Started working on generate_pairs.py script to generate sorted profile pairs.

lib/scripts/generate_pairs.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+# Copyright or Copr. Centre National de la Recherche Scientifique (CNRS) (2018)
+# Contributors:
+# - Vincent Lanore <vincent.lanore@gmail.com>
+
+# This software is a computer program whose purpose is to provide a set of scripts for pre and post processing of data for
+# convergence detection programs.
+
+# This software is governed by the CeCILL-C license under French law and abiding by the rules of distribution of free software.
+# You can use, modify and/ or redistribute the software under the terms of the CeCILL-C license as circulated by CEA, CNRS and
+# INRIA at the following URL "http://www.cecill.info".
+
+# As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users
+# are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive
+# licensors have only limited liability.
+
+# In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or
+# reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated
+# to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth
+# computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements
+# in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in
+# the same conditions as regards security.
+
+# The fact that you are presently reading this means that you have had knowledge of the CeCILL-C license and that you accept
+# its terms.
+
+"""Scripts that reads aminoacid profiles from a file, draws random pairs among them,
+and outputs said pairs sorted in distance classes.
+
+Usage:
+  generate_pairs.py [options...] -o <output-file> <profiles-file>
+
+Positional arguments:
+  profiles-file            the file to read profile from
+
+Options:
+  -h, --help            show this help message and exit
+  -o, --output-file <filename>
+                        output file"""
+
+from diffsel_script_utils import *
+
+#===================================================================================================
+STEP("Parsing command line arguments")
+from docopt import docopt
+
+args = docopt(__doc__)
+profiles_file = args["<profiles-file>"]
+MESSAGE("Profile file is " + param(profiles_file))
+out = args["--output-file"]
+MESSAGE("Output file is " + param(out))
+
+#===================================================================================================
+STEP("Reading profiles from file")
+import pandas as pd
+
+MESSAGE("Reading tsv file")
+profiles = pd.read_csv(profiles_file, sep=" ", header=None).transpose()
+print(profiles.shape)
+print(profiles)