TSUMUGI 1.0.1__py3-none-any.whl

TSUMUGI/main.py

@@ -0,0 +1,300 @@
+from __future__ import annotations
+
+import logging
+import sys
+from pathlib import Path
+
+from TSUMUGI import argparser, core, validator
+from TSUMUGI.subcommands import (
+    count_filterer,
+    genes_filterer,
+    graphml_builder,
+    life_stage_filterer,
+    mp_filterer,
+    score_filterer,
+    sex_filterer,
+    webapp_builder,
+    zygosity_filterer,
+)
+
+logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(levelname)s - %(message)s")
+
+
+def main() -> None:
+    args = argparser.parse_args()
+
+    logging.info(f"TSUMUGI version: {args.version}")
+
+    ###########################################################
+    # Load and validate data
+    ###########################################################
+
+    if getattr(args, "statistical_results", None):
+        validator.validate_statistical_results(args.statistical_results)
+
+    if getattr(args, "mp_obo", None):
+        validator.validate_obo_file(args.mp_obo)
+
+    if getattr(args, "impc_phenodigm", None):
+        validator.validate_phenodigm_file(args.impc_phenodigm)
+
+    if getattr(args, "mp_obo", None) and (getattr(args, "exclude", None) or getattr(args, "include", None)):
+        mp_term_id = args.exclude or args.include
+        validator.validate_mp_term_id(mp_term_id, args.mp_obo)
+
+    ###########################################################
+    # Run commands
+    ###########################################################
+
+    if args.cmd == "run":
+        logging.info("Running TSUMUGI pipeline")
+        Path(args.output_dir).mkdir(parents=True, exist_ok=True)
+        core.run_pipeline(args)
+
+    # ===========================================================
+    # Subcommands for filtering pairwise similarity annotations
+    # ===========================================================
+
+    # -----------------------------------------------------
+    # MP term inclusion/exclusion
+    # -----------------------------------------------------
+    if args.cmd == "mp":
+        if args.include:
+            if args.pairwise:
+                logging.info(f"Including gene pairs with phenotypes related to MP term: {args.include}")
+                mp_filterer.include_specific_phenotype(
+                    path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                    path_genewise_phenotype_annotations=None,
+                    path_obo=args.mp_obo,
+                    mp_term_id=args.include,
+                    life_stage=args.life_stage,
+                    sex=args.sex,
+                    zygosity=args.zygosity,
+                    is_pairwise=True,
+                )
+            else:
+                logging.info(f"Including genes with phenotypes related to MP term: {args.include}")
+                mp_filterer.include_specific_phenotype(
+                    path_pairwise_similarity_annotations=None,
+                    path_genewise_phenotype_annotations=args.path_genewise,
+                    path_obo=args.mp_obo,
+                    mp_term_id=args.include,
+                    life_stage=args.life_stage,
+                    sex=args.sex,
+                    zygosity=args.zygosity,
+                    is_pairwise=False,
+                )
+        if args.exclude:
+            if args.pairwise:
+                logging.info(f"Excluding gene pairs with phenotypes related to MP term: {args.exclude}")
+                mp_filterer.exclude_specific_phenotype(
+                    path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                    path_genewise_phenotype_annotations=args.path_genewise,
+                    path_obo=args.mp_obo,
+                    mp_term_id=args.exclude,
+                    life_stage=args.life_stage,
+                    sex=args.sex,
+                    zygosity=args.zygosity,
+                    is_pairwise=True,
+                )
+            else:
+                logging.info(f"Excluding genes with phenotypes related to MP term: {args.exclude}")
+                mp_filterer.exclude_specific_phenotype(
+                    path_pairwise_similarity_annotations=None,
+                    path_genewise_phenotype_annotations=args.path_genewise,
+                    path_obo=args.mp_obo,
+                    mp_term_id=args.exclude,
+                    life_stage=args.life_stage,
+                    sex=args.sex,
+                    zygosity=args.zygosity,
+                    is_pairwise=False,
+                )
+
+    # -----------------------------------------------------
+    # Number of phenotypes per gene/pair
+    # -----------------------------------------------------
+    if args.cmd == "count":
+        logging.info("Filtering gene pairs based on number of phenotypes per gene")
+        if args.genewise:
+            count_filterer.filter_by_number_of_phenotypes_per_gene(
+                path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                path_genewise_phenotype_annotations=args.path_genewise,
+                min_phenotypes=args.min,
+                max_phenotypes=args.max,
+            )
+        elif args.pairwise:
+            count_filterer.filter_by_number_of_phenotypes_per_pair(
+                path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                min_phenotypes=args.min,
+                max_phenotypes=args.max,
+            )
+
+    # -----------------------------------------------------
+    # Score of phenotype similarity per gene/pair
+    # -----------------------------------------------------
+    if args.cmd == "score":
+        logging.info("Filtering gene pairs based on the score of phenotype similarity per gene")
+        score_filterer.filter_by_score_of_phenotypes_per_pair(
+            path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+            min_phenotypes=args.min,
+            max_phenotypes=args.max,
+        )
+
+    # -----------------------------------------------------
+    # gene lists filterer
+    # -----------------------------------------------------
+    if args.cmd == "genes":
+        if args.genewise:
+            if args.keep:
+                if Path(args.keep).is_file():
+                    gene_list = set(Path(args.keep).read_text().splitlines())
+                else:
+                    gene_list = set(args.keep.split(","))
+
+                if len(gene_list) == 0:
+                    raise ValueError("Gene list is empty. Please provide at least one gene symbol.")
