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Commit 02ee3ac5 authored by Amandine PERRIN's avatar Amandine PERRIN
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add licence header for pangenome module

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PanACoTA/pangenome_module/mmseqs_functions.py
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#!/usr/bin/env python3 #!/usr/bin/env python3
# coding: utf-8 # 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 Functions to use mmseqs to create a pangenome
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PanACoTA/pangenome_module/post_treatment.py
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View file @ 02ee3ac5
#!/usr/bin/env python3 #!/usr/bin/env python3
# coding: utf-8 # 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 Functions to generate the matrix pan_quali, pan_quanti, as well
as a summary file for the pangenome. as a summary file for the pangenome.
...@@ -161,7 +193,7 @@ def generate_and_write_outputs(fams_by_strain, families, all_strains, panquali, ...@@ -161,7 +193,7 @@ def generate_and_write_outputs(fams_by_strain, families, all_strains, panquali,
matrix_quanti = np.vstack((header, matrix_quanti)) matrix_quanti = np.vstack((header, matrix_quanti))
# Transpose matrix: lines = genomes, columns = families # Transpose matrix: lines = genomes, columns = families
tmatrix_quali = matrix_quali.transpose() 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() 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 return qualis, quantis, summaries
PanACoTA/pangenome_module/protein_seq_functions.py
+ 32
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View file @ 02ee3ac5
#!/usr/bin/env python3 #!/usr/bin/env python3
# coding: utf-8 # 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 Functions to build a bank of all proteins to include in the pangenome
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