From a53aadbdb5b40049ef688822fce6eff9ee564500 Mon Sep 17 00:00:00 2001 From: Amandine PERRIN <amandine.perrin@pasteur.fr> Date: Wed, 2 Sep 2020 16:07:49 +0200 Subject: [PATCH] add licence header for subcommands --- PanACoTA/subcommands/align.py | 36 +++++++++++++++++++++++++++++-- PanACoTA/subcommands/annotate.py | 32 +++++++++++++++++++++++++++ PanACoTA/subcommands/corepers.py | 32 +++++++++++++++++++++++++++ PanACoTA/subcommands/pangenome.py | 32 +++++++++++++++++++++++++++ PanACoTA/subcommands/prepare.py | 32 +++++++++++++++++++++++++++ PanACoTA/subcommands/tree.py | 32 +++++++++++++++++++++++++++ 6 files changed, 194 insertions(+), 2 deletions(-) diff --git a/PanACoTA/subcommands/align.py b/PanACoTA/subcommands/align.py index 20ec5613..931e4fc0 100755 --- a/PanACoTA/subcommands/align.py +++ b/PanACoTA/subcommands/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/>. # +# ############################################################################### + """ align is a subcommand of PanACoTA @@ -23,7 +55,7 @@ def main_from_parse(args): result of argparse parsing of all arguments in command line """ cmd = "PanACoTA " + ' '.join(args.argv) - main(cmd, args.corepers, args.list_genomes, args.dataset_name, args.dbpath, + main(cmd, args.corepers, args.list_genomes, args.dataset_name, args.dbpath, args.outdir, args.threads, args.force, args.verbose, args.quiet) @@ -99,7 +131,7 @@ def main(cmd, corepers, list_genomes, dname, dbpath, outdir, threads, force, ver # generate required files gseqs.get_all_seqs(all_genomes, dname, dbpath, listdir, aldir, fam_nums, quiet) prefix = os.path.join(aldir, dname) - + # Align all families status = ali.align_all_families(prefix, fam_nums, len(all_genomes), dname, quiet, threads) if not status: diff --git a/PanACoTA/subcommands/annotate.py b/PanACoTA/subcommands/annotate.py index 54e94539..b406a88f 100755 --- a/PanACoTA/subcommands/annotate.py +++ b/PanACoTA/subcommands/annotate.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/>. # +# ############################################################################### + """ annotate is a subcommand of PanACoTA diff --git a/PanACoTA/subcommands/corepers.py b/PanACoTA/subcommands/corepers.py index ad60a87c..8b6db02b 100755 --- a/PanACoTA/subcommands/corepers.py +++ b/PanACoTA/subcommands/corepers.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/>. # +# ############################################################################### + """ corepers is a subcommand of PanACoTA diff --git a/PanACoTA/subcommands/pangenome.py b/PanACoTA/subcommands/pangenome.py index d52d7c7a..202b15e5 100755 --- a/PanACoTA/subcommands/pangenome.py +++ b/PanACoTA/subcommands/pangenome.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/>. # +# ############################################################################### + """ pangenome is a subcommand of PanACoTA diff --git a/PanACoTA/subcommands/prepare.py b/PanACoTA/subcommands/prepare.py index 4079c14a..6a9c7659 100644 --- a/PanACoTA/subcommands/prepare.py +++ b/PanACoTA/subcommands/prepare.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/>. # +# ############################################################################### + """ Subcommand to prepare a dataset: diff --git a/PanACoTA/subcommands/tree.py b/PanACoTA/subcommands/tree.py index 9ea6e9fb..0e7aa537 100755 --- a/PanACoTA/subcommands/tree.py +++ b/PanACoTA/subcommands/tree.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/>. # +# ############################################################################### + """ tree is a subcommand of PanACoTA -- GitLab