From 81107fa655e9c697e45f2dfbc9573b53de183913 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 2 Sep 2020 16:03:31 +0200
Subject: [PATCH] add licence header for align module

---
 PanACoTA/align_module/__init__.py         | 32 +++++++++++++++++++++
 PanACoTA/align_module/alignment.py        | 32 +++++++++++++++++++++
 PanACoTA/align_module/get_seqs.py         | 34 ++++++++++++++++++++++-
 PanACoTA/align_module/pan_to_pergenome.py | 32 +++++++++++++++++++++
 PanACoTA/align_module/post_align.py       | 32 +++++++++++++++++++++
 5 files changed, 161 insertions(+), 1 deletion(-)

diff --git a/PanACoTA/align_module/__init__.py b/PanACoTA/align_module/__init__.py
index 494d571b..abc8c3e4 100755
--- a/PanACoTA/align_module/__init__.py
+++ b/PanACoTA/align_module/__init__.py
@@ -1,3 +1,35 @@
+# ###############################################################################
+# This file is part of PanACOTA.                                                #
+#                                                                               #
+# Authors: Amandine Perrin                                                      #
+# Copyright © 2018-2020 Institut Pasteur (Paris).                               #
+# See the COPYRIGHT file for details.                                           #
+#                                                                               #
+# PanACOTA is a software providing tools for large scale bacterial comparative  #
+# genomics. From a set of complete and/or draft genomes, you can:               #
+#    -  Do a quality control of your strains, to eliminate poor quality         #
+# genomes, which would not give any information for the comparative study       #
+#    -  Uniformly annotate all genomes                                          #
+#    -  Do a Pan-genome                                                         #
+#    -  Do a Core or Persistent genome                                          #
+#    -  Align all Core/Persistent families                                      #
+#    -  Infer a phylogenetic tree from the Core/Persistent families             #
+#                                                                               #
+# PanACOTA is free software: you can redistribute it and/or modify it under the #
+# terms of the Affero GNU General Public License as published by the Free       #
+# Software Foundation, either version 3 of the License, or (at your option)     #
+# any later version.                                                            #
+#                                                                               #
+# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY   #
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS     #
+# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License           #
+# for more details.                                                             #
+#                                                                               #
+# You should have received a copy of the Affero GNU General Public License      #
+# along with PanACOTA (COPYING file).                                           #
+# If not, see <https://www.gnu.org/licenses/>.                                  #
+# ###############################################################################
+
 """
 PanACoTA align submodule
 """
diff --git a/PanACoTA/align_module/alignment.py b/PanACoTA/align_module/alignment.py
index 2ea7c08a..a34c0c9b 100755
--- a/PanACoTA/align_module/alignment.py
+++ b/PanACoTA/align_module/alignment.py
@@ -1,6 +1,38 @@
 #!/usr/bin/env python3
 # coding: utf-8
 
+# ###############################################################################
+# This file is part of PanACOTA.                                                #
+#                                                                               #
+# Authors: Amandine Perrin                                                      #
+# Copyright © 2018-2020 Institut Pasteur (Paris).                               #
+# See the COPYRIGHT file for details.                                           #
+#                                                                               #
+# PanACOTA is a software providing tools for large scale bacterial comparative  #
+# genomics. From a set of complete and/or draft genomes, you can:               #
+#    -  Do a quality control of your strains, to eliminate poor quality         #
+# genomes, which would not give any information for the comparative study       #
+#    -  Uniformly annotate all genomes                                          #
+#    -  Do a Pan-genome                                                         #
+#    -  Do a Core or Persistent genome                                          #
+#    -  Align all Core/Persistent families                                      #
+#    -  Infer a phylogenetic tree from the Core/Persistent families             #
+#                                                                               #
+# PanACOTA is free software: you can redistribute it and/or modify it under the #
+# terms of the Affero GNU General Public License as published by the Free       #
+# Software Foundation, either version 3 of the License, or (at your option)     #
+# any later version.                                                            #
+#                                                                               #
+# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY   #
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS     #
+# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License           #
+# for more details.                                                             #
+#                                                                               #
+# You should have received a copy of the Affero GNU General Public License      #
+# along with PanACOTA (COPYING file).                                           #
+# If not, see <https://www.gnu.org/licenses/>.                                  #
+# ###############################################################################
+
 """
 For a given family:
 
diff --git a/PanACoTA/align_module/get_seqs.py b/PanACoTA/align_module/get_seqs.py
index 15da584b..dd7d849f 100755
--- a/PanACoTA/align_module/get_seqs.py
+++ b/PanACoTA/align_module/get_seqs.py
@@ -1,6 +1,38 @@
 #!/usr/bin/env python3
 # coding: utf-8
 
