two columns, geneset and gene_id, geneset filled with score_names and gene_id with gene_list, one row per element
+    geneset_df = pd.DataFrame(
+        {
+            "gene_id": gene_list,
+            "geneset": score_name,
+        }
+    )
+    # run decoupler's run_aucell
+    dc.run_aucell(
+        adata, net=geneset_df, source="geneset", target="gene_id", use_raw=use_raw
+    )
+    # copy .obsm['aucell_estimate'] matrix columns to adata.obs using the column names
+    adata.obs[score_name] = adata.obsm["aucell_estimate"][score_name]
+
+
+def run_for_genelists(
+    adata, gene_lists, score_names, use_raw=False, gene_symbols_field="gene_symbols"
+):
+    if len(gene_lists) == len(score_names):
+        for gene_list, score_names in zip(gene_lists, score_names):
+            genes = gene_list.split(",")
+            ens_gene_ids = adata.var[adata.var[gene_symbols_field].isin(genes)].index
+            score_genes_aucell(
+                adata,
+                ens_gene_ids,
+                f"AUCell_{score_names}",
+                use_raw,
+            )
+    else:
+        raise ValueError(
+            "The number of gene lists (separated by :) and score names (separated by :) must be the same"
+        )
+
+
+if __name__ == "__main__":
+    # Create command-line arguments parser
+    parser = argparse.ArgumentParser(description="Score genes using Aucell")
+    parser.add_argument("--input_file", type=str, help="Path to input AnnData file")
+    parser.add_argument("--output_file", type=str, help="Path to output file")
+    parser.add_argument("--gmt_file", type=str, help="Path to GMT file", required=False)
+    # add argument for gene sets to score
+    parser.add_argument(
+        "--gene_sets_to_score",
+        type=str,
+        required=False,
+        help="Comma separated list of gene sets to score (the need to be in the gmt file)",
+    )
+    # add argument for gene list (comma separated) to score
+    parser.add_argument(
+        "--gene_lists_to_score",
+        type=str,
+        required=False,
+        help="Comma separated list of genes to score. You can have more than one set of genes, separated by colon :",
+    )
+    # argument for the score name when using the gene list
+    parser.add_argument(
+        "--score_names",
+        type=str,
+        required=False,
+        help="Name of the score column when using the gene list. You can have more than one set of score names, separated by colon :. It should be the same length as the number of gene lists.",
+    )
+    parser.add_argument(
+        "--gene_symbols_field",
+        type=str,
+        help="Name of the gene symbols field in the AnnData object",
+    )
+    parser.add_argument("--use_raw", action="store_true", help="Use raw data")
+    parser.add_argument(
+        "--write_anndata", action="store_true", help="Write the modified AnnData object"
+    )
+
+    # Parse command-line arguments
+    args = parser.parse_args()
+
+    # Load input AnnData object
+    adata = anndata.read_h5ad(args.input_file)
+
+    if args.gene_sets_to_score is not None and args.gmt_file is not None:
+        # Load MSigDB file in GMT format
+        msigdb = read_gmt(args.gmt_file)
+
+        gene_sets_to_score = args.gene_sets_to_score.split(",")
+        # Score genes by their ensembl ids using the score_genes_aucell function
+        for _, row in msigdb.iterrows():
+            gene_set_name = row["gene_set_name"]
+            if gene_set_name in gene_sets_to_score:
+                genes = row["genes"].split(",")
+                # Convert gene symbols to ensembl ids by using the columns gene_symbols and index in adata.var specific to the gene set
+                ens_gene_ids = adata.var[
+                    adata.var[args.gene_symbols_field].isin(genes)
+                ].index
+                score_genes_aucell(
+                    adata, ens_gene_ids, f"AUCell_{gene_set_name}", args.use_raw
+                )
+    elif args.gene_lists_to_score is not None and args.score_names is not None:
+        gene_lists = args.gene_lists_to_score.split(":")
+        score_names = args.score_names.split(",")
+        run_for_genelists(
+            adata, gene_lists, score_names, args.use_raw, args.gene_symbols_field
+        )
+
+    # Save the modified AnnData object or generate a file with cells as rows and the new score_names columns
+    if args.write_anndata:
+        adata.write_h5ad(args.output_file)
+    else:
+        new_columns = [col for col in adata.obs.columns if col.startswith("AUCell_")]
+        adata.obs[new_columns].to_csv(args.output_file, sep="\t", index=True)