Initial commit

.gitignore

+./.idea
+./.vscode
\ No newline at end of file

data/sequences_P2Q3.csv

+"Gorilla","tttttttaggtcttcctgacacaaaaaccgcgccacctggtattgtgcgttaactcgctgggtagttaactgacgcactacgctcacatggttttgtaaa"
+"Human","ctggatgatgccacacctaaattaaagatgagttgttgagtaaactggttcagttccccacgcggttatctagtgcccaactttcgagagggacgattgg"
+"Chimp","gagttttagggcctagctaggctaggtccgaattgacgagcgaactggctcacttaatcagggaataatccagtgcccaaccctcgagaggtagggtgag"
+

data/sequences_P3.csv

+"Virus0","cattgagattgccttataccgctgcccccacttgttttgctcccttttgagtcaacgtagttgacgagggtggtatacgatgtacgagccgagtgcgaccgtcctttctgtccctagccacaatggttgaagcatcagcatactggaggtcaatagaaccatccaacgcaatcgctagttcttgtatacgtcgacgataa"
+"Alger","aatccgaagagctctactgcaccactgctacttatattgcgccagtctggatggactttaattccggagtacctatgctgcgtaccagacgagtccggcggtacctttgatcaccgggcgcgatggtcgaagcattactggagcgaaggactacgggattaccttatgctcttgttggagaccggagggtcagccgacta"
+"Amsterdam","cattgggatggcatgataccggttccttcacttattctgcgccaatgtggatcgacgaagaattcggcatcagtctgtgccgtgccagccgtgtgcggcagttcttcccgtccctagacacatcgcttgaagcatctccgtaacgaacgaccatagaatcaacctgagcccgcgctagttcctagagatttcgacgataa"
+"Belfast","cattcctattgcttgagggcggatcccccccttcgggcccgcccgcgcaaaccgacttaggtgtaggaggtaggaagtgacgcgccatacgtgtgaggcagatctttcggggcttacgccaaatggctggttcctcccagcatcgaaggggaatagtctcaccgagaactcgcgctactttccagatatatcggcgatta"
+"Bologne","cacgagaatggctttttatgggctctgctacttattttgcgcaagtgcagatggattcggatgccggagtcagtatgcagcgcactagcggagtgcggcggcccatgcgagcaccgaacgcaatggtcgaagcactagcgaaaagaaggaatccacgataatctattccccgcgctaatctctagagattgcgtcgataa"
+"Bruxelles","cattgggatgactttataccggttccgccacttattttgcgccaatgtgggtctacgtagatgtcggcgtcagtctgtgacgtgccagccgtctgcggcgctcctttccgtccctaggcgcaatgattgaagcatcaccgtaacgaaggaccatagaatcatgcagagcccgcgctagttcctggatatttcgacgataa"
+"Casablanca","aatgctagaacctctatagcacctctgctagtgataatgcgtctctctcgatggactttaatgcgggagaattgatgcgacggacccgacgagtgccagggtccctagcagaaccgaacgcgatggtcgagacattaccacgaggaagtagaatccggtaatccagtgctttcggtcgcgagtgggaagtcagccgatga"
+"Cork","cattcaaattgcctgagggagggtcccccccttcgggcccgtcagcgcaacccgagttgggtgtcagaggtgggaagtgatgcgccatacgtgtggggcggatctttagggccttacgccaaatggtaggatcaggccagtatcggaaggggaccgtcccaccgagaactcgcgctactttccagatatttcgctgatta"
+"Dublin","cattcaaattgcttgagaccggatcccctccttcgggcccgctagcgcaactcgacttgggtgtcggaggtgggaagtgacgcgccatacgtgtgaggcggggctttcgggccttacgccaaatgattggatcagcccagtatcggagggggatagactcaccgagaactcgtgctactttccagatatatcggcgatta"
