From 5b1c37b036bab543c18bd32b19d2a0c8e8cf5061 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Fri, 21 Aug 2020 19:48:06 +0200
Subject: [PATCH] update typo README
---
Examples/commands/1-Annotate.sh | 2 +-
README.md | 1 +
test/test_unit/test_annotate/test_format_prodigal.py | 6 ++++++
3 files changed, 8 insertions(+), 1 deletion(-)
diff --git a/Examples/commands/1-Annotate.sh b/Examples/commands/1-Annotate.sh
index 5be2fef6..0cbf1f76 100644
--- a/Examples/commands/1-Annotate.sh
+++ b/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
diff --git a/README.md b/README.md
index ffafd179..a0315398 100755
--- a/README.md
+++ b/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)
diff --git a/test/test_unit/test_annotate/test_format_prodigal.py b/test/test_unit/test_annotate/test_format_prodigal.py
index 61c291cf..31806890 100644
--- a/test/test_unit/test_annotate/test_format_prodigal.py
+++ b/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
--
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