diff --git a/containers/crosswalking/options.yml b/containers/crosswalking/options.yml index 99a3418..418371b 100644 --- a/containers/crosswalking/options.yml +++ b/containers/crosswalking/options.yml @@ -2,6 +2,21 @@ type: record name: options label: crosswalking options fields: + annotationColumn: + type: string? + label: Annotation column + inputBinding: + prefix: --annotation-column + clidColumn: + type: string? + label: Output clid column name + inputBinding: + prefix: --clid-column + matchColumn: + type: string? + label: Output match type column name + inputBinding: + prefix: --match-column table: type: File? label: Crosswalk CSV file @@ -27,23 +42,13 @@ fields: label: CL ID column in crosswalk table inputBinding: prefix: --crosswalk-table-clid-column + tableClidLabelColumn: + type: string? + label: CL label column in crosswalk table + inputBinding:: + prefix: --crosswalk-table-clid-label-column tableMatchColumn: type: string? label: Match type column in crosswalk table inputBinding: prefix: --crosswalk-table-match-column - annotationColumn: - type: string? - label: Annotation column - inputBinding: - prefix: --annotation-column - clidColumn: - type: string? - label: Output clid column name - inputBinding: - prefix: --clid-column - matchColumn: - type: string? - label: Output match type column name - inputBinding: - prefix: --match-column diff --git a/containers/gene-expression/context/main.py b/containers/gene-expression/context/main.py index 80c5add..5f5b6f8 100644 --- a/containers/gene-expression/context/main.py +++ b/containers/gene-expression/context/main.py @@ -8,6 +8,9 @@ import pandas as pd import scanpy as sc +from src.util.ensemble import add_ensemble_data + + MIN_CELLS_PER_CT = 2 # need a filter to reomve CTs with one cell as sc.tl.rank_genes_groups gives an error @@ -67,12 +70,17 @@ def get_mean_expr_value( def get_marker_genes_with_expr( - matrix: anndata.AnnData, clid_column: str, cell_type: str, marker_genes: str + matrix: anndata.AnnData, + gene_data: pd.DataFrame, + clid_column: str, + cell_type: str, + marker_genes: str, ) -> t.List[dict]: """Get the mean expression for all marker genes. Args: matrix (anndata.AnnData): Data + gene_data (pd.DataFrame): Data frame with additional gene data indexed by gene clid_column (str): Cell type id column cell_type (str): Cell type name gene (str): Gene name @@ -82,9 +90,12 @@ def get_marker_genes_with_expr( """ output = [] for gene in marker_genes: + data = gene_data.loc[gene] output.append( { - "gene_label": gene, + "gene_id": data["hgnc"], + "gene_label": data["gene_name"], + "ensembl_id": gene, "mean_gene_expr_value": get_mean_expr_value( matrix, clid_column, cell_type, gene ), @@ -94,12 +105,13 @@ def get_marker_genes_with_expr( def get_gene_expr( - matrix: anndata.AnnData, clid_column: str, gene_expr_column: str + matrix: anndata.AnnData, ensemble: Path, clid_column: str, gene_expr_column: str ) -> anndata.AnnData: """Computes and adds gene mean expressions for all cells in the annotated data. Args: matrix (anndata.AnnData): Data + ensemble (Path): Ensemble lookup data path clid_column (str): Cell type id column gene_expr_column (str): Column to store gene expression on @@ -108,6 +120,7 @@ def get_gene_expr( """ matrix.raw = matrix # for getting gene names as output for sc.tl.rank_genes_groups filtered_matrix = filter_matrix(matrix, clid_column) + filtered_matrix = add_ensemble_data(filtered_matrix, ensemble) sc.tl.rank_genes_groups(filtered_matrix, groupby=clid_column, n_genes=10) ct_marker_genes_df = format_marker_genes_df( pd.DataFrame(filtered_matrix.uns["rank_genes_groups"]["names"]), @@ -116,7 +129,11 @@ def get_gene_expr( ct_marker_genes_df[gene_expr_column] = ct_marker_genes_df.apply( lambda row: get_marker_genes_with_expr( - matrix, clid_column, row[clid_column], row["marker_genes"] + matrix, + filtered_matrix.var, + clid_column, + row[clid_column], + row["marker_genes"], ), axis=1, ) @@ -139,13 +156,20 @@ def main(args: argparse.Namespace): CLI arguments, must contain "matrix", "clid_column", "gene_expr_column", and "output_matrix" """ - matrix = get_gene_expr(args.matrix, args.clid_column, args.gene_expr_column) + matrix = get_gene_expr( + args.matrix, args.ensemble_lookup, args.clid_column, args.gene_expr_column + ) matrix.write_h5ad(args.output_matrix) def _get_arg_parser() -> argparse.ArgumentParser: parser = argparse.ArgumentParser(description="Add gene expressions to h5ad data") parser.add_argument("matrix", type=anndata.read_h5ad, help="h5ad data file") + parser.add_argument( + "--ensemble-lookup", + default="/src/assets/ensemble-lookup.csv", + help="Ensemble lookup data csv", + ) parser.add_argument("--clid-column", default="clid", help="Column with cell id") parser.add_argument( "--gene-expr-column", default="gene_expr", help="Column for gene_expr" diff --git a/containers/gene-expression/options.yml b/containers/gene-expression/options.yml index 5d8986d..cd46a90 100644 --- a/containers/gene-expression/options.yml +++ b/containers/gene-expression/options.yml @@ -12,3 +12,7 @@ fields: label: Gene expression column inputBinding: prefix: --gene-expr-column + ensembleLookup: + type: File? + inputBinding: + prefix: --ensemble-lookup diff --git a/src/assets/ensemble-lookup.csv b/src/assets/ensemble-lookup.csv new file mode 100644 index 0000000..7c1c32e --- /dev/null +++ b/src/assets/ensemble-lookup.csv @@ -0,0 +1,41002 @@ +ensemble,gene_name,hgnc +ENSG00000207005,RNU1-2,HGNC:10123 +ENSG00000207389,RNU1-4,HGNC:10128 +ENSG00000207513,RNU1-3,HGNC:10130 +ENSG00000207340,RNVU1-1,HGNC:10133 +ENSG00000206702,RNU1-11P,HGNC:10137 +ENSG00000199629,RNU1-14P,HGNC:10139 +ENSG00000186716,BCR,HGNC:1014 +ENSG00000195024,RNU1-15P,HGNC:10140 +ENSG00000274585,RNU2-1,HGNC:10142 +ENSG00000207280,SNORD20,HGNC:10143 +ENSG00000206680,SNORD21,HGNC:10144 +ENSG00000277194,SNORD22,HGNC:10145 +ENSG00000206611,SNORD24,HGNC:10146 +ENSG00000275043,SNORD25,HGNC:10147 +ENSG00000276788,SNORD26,HGNC:10148 +ENSG00000275996,SNORD27,HGNC:10149 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+ENSG00000163882,POLR2H,HGNC:9195 +ENSG00000105258,POLR2I,HGNC:9196 +ENSG00000005075,POLR2J,HGNC:9197 +ENSG00000147669,POLR2K,HGNC:9198 +ENSG00000177700,POLR2L,HGNC:9199 +ENSG00000072778,ACADVL,HGNC:92 +ENSG00000183778,B3GALT5,HGNC:920 +ENSG00000099821,POLRMT,HGNC:9200 +ENSG00000115138,POMC,HGNC:9201 +ENSG00000130714,POMT1,HGNC:9202 +ENSG00000146707,POMZP3,HGNC:9203 diff --git a/src/util/__init__.py b/src/util/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/util/ensemble.py b/src/util/ensemble.py new file mode 100644 index 0000000..3e4514b --- /dev/null +++ b/src/util/ensemble.py @@ -0,0 +1,59 @@ +import os +import re +import typing as t + +import anndata +import pandas as pd + + +_ENSEMBLE_COLUMN = "ensemble" +_GENE_COLUMN = "hgnc" +_GENE_NAME_COLUMN = "gene_name" + +_ENSEMBLE_VERSION_REPLACE_REGEX = re.compile(r"\.\d+$") + + +def strip_version(value: str) -> str: + return re.sub(_ENSEMBLE_VERSION_REPLACE_REGEX, "", value) + + +def add_ensemble_data( + matrix: anndata.AnnData, ensemble: t.Union[str, bytes, os.PathLike, pd.DataFrame] +) -> anndata.AnnData: + if not isinstance(ensemble, pd.DataFrame): + ensemble = pd.read_csv(ensemble, dtype=str) + ensemble = ensemble.drop_duplicates(_ENSEMBLE_COLUMN) + + index = matrix.var.index + keys = index.map(strip_version) + merged_var = matrix.var.merge( + ensemble, how="left", left_on=keys, right_on=_ENSEMBLE_COLUMN + ) + merged_var.index = index + merged_var[_GENE_COLUMN].fillna(index.to_series().map(_create_default_gene_id), inplace=True) + merged_var[_GENE_NAME_COLUMN].fillna(index.to_series(), inplace=True) + + result = matrix.copy() + result.var = merged_var + return result + + +def _create_temp_asctb_id(value: str) -> str: + """Create a temporary IRI based on a label. + + Args: + value (str): Label for the row + + Returns: + str: Temporary IRI + """ + suffix = value.lower().strip() + suffix = re.sub(r"\W+", "-", suffix) + suffix = re.sub(r"[^a-z0-9-]+", "", suffix) + return "ASCTB-TEMP:" + suffix + + +def _create_default_gene_id(value: str) -> str: + if value.lower().startswith('ens'): + return 'ensembl:' + value + return _create_temp_asctb_id(value)