From 2de80c26ba343237581751609aed9131999f0d61 Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Wed, 2 Sep 2020 16:06:44 +0200 Subject: [PATCH] add licence header for tree module --- PanACoTA/tree_module/fastme_func.py | 32 ++++++++++++++++++++++++++ PanACoTA/tree_module/fasttree_func.py | 32 ++++++++++++++++++++++++++ PanACoTA/tree_module/iqtree_func.py | 32 ++++++++++++++++++++++++++ PanACoTA/tree_module/quicktree_func.py | 32 ++++++++++++++++++++++++++ 4 files changed, 128 insertions(+) diff --git a/PanACoTA/tree_module/fastme_func.py b/PanACoTA/tree_module/fastme_func.py index 03b548e2..98b77fa9 100755 --- a/PanACoTA/tree_module/fastme_func.py +++ b/PanACoTA/tree_module/fastme_func.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/>. # +# ############################################################################### + """ Functions to infer a phylogenetic tree with fastME diff --git a/PanACoTA/tree_module/fasttree_func.py b/PanACoTA/tree_module/fasttree_func.py index eb2a60ab..e761204c 100755 --- a/PanACoTA/tree_module/fasttree_func.py +++ b/PanACoTA/tree_module/fasttree_func.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/>. # +# ############################################################################### + """ Function to infer a phylogenetic tree from a persistent genome, using FastTree diff --git a/PanACoTA/tree_module/iqtree_func.py b/PanACoTA/tree_module/iqtree_func.py index 7938d4f5..73d4ad85 100644 --- a/PanACoTA/tree_module/iqtree_func.py +++ b/PanACoTA/tree_module/iqtree_func.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/>. # +# ############################################################################### + """ Function to infer a phylogenetic tree from a persistent genome, using IQtree diff --git a/PanACoTA/tree_module/quicktree_func.py b/PanACoTA/tree_module/quicktree_func.py index 5761a9ad..d1babbdc 100755 --- a/PanACoTA/tree_module/quicktree_func.py +++ b/PanACoTA/tree_module/quicktree_func.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/>. # +# ############################################################################### + """ Functions to infer a phylogenetic tree with quicktree -- GitLab