From bbb55a545e4837e7b058551a4d88b68a8779c7c1 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 2 Sep 2020 16:05:58 +0200
Subject: [PATCH] add licence header for prepare module
---
.../prepare_module/download_genomes_func.py | 32 +++++++++++++++++
PanACoTA/prepare_module/filter_genomes.py | 34 ++++++++++++++++++-
2 files changed, 65 insertions(+), 1 deletion(-)
diff --git a/PanACoTA/prepare_module/download_genomes_func.py b/PanACoTA/prepare_module/download_genomes_func.py
index f1d9859c..bbab0ad9 100644
--- a/PanACoTA/prepare_module/download_genomes_func.py
+++ b/PanACoTA/prepare_module/download_genomes_func.py
@@ -1,5 +1,37 @@
#!/usr/bin/env python3
+# ###############################################################################
+# 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 helping for downloading refseq genomes of a species,
gunzip them, adding complete genomes...
diff --git a/PanACoTA/prepare_module/filter_genomes.py b/PanACoTA/prepare_module/filter_genomes.py
index 4736862c..aa3d7167 100755
--- a/PanACoTA/prepare_module/filter_genomes.py
+++ b/PanACoTA/prepare_module/filter_genomes.py
@@ -1,5 +1,37 @@
#!/usr/bin/env python3
+# ###############################################################################
+# 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 helping for doing quality control on genomes in order to eliminate
bad quality sequences, and then run Mash loops in order to discard too close genomes.
@@ -158,7 +190,7 @@ def iterative_mash(sorted_genomes, genomes, outdir, species_linked, min_dist, ma
# Sketch genomes
sketch_all(genomes, sorted_genomes, outdir, list_reps, out_msh, mash_log, threads)
-
+
# Compute pairwise distances
compare_all(out_msh, matrix, sparse_mat, mash_log, threads)
# Iteratively discard genomes
--
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