From 40cf4cabaea7a51a60567c341db03a983c3dacd5 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 16 Sep 2021 14:35:31 +0200
Subject: [PATCH] add warning on protein names for align step
---
doc/source/usage.rst | 2 ++
1 file changed, 2 insertions(+)
diff --git a/doc/source/usage.rst b/doc/source/usage.rst
index 4f9f3095..3adffcdf 100755
--- a/doc/source/usage.rst
+++ b/doc/source/usage.rst
@@ -893,6 +893,8 @@ All other information than the genome names in the first columns will be ignored
- a ``Genes`` folder, containing at list the following files: ``ESCO.0217.00001.gen``, ``ESCO.0217.00002.gen``, ``ESCO.0217.00003.gen`` and ``ESCO.0217.00004.gen``.
- a ``Proteins`` folder, containing at list the following files: ``ESCO.0217.00001.prt``, ``ESCO.0217.00002.prt``, ``ESCO.0217.00003.prt`` and ``ESCO.0217.00004.prt``.
+.. warning:: Inside those files, each fasta entry must start with the genome name, and end with a protein number separated by a `_`. For example, in ``ESCO.0217.00003.prt``, all gene names should start with ``>ESCO.0217.00003``. Examples of good names: ``ESCO.0217.00003_12345``, ``ESCO.0217.00003.toto_12345``. Bad name: ``toto.ESCO.0217.00003_12345``.
+
Those folders and files are automatically created by the 'annotate' subcommand, in the given ``<outdir>``.
.. _outalign:
--
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