+"Edimbourg","cattcagattgttttatatcgaatcccctccctcggtcccgctcgggatggtcgacttgggtgtctgggcgagtccgtgacgcgccatacgtgtgatgctgtgctttcgggtcccatgtgaaatgcgttaatcattacagtacctgggagcgatagacccgtcgagaacctgcgctagttcccaggtatattggcgataa"
+"Glasgow","cattgagagtgctttgtatcggatcccctccttaggtcccgctcatgaaggtcaacttgggtttctgggcgagtccgtgacgtgccatacgtgtggtgctgtgcgttcgagtcctatgtaaaatgagtgaatcatcacagtaactgggagcgatagaatcgttgagaacctgcacttgttcttaggtatatcggcgatag"
+"Lilles","cattgggatggttgtctgtgggtttctccatttgttttgcgctcgtatgggtccacgtagaggccgcaatcagcctgtgacgtgccagccgtgcgtggtggtcgaggacgtccatggacgcaaaggccgaagcgccaccgaaacgaaggaccatagcaccatccagtacccgcgctagttcccagatatttaggggacaa"
+"Ljubljana","catgcaaatggctttatcccggctctgcagcttattgtgcgcaaatgcagatggactaggatgcccgagtctgtatgtcgagtactagcgaagtgcggcggaccttgcgagccccaaacacaatggtcgaagcataagcggaacgctggaacacaggatcatccgctccccgcgctaatctctagagattgcgtcgatta"
+"Londres","cactaagatcactttaccttggttccttcacttagaaacaccgcatgtatgtcgacttagttgtcgggggaggtcagcgatccgccagtactgcgcggccagtctttcagttcccaggggcaatgattgtagcgtgactgtaacggaggtccacggaatcctccagagcccgcgctctttccttgatatagcggcgataa"
+"Manchester","tattgagattactttacatcggttccctcacttaagaaccacccatgcagacaaacttagttggcgggggtggtctgcgataggccagtcgtgtgcggccgttatctcagttctgaggagcaaagagtggagcgataccatactgtagcgtcacagaatcatccaccgcccgcgctaactccttgatatagcggcgaaaa"
+"Marrakech","aatactagaacctctatcgcacctctgctagtggtaatgcgtctctctcgatggtctttaatgcgggagaattgatgcgtcggacccgacgcgtgccagggtccctaggagaaccgaactcgatggtcgagacatcaccaggaggaagtagaatccggtactccagagctttccgttgcgagtggggagtctgccgatga"
+"Marseille","cattggaacggctttatatcacctcggctactcattttgcgcccttggggatggacgtggatgccggtgtcactatgtgacgtgcgagccgagtgcggcggtcgttgccgtctccggacgcaatggtggaagcatcaccgaaacgaaggaatataggactatccagtccccgcgcaagtttccagagatttcgccgatta"
+"Milan","catgggaatggctttatatcggctctaccacttattttgcgtcagtgcagatggacttggatgccggagtcagtatgcggcgtactagccgagcgcgccggtccctgcgatcaccggacgctatggtcggagcattaccgaaacgaaggaatataggatcatctactccctgcgctagcctctatacattacgccgatta"
+"Paris","catcggaatggctttctattacctcggctacttattttgcgcccgtgcggatagacgtggatgccggagtcagtatgtgacgtgccagccgagttcggcagtccttagcgtcaccgaacgcaatggtcgaagcatcaccgaaacgaagggatataggatgatccagtcaccgcgttagttcctagagatttcgccgatta"
+"Tunis","aatgcgagaacctttatagcatctctgttagtgataacgcgtcactctggatgggctctaatgcgcgagaattgatagggcggaccagacgagtgcaagggtcccttcgagagcggaacgcaatggtccagacgttaccgaaacgaaggaaaattggggaattcaatgctttcggtgtttagcggagagtccgccgatga"
+"Venise","cacgagaatggcttgatatgggctctgctacttattttgcgccagtgcagatggactaggctgccggagtcagtatgcagcgtactagcggagtgcggcggcccgtgcgcgcactgaacgcaatgttcgaagcactagcgaaaccaaggaataaaggataatctattccccgcgctaatctctagagattgcgtcgatta"

