update typo README

Examples/commands/1-Annotate.sh

@@ -3,4 +3,4 @@ PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prokka -l Examples/
 
 
 # With prodigal
-PanACoTA annotate -d Examples/genomes_init -l Examples/input_files/list_genomes.lst -n EXAM -r Examples/1-res-Annotate-prodigal --prodigal --small
+PanACoTA annotate -d Examples/genomes_init -r Examples/1-res-prodigal -l Examples/input_files/list_genomes.lst -n EXAM  --l90 3 --prodigal --small 

README.md

@@ -111,6 +111,7 @@ If you installed the dependencies (such as prokka) via our installation script,
 ## Quick run
 
 `PanACoTA` contains 5 different subcommands:
+
 - `annotate` (annotate all genomes of the dataset, after a quality control)
 - `pangenome` (generate pan-genome)
 - `corepers` (generate core-genome or persistent-genome)

test/test_unit/test_annotate/test_format_prodigal.py

@@ -271,6 +271,12 @@ def test_create_prt_not_moreprots_lst(caplog):
     assert ("Protein test.0417.00002.0007b_00015 is in .lst file but its sequence is not "
             "in the protein file generated by prodigal.") in caplog.text
 
+
+def test_format_1genome(caplog):
+    """
+    Test that when prodigal results are ok, all files are
+    generated as expected.
+    """
 # # def test_tbl_to_lst_not_changed_names(caplog):
 #     """
 #     Check that generated lstinfo file is as expected, when the genome name is the same as