+
+                logging.info(f"Keeping phenotype annotations matching {len(gene_list)} genes")
+                genes_filterer.filter_annotations_by_genes(
+                    path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                    gene_list=gene_list,
+                    keep=True,
+                )
+            elif args.drop:
+                if Path(args.drop).is_file():
+                    gene_list = set(Path(args.drop).read_text().splitlines())
+                else:
+                    gene_list = set(args.drop.split(","))
+                if len(gene_list) == 0:
+                    raise ValueError("Gene list is empty. Please provide at least one gene symbol.")
+
+                logging.info(f"Dropping phenotype annotations matching {len(gene_list)} genes")
+                genes_filterer.filter_annotations_by_genes(
+                    path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                    gene_list=gene_list,
+                    drop=True,
+                )
+        else:
+            if args.keep:
+                gene_pairs = set()
+                for record in Path(args.keep).read_text().splitlines():
+                    # TSV
+                    if "\t" in record:
+                        gene1, gene2 = record.split("\t")
+                    # CSV
+                    elif "," in record:
+                        gene1, gene2 = record.split(",")
+                    gene_pairs.add(frozenset([gene1, gene2]))
+
+                if len(gene_pairs) == 0:
+                    raise ValueError(f"Gene list is empty. Please provide at least one gene pair in {args.keep}.")
+
+                logging.info(f"Keeping phenotype annotations matching {len(gene_pairs)} gene pairs")
+                genes_filterer.filter_annotations_by_gene_pairs(
+                    path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                    gene_pairs=gene_pairs,
+                    keep=True,
+                )
+            elif args.drop:
+                gene_pairs = set()
+                for record in Path(args.drop).read_text().splitlines():
+                    # TSV
+                    if "\t" in record:
+                        gene1, gene2 = record.split("\t")
+                    # CSV
+                    elif "," in record:
+                        gene1, gene2 = record.split(",")
+                    gene_pairs.add(frozenset([gene1, gene2]))
+
+                if len(gene_pairs) == 0:
+                    raise ValueError(f"Gene list is empty. Please provide at least one gene pair in {args.drop}.")
+
+                logging.info(f"Dropping phenotype annotations matching {len(gene_pairs)} gene pairs")
+                genes_filterer.filter_annotations_by_gene_pairs(
+                    path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                    gene_pairs=gene_pairs,
+                    drop=True,
+                )
+
+    # -----------------------------------------------------
+    # Life stage filterer
+    # -----------------------------------------------------
+    if args.cmd == "life-stage":
+        if args.keep:
+            logging.info(f"Keeping phenotype annotations matching life stage: {args.keep}")
+            life_stage_filterer.filter_annotations_by_life_stage(
+                path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                life_stage=args.keep,
+                keep=True,
+            )
+        elif args.drop:
+            logging.info(f"Dropping phenotype annotations matching life stage: {args.drop}")
+            life_stage_filterer.filter_annotations_by_life_stage(
+                path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                life_stage=args.drop,
+                drop=True,
+            )
+
+    # -----------------------------------------------------
+    # Sex filterer
+    # -----------------------------------------------------
+    if args.cmd == "sex":
+        if args.keep:
+            logging.info(f"Keeping phenotype annotations matching sex: {args.keep}")
+            sex_filterer.filter_annotations_by_sex(
+                path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                sex=args.keep,
+                keep=True,
+            )
+        elif args.drop:
+            logging.info(f"Dropping phenotype annotations matching sex: {args.drop}")
+            sex_filterer.filter_annotations_by_sex(
+                path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                sex=args.drop,
+                drop=True,
+            )
+
+    # -----------------------------------------------------
+    # Zygosity filterer
+    # -----------------------------------------------------
+    if args.cmd == "zygosity":
+        if args.keep:
+            logging.info(f"Keeping phenotype annotations matching zygosity: {args.keep}")
+            zygosity_filterer.filter_annotations_by_zygosity(
+                path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                zygosity=args.keep,
+                keep=True,
+            )
+        elif args.drop:
+            logging.info(f"Dropping phenotype annotations matching zygosity: {args.drop}")
+            zygosity_filterer.filter_annotations_by_zygosity(
+                path_pairwise_similarity_annotations=args.path_pairwise or sys.stdin,
+                zygosity=args.drop,
+                drop=True,
+            )
+
+    # -----------------------------------------------------
+    # Build GraphML
+    # -----------------------------------------------------
+    if args.cmd == "build-graphml":
+        logging.info("Building GraphML from pairwise similarity annotations")
+
+        graphml_builder.write_graphml_to_stdout(
+            pairwise_path=args.path_pairwise or sys.stdin,
+            genewise_path=args.path_genewise,
+        )
+    # -----------------------------------------------------
+    # Build Webapp
+    # -----------------------------------------------------
+    if args.cmd == "build-webapp":
+        logging.info("Building webapp network from pairwise similarity annotations")
+
+        webapp_builder.build_and_save_webapp_network(
+            genewise_path=args.path_genewise,
+            pairwise_path=args.path_pairwise or sys.stdin,
+            output_dir=args.output_dir,
+        )
+
+
+if __name__ == "__main__":
+    main()