data/transition_matrix_P1Q3.csv

+0.8860516969572614, 0.04737184130589218, 0.03104758075742727, 0.03552888097941914
+0.011842960326473046, 0.91799183092612, 0.023685920652946092, 0.04647928809446081
+0.01552379037871363, 0.04737184130589217, 0.901575487335975, 0.035528880979419135
+0.011842960326473044, 0.061972384125947765, 0.02368592065294609, 0.9024987348946332
\ No newline at end of file

startingcode.py

+# Code et données pour le projet du cours MATH1222
+
+# Classe simple pour représenter un arbre phylogénétique (noeud)
+
+# Pour visualiser un arbre de racine root, vous pouvez utiliser
+# root.toNewick() pour générer une représenter newick de l'arbre que
+# vous pouvez visualiser par exemple sur le site https://beta.phylo.io/
+
+
+class PTNode:
+    def __init__(self, name, length, treeleft=None, treeright=None):
+        self.length = length
+        self.name = name
+        self.parent = None
+        self.left = None
+        self.right = None
+        if treeleft != None:
+            self.left = treeleft
+            self.left.parent = self
+        if treeright != None:
+            self.right = treeright
+            self.right.parent = self
+
+    def toNewick(self):
+        """output a newick representation of the tree"""
+        namestr = ""
+        if self.name != None:
+            namestr += self.name
+        if self.length != None:
+            namestr += ":" + str(self.length)
+        if self.left == None:
+            return namestr
+        if self.parent is None:
+            namestr += ";"
+        return "(" + self.left.toNewick() + "," + self.right.toNewick() + ")" + namestr
+
+
+# Données pour les différentes sous-questions
+
+# Partie 1
+# ========
+
+# 2) Matrice de transition d'une chaîne réversible
+
+Prev = [
+    [0.8860516969572614, 0.04737184130589218, 0.03104758075742727, 0.03552888097941914],
+    [0.011842960326473046, 0.91799183092612, 0.023685920652946092, 0.04647928809446081],
+    [0.01552379037871363, 0.04737184130589217, 0.901575487335975, 0.035528880979419135],
+    [0.011842960326473044, 0.061972384125947765, 0.02368592065294609, 0.9024987348946332]
+]
+
+# Partie 2
+# ========
+
+# Question 1
+
+tree_P2Q1a = PTNode("ROOT", None, PTNode("S1", 1), PTNode("S2", 4))
+print("tree_P2Q1a: ", tree_P2Q1a.toNewick())
+tree_P2Q1b = PTNode("ROOT", None, PTNode("S1", 3), PTNode("S2", 2))
+print("tree_P2Q1b: ", tree_P2Q1b.toNewick())
+
+sequences_P2Q1 = {"S1": "ccat", "S2": "ccgt"}
+
+# Question 2
+
+tree_P2Q2 = PTNode(
+    "ROOT",
+    None,
+    PTNode(
+        "N3",
+        2,
+        PTNode(
+            "N2", 6, PTNode("N1", 2, PTNode("S1", 1), PTNode("S2", 4)), PTNode("S3", 1)
+        ),
+        PTNode("S4", 9),
+    ),
+    PTNode("S5", 9),
+)
+print("tree_P2Q2: ", tree_P2Q2.toNewick())
+
+sequences_P2Q2 = {
+    "S1": "aatta",
