diff --git a/PanACoTA/pangenome_module/mmseqs_functions.py b/PanACoTA/pangenome_module/mmseqs_functions.py index 13ba81319ad9777913e70b4c1aafe0e8d1c140ca..b57bbc141ff3eb594b8bd42de352804d252a9301 100755 --- a/PanACoTA/pangenome_module/mmseqs_functions.py +++ b/PanACoTA/pangenome_module/mmseqs_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 use mmseqs to create a pangenome diff --git a/PanACoTA/pangenome_module/post_treatment.py b/PanACoTA/pangenome_module/post_treatment.py index 21528a78a6154bdd32682e294e09c1f51047dbdb..6c40c2ee490094d311e457778ded8b3d2621f9f1 100755 --- a/PanACoTA/pangenome_module/post_treatment.py +++ b/PanACoTA/pangenome_module/post_treatment.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 generate the matrix pan_quali, pan_quanti, as well as a summary file for the pangenome. @@ -161,7 +193,7 @@ def generate_and_write_outputs(fams_by_strain, families, all_strains, panquali, matrix_quanti = np.vstack((header, matrix_quanti)) # Transpose matrix: lines = genomes, columns = families tmatrix_quali = matrix_quali.transpose() - np.savetxt(panquali, tmatrix_quali, delimiter=",", fmt="%s") + np.savetxt(panquali, tmatrix_quali, delimiter=",", fmt="%s") tmatrix_quanti = matrix_quanti.transpose() - np.savetxt(panquanti, tmatrix_quanti, delimiter=",", fmt="%s") + np.savetxt(panquanti, tmatrix_quanti, delimiter=",", fmt="%s") return qualis, quantis, summaries diff --git a/PanACoTA/pangenome_module/protein_seq_functions.py b/PanACoTA/pangenome_module/protein_seq_functions.py index 43daf95a2b6ba40744c7ee53a62e3e5d91e6b2f1..9ce2a97b2385c69ee6a91f97f9c16abb03a64d6a 100755 --- a/PanACoTA/pangenome_module/protein_seq_functions.py +++ b/PanACoTA/pangenome_module/protein_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 build a bank of all proteins to include in the pangenome