docs(README): add option for gene_list

Former-commit-id: ce32c1e9e4ccb99c4bad371535809ef46ef661b2

README.md

@@ -45,6 +45,16 @@ streamlit run phenogenius_app.py
 poetry shell
 python phenogenius_cli.py --hpo_list HP:0000107,HP:0000108,HP:0001407,HP:0005562 --result_file PKD1.tsv
 ```
+```
+Usage: phenogenius_cli.py [OPTIONS]
+
+Options:
+  --result_file TEXT  Output file name, default = match.tsv
+  --hpo_list TEXT     (Mandatory) List of HPO terms to match, separated with
+                      commas
+  --gene_list TEXT    (Optional) List of genes in NCBI ID format to match,
+                      separated with commas
+```
 
 ## Explore interactive graphs of symptoms interactions
 

phenogenius_cli.py

@@ -127,9 +127,9 @@ def add_hpo_description_implicated(x, annot_dict):
         return None
     
 @click.command()
-@click.option("--result_file", default="match.tsv")
-@click.option("--hpo_list", default=None, help="List of HPO terms to match, separated with commas")
-@click.option("--gene_list", default=None, help="List of genes in NCBI ID format to match, separated with commas")
+@click.option("--result_file", default="match.tsv", help="Output file name, default = match.tsv")
+@click.option("--hpo_list", default=None, help="(Mandatory) List of HPO terms to match, separated with commas")
+@click.option("--gene_list", default=None, help="(Optional) List of genes in NCBI ID format to match, separated with commas")
 def evaluate_matching(result_file, hpo_list, gene_list):
     logging.info("INFO: load databases")
     ncbi, symbol = symbol_to_id_to_dict()