+    "S2": "aatca",
+    "S3": "aacca",
+    "S4": "aaaca",
+    "S5": "aacca",
+}
+
+# Question 3
+
+d = 4
+
+tree_P2Q3a = PTNode(
+    None,
+    None,
+    PTNode("Chimp", 25),
+    PTNode(None, d, PTNode("Human", 25 - d), PTNode("Gorilla", 25 - d)),
+)
+print("tree_P2Q3a: ", tree_P2Q3a.toNewick())
+
+tree_P2Q3b = PTNode(
+    None,
+    None,
+    PTNode("Gorilla", 25),
+    PTNode(None, d, PTNode("Human", 25 - d), PTNode("Chimp", 25 - d)),
+)
+print("tree_P2Q3b: ", tree_P2Q3b.toNewick())
+
+sequences_P2Q3 = {
+    "Gorilla": "tttttttaggtcttcctgacacaaaaaccgcgccacctggtattgtgcgttaactcgctgggtagttaactgacgcactacgctcacatggttttgtaaa",
+    "Human": "ctggatgatgccacacctaaattaaagatgagttgttgagtaaactggttcagttccccacgcggttatctagtgcccaactttcgagagggacgattgg",
+    "Chimp": "gagttttagggcctagctaggctaggtccgaattgacgagcgaactggctcacttaatcagggaataatccagtgcccaaccctcgagaggtagggtgag",
+}
+
+# Partie 3
+# ========
+
+# L'outgroup est la séquence "Virus0". Le nom de la séquence est la ville
+# dans laquelle le variant du virus a été trouvé.
+
+sequences_P3 = {
+    "Virus0": "cattgagattgccttataccgctgcccccacttgttttgctcccttttgagtcaacgtagttgacgagggtggtatacgatgtacgagccgagtgcgaccgtcctttctgtccctagccacaatggttgaagcatcagcatactggaggtcaatagaaccatccaacgcaatcgctagttcttgtatacgtcgacgataa",
+    "Alger": "aatccgaagagctctactgcaccactgctacttatattgcgccagtctggatggactttaattccggagtacctatgctgcgtaccagacgagtccggcggtacctttgatcaccgggcgcgatggtcgaagcattactggagcgaaggactacgggattaccttatgctcttgttggagaccggagggtcagccgacta",
+    "Amsterdam": "cattgggatggcatgataccggttccttcacttattctgcgccaatgtggatcgacgaagaattcggcatcagtctgtgccgtgccagccgtgtgcggcagttcttcccgtccctagacacatcgcttgaagcatctccgtaacgaacgaccatagaatcaacctgagcccgcgctagttcctagagatttcgacgataa",
+    "Belfast": "cattcctattgcttgagggcggatcccccccttcgggcccgcccgcgcaaaccgacttaggtgtaggaggtaggaagtgacgcgccatacgtgtgaggcagatctttcggggcttacgccaaatggctggttcctcccagcatcgaaggggaatagtctcaccgagaactcgcgctactttccagatatatcggcgatta",
+    "Bologne": "cacgagaatggctttttatgggctctgctacttattttgcgcaagtgcagatggattcggatgccggagtcagtatgcagcgcactagcggagtgcggcggcccatgcgagcaccgaacgcaatggtcgaagcactagcgaaaagaaggaatccacgataatctattccccgcgctaatctctagagattgcgtcgataa",
+    "Bruxelles": "cattgggatgactttataccggttccgccacttattttgcgccaatgtgggtctacgtagatgtcggcgtcagtctgtgacgtgccagccgtctgcggcgctcctttccgtccctaggcgcaatgattgaagcatcaccgtaacgaaggaccatagaatcatgcagagcccgcgctagttcctggatatttcgacgataa",
+    "Casablanca": "aatgctagaacctctatagcacctctgctagtgataatgcgtctctctcgatggactttaatgcgggagaattgatgcgacggacccgacgagtgccagggtccctagcagaaccgaacgcgatggtcgagacattaccacgaggaagtagaatccggtaatccagtgctttcggtcgcgagtgggaagtcagccgatga",
+    "Cork": "cattcaaattgcctgagggagggtcccccccttcgggcccgtcagcgcaacccgagttgggtgtcagaggtgggaagtgatgcgccatacgtgtggggcggatctttagggccttacgccaaatggtaggatcaggccagtatcggaaggggaccgtcccaccgagaactcgcgctactttccagatatttcgctgatta",
+    "Dublin": "cattcaaattgcttgagaccggatcccctccttcgggcccgctagcgcaactcgacttgggtgtcggaggtgggaagtgacgcgccatacgtgtgaggcggggctttcgggccttacgccaaatgattggatcagcccagtatcggagggggatagactcaccgagaactcgtgctactttccagatatatcggcgatta",
+    "Edimbourg": "cattcagattgttttatatcgaatcccctccctcggtcccgctcgggatggtcgacttgggtgtctgggcgagtccgtgacgcgccatacgtgtgatgctgtgctttcgggtcccatgtgaaatgcgttaatcattacagtacctgggagcgatagacccgtcgagaacctgcgctagttcccaggtatattggcgataa",
+    "Glasgow": "cattgagagtgctttgtatcggatcccctccttaggtcccgctcatgaaggtcaacttgggtttctgggcgagtccgtgacgtgccatacgtgtggtgctgtgcgttcgagtcctatgtaaaatgagtgaatcatcacagtaactgggagcgatagaatcgttgagaacctgcacttgttcttaggtatatcggcgatag",
+    "Lilles": "cattgggatggttgtctgtgggtttctccatttgttttgcgctcgtatgggtccacgtagaggccgcaatcagcctgtgacgtgccagccgtgcgtggtggtcgaggacgtccatggacgcaaaggccgaagcgccaccgaaacgaaggaccatagcaccatccagtacccgcgctagttcccagatatttaggggacaa",
+    "Ljubljana": "catgcaaatggctttatcccggctctgcagcttattgtgcgcaaatgcagatggactaggatgcccgagtctgtatgtcgagtactagcgaagtgcggcggaccttgcgagccccaaacacaatggtcgaagcataagcggaacgctggaacacaggatcatccgctccccgcgctaatctctagagattgcgtcgatta",
+    "Londres": "cactaagatcactttaccttggttccttcacttagaaacaccgcatgtatgtcgacttagttgtcgggggaggtcagcgatccgccagtactgcgcggccagtctttcagttcccaggggcaatgattgtagcgtgactgtaacggaggtccacggaatcctccagagcccgcgctctttccttgatatagcggcgataa",
+    "Manchester": "tattgagattactttacatcggttccctcacttaagaaccacccatgcagacaaacttagttggcgggggtggtctgcgataggccagtcgtgtgcggccgttatctcagttctgaggagcaaagagtggagcgataccatactgtagcgtcacagaatcatccaccgcccgcgctaactccttgatatagcggcgaaaa",
+    "Marrakech": "aatactagaacctctatcgcacctctgctagtggtaatgcgtctctctcgatggtctttaatgcgggagaattgatgcgtcggacccgacgcgtgccagggtccctaggagaaccgaactcgatggtcgagacatcaccaggaggaagtagaatccggtactccagagctttccgttgcgagtggggagtctgccgatga",
+    "Marseille": "cattggaacggctttatatcacctcggctactcattttgcgcccttggggatggacgtggatgccggtgtcactatgtgacgtgcgagccgagtgcggcggtcgttgccgtctccggacgcaatggtggaagcatcaccgaaacgaaggaatataggactatccagtccccgcgcaagtttccagagatttcgccgatta",
+    "Milan": "catgggaatggctttatatcggctctaccacttattttgcgtcagtgcagatggacttggatgccggagtcagtatgcggcgtactagccgagcgcgccggtccctgcgatcaccggacgctatggtcggagcattaccgaaacgaaggaatataggatcatctactccctgcgctagcctctatacattacgccgatta",
+    "Paris": "catcggaatggctttctattacctcggctacttattttgcgcccgtgcggatagacgtggatgccggagtcagtatgtgacgtgccagccgagttcggcagtccttagcgtcaccgaacgcaatggtcgaagcatcaccgaaacgaagggatataggatgatccagtcaccgcgttagttcctagagatttcgccgatta",
+    "Tunis": "aatgcgagaacctttatagcatctctgttagtgataacgcgtcactctggatgggctctaatgcgcgagaattgatagggcggaccagacgagtgcaagggtcccttcgagagcggaacgcaatggtccagacgttaccgaaacgaaggaaaattggggaattcaatgctttcggtgtttagcggagagtccgccgatga",
+    "Venise": "cacgagaatggcttgatatgggctctgctacttattttgcgccagtgcagatggactaggctgccggagtcagtatgcagcgtactagcggagtgcggcggcccgtgcgcgcactgaacgcaatgttcgaagcactagcgaaaccaaggaataaaggataatctattccccgcgctaatctctagagattgcgtcgatta",
+}