+# ###############################################################################
+# This file is part of PanACOTA.                                                #
+#                                                                               #
+# Authors: Amandine Perrin                                                      #
+# Copyright © 2018-2020 Institut Pasteur (Paris).                               #
+# See the COPYRIGHT file for details.                                           #
+#                                                                               #
+# PanACOTA is a software providing tools for large scale bacterial comparative  #
+# genomics. From a set of complete and/or draft genomes, you can:               #
+#    -  Do a quality control of your strains, to eliminate poor quality         #
+# genomes, which would not give any information for the comparative study       #
+#    -  Uniformly annotate all genomes                                          #
+#    -  Do a Pan-genome                                                         #
+#    -  Do a Core or Persistent genome                                          #
+#    -  Align all Core/Persistent families                                      #
+#    -  Infer a phylogenetic tree from the Core/Persistent families             #
+#                                                                               #
+# PanACOTA is free software: you can redistribute it and/or modify it under the #
+# terms of the Affero GNU General Public License as published by the Free       #
+# Software Foundation, either version 3 of the License, or (at your option)     #
+# any later version.                                                            #
+#                                                                               #
+# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY   #
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS     #
+# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License           #
+# for more details.                                                             #
+#                                                                               #
+# You should have received a copy of the Affero GNU General Public License      #
+# along with PanACOTA (COPYING file).                                           #
+# If not, see <https://www.gnu.org/licenses/>.                                  #
+# ###############################################################################
+
 import sys
 import os
 import logging
@@ -225,7 +257,7 @@ def extract_sequences(to_extract, fasf, files_todo=None, outf=None):
 
     # State machine variables
     previous_fp = None
-    
+
     for line in fasf:
         if line[0] == '>':
             # Close previous file if needed
diff --git a/PanACoTA/align_module/pan_to_pergenome.py b/PanACoTA/align_module/pan_to_pergenome.py
index 7d5a48aa..86d20b50 100755
--- a/PanACoTA/align_module/pan_to_pergenome.py
+++ b/PanACoTA/align_module/pan_to_pergenome.py
@@ -1,6 +1,38 @@
 #!/usr/bin/env python3
 # coding: utf-8
 
+# ###############################################################################
+# This file is part of PanACOTA.                                                #
+#                                                                               #
+# Authors: Amandine Perrin                                                      #
+# Copyright © 2018-2020 Institut Pasteur (Paris).                               #
+# See the COPYRIGHT file for details.                                           #
+#                                                                               #
+# PanACOTA is a software providing tools for large scale bacterial comparative  #
+# genomics. From a set of complete and/or draft genomes, you can:               #
+#    -  Do a quality control of your strains, to eliminate poor quality         #
+# genomes, which would not give any information for the comparative study       #
+#    -  Uniformly annotate all genomes                                          #
+#    -  Do a Pan-genome                                                         #
+#    -  Do a Core or Persistent genome                                          #
+#    -  Align all Core/Persistent families                                      #
+#    -  Infer a phylogenetic tree from the Core/Persistent families             #
+#                                                                               #
+# PanACOTA is free software: you can redistribute it and/or modify it under the #
+# terms of the Affero GNU General Public License as published by the Free       #
+# Software Foundation, either version 3 of the License, or (at your option)     #
+# any later version.                                                            #
+#                                                                               #
+# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY   #
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS     #
+# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License           #
+# for more details.                                                             #
+#                                                                               #
+# You should have received a copy of the Affero GNU General Public License      #
+# along with PanACOTA (COPYING file).                                           #
+# If not, see <https://www.gnu.org/licenses/>.                                  #
+# ###############################################################################
+
 """
 From the Persistent Genome file, group all persistent proteins per genome, in order to be
 able to extract them faster after.
diff --git a/PanACoTA/align_module/post_align.py b/PanACoTA/align_module/post_align.py
index 6b9a7e4a..c0149a34 100755
--- a/PanACoTA/align_module/post_align.py
+++ b/PanACoTA/align_module/post_align.py
@@ -1,6 +1,38 @@
 #!/usr/bin/env python3
 # coding: utf-8
 
+# ###############################################################################
+# This file is part of PanACOTA.                                                #
+#                                                                               #
+# Authors: Amandine Perrin                                                      #
+# Copyright © 2018-2020 Institut Pasteur (Paris).                               #
+# See the COPYRIGHT file for details.                                           #
+#                                                                               #
+# PanACOTA is a software providing tools for large scale bacterial comparative  #
+# genomics. From a set of complete and/or draft genomes, you can:               #
+#    -  Do a quality control of your strains, to eliminate poor quality         #
+# genomes, which would not give any information for the comparative study       #
+#    -  Uniformly annotate all genomes                                          #
+#    -  Do a Pan-genome                                                         #
+#    -  Do a Core or Persistent genome                                          #
+#    -  Align all Core/Persistent families                                      #
+#    -  Infer a phylogenetic tree from the Core/Persistent families             #
+#                                                                               #
+# PanACOTA is free software: you can redistribute it and/or modify it under the #
+# terms of the Affero GNU General Public License as published by the Free       #
+# Software Foundation, either version 3 of the License, or (at your option)     #
+# any later version.                                                            #
+#                                                                               #
+# PanACOTA is distributed in the hope that it will be useful, but WITHOUT ANY   #
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS     #
+# FOR A PARTICULAR PURPOSE. See the Affero GNU General Public License           #
+# for more details.                                                             #
+#                                                                               #
+# You should have received a copy of the Affero GNU General Public License      #
+# along with PanACOTA (COPYING file).                                           #
+# If not, see <https://www.gnu.org/licenses/>.                                  #
+# ###############################################################################
+
 """
 Concatenate all alignment files of all families. Then,
 group alignments by genome.
-- 
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