From 2678606ea7a9ac8d4287339b2071edb4a6ca0724 Mon Sep 17 00:00:00 2001 From: Rafael Goncalves Date: Wed, 5 Jun 2024 16:17:09 -0400 Subject: [PATCH] Minor updates to CLI help messages --- text2term/__main__.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/text2term/__main__.py b/text2term/__main__.py index 9560fac..ed94223 100644 --- a/text2term/__main__.py +++ b/text2term/__main__.py @@ -4,7 +4,6 @@ from t2t import map_terms, cache_ontology from onto_cache import cache_exists from mapper import Mapper -from term import OntologyTermType if __name__ == "__main__": parser = argparse.ArgumentParser(description='A tool for mapping free-text descriptions of (biomedical) ' @@ -25,7 +24,7 @@ "that contains the terms to map, optionally followed by the name of the column that " "contains identifiers for the terms (eg 'my_terms,my_term_ids')") parser.add_argument("-sep", "--separator", required=False, type=str, default=',', - help="Specifies the cell separator to be used when reading a non-comma-separated tabular file") + help="Specifies the cell separator to be used when reading a table") parser.add_argument("-top", "--top_mappings", required=False, type=int, default=3, help="Maximum number of top-ranked mappings returned per source term (default=3)") parser.add_argument("-min", "--min_score", required=False, type=float, default=0.5, @@ -38,9 +37,9 @@ parser.add_argument("-g", "--save_term_graphs", required=False, default=False, action="store_true", help="Save vis.js graphs representing the neighborhood of each ontology term (default=False)") parser.add_argument("-c", "--store_in_cache", required=False, type=str, default="", - help="Store the target ontology into local cache under acronym") + help="Cache the target ontology using the name given here") parser.add_argument("-type", "--term_type", required=False, type=str, default="class", - help="Define whether to return ontology classes, properties, or both") + help="Define whether to map to ontology classes, properties, or both") parser.add_argument('-u', "--incl_unmapped", required=False, default=False, action="store_true", help="Include all unmapped terms in the output")