From 02ee3ac527329263cd351ac6a5e7bb0ef4baa9c3 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 2 Sep 2020 16:05:36 +0200
Subject: [PATCH] add licence header for pangenome module
---
PanACoTA/pangenome_module/mmseqs_functions.py | 32 +++++++++++++++++
PanACoTA/pangenome_module/post_treatment.py | 36 +++++++++++++++++--
.../pangenome_module/protein_seq_functions.py | 32 +++++++++++++++++
3 files changed, 98 insertions(+), 2 deletions(-)
diff --git a/PanACoTA/pangenome_module/mmseqs_functions.py b/PanACoTA/pangenome_module/mmseqs_functions.py
index 13ba8131..b57bbc14 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 21528a78..6c40c2ee 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 43daf95a..9ce2a97b 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
--
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