diff --git a/PanACoTA/annotate_module/annotation_functions.py b/PanACoTA/annotate_module/annotation_functions.py index 1750a723edff9182a83719f7e44696bf0b151e20..bdf47ee2a15ae863273ab70fd452821468e5d1f3 100755 --- a/PanACoTA/annotate_module/annotation_functions.py +++ b/PanACoTA/annotate_module/annotation_functions.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 deal with prokka or prodigal only, according to user request diff --git a/PanACoTA/annotate_module/format_prodigal.py b/PanACoTA/annotate_module/format_prodigal.py index 89066cbd03665c4644f502af8f876e572fd78b83..1981d11c6dec15106bc31d9be4ef089d211b0a26 100644 --- a/PanACoTA/annotate_module/format_prodigal.py +++ b/PanACoTA/annotate_module/format_prodigal.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 convert prodigal result files to gembase format. diff --git a/PanACoTA/annotate_module/format_prokka.py b/PanACoTA/annotate_module/format_prokka.py index 0f82d936d6575b17b84048faa6fe2c0b9d7cf9e0..3824e3dedd582e613cc6d7fb0907fa23473774a9 100644 --- a/PanACoTA/annotate_module/format_prokka.py +++ b/PanACoTA/annotate_module/format_prokka.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: diff --git a/PanACoTA/annotate_module/general_format_functions.py b/PanACoTA/annotate_module/general_format_functions.py index 023e66ff558720f24cc3fe0d6d98ea0850568208..a1643d0691af5c0c8c1ea1bbfe3719cb8cd3e715 100644 --- a/PanACoTA/annotate_module/general_format_functions.py +++ b/PanACoTA/annotate_module/general_format_functions.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 convert prokka or prodigal results to gembase format: diff --git a/PanACoTA/annotate_module/genome_seq_functions.py b/PanACoTA/annotate_module/genome_seq_functions.py index 509d8d998656d06320d119d6cad61ab238e7bb74..639a4f9f0c31e6ed5c956d0bebaa70212491631b 100755 --- a/PanACoTA/annotate_module/genome_seq_functions.py +++ b/PanACoTA/annotate_module/genome_seq_functions.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: