From f0499afb5b5470eeb1060bb1054608ca85a8c287 Mon Sep 17 00:00:00 2001
From: Nico Maillet <nicolas.maillet@pasteur.fr>
Date: Wed, 27 Sep 2023 12:07:53 +0200
Subject: [PATCH] Add TP 3 skeleton
---
3-Needleman-Wunsch/tp3_skeleton.py | 158 +++++++++++++++++++++++++++++
1 file changed, 158 insertions(+)
create mode 100644 3-Needleman-Wunsch/tp3_skeleton.py
diff --git a/3-Needleman-Wunsch/tp3_skeleton.py b/3-Needleman-Wunsch/tp3_skeleton.py
new file mode 100644
index 0000000..d10ef52
--- /dev/null
+++ b/3-Needleman-Wunsch/tp3_skeleton.py
@@ -0,0 +1,158 @@
+""" TP3 where we code a global alignment program
+ based on Needleman-Wunsch algorithm """
+
+def simple_display(seq_top, seq_left, score):
+ """ Do a simple display """
+ print("Seq_top: {}\nSeq_left: {}\nScore: {}".format(seq_top[::-1], seq_left[::-1], score))
+
+def nice_display(seq_top, seq_left, score):
+ """ Do a nice display """
+ # What will be printed
+ to_print = ""
+
+ # Print seq_top
+ # For each positions in a sequence
+ for i, _ in enumerate(seq_top):
+ # Add the corresponding letter (reverse order)
+ to_print += seq_top[-(i+1)]
+ # Print a next line after printing the seq_top
+ to_print += "\n"
+
+ # Print middle line
+ # For each positions in a sequence
+ for i, _ in enumerate(seq_top):
+ # If it is a match between the two sequences
+ if seq_top[-(i+1)] == seq_left[-(i+1)]:
+ # Print a pipe
+ to_print += "|"
+ # Otherwise
+ else:
+ # Print a space
+ to_print += " "
+ # Print a next line after printing the middle line
+ to_print += "\n"
+
+ # Print seq_left
+ # For each positions in a sequence
+ for i, _ in enumerate(seq_top):
+ # Add the corresponding letter (reverse order)
+ to_print += seq_left[-(i+1)]
+
+ # Add the score at the end
+ to_print += "\nScore: {}\n".format(score)
+ # Print everything!
+ print(to_print)
+
+
+class DynamicMatrix:
+ """ Class to generate an empty matrix """
+ def __init__(self, seq_top, seq_left, match, mismatch, indel):
+ # Init all "self" variables
+
+ # Create the matrix of Cell()
+
+ # self representation for print
+ def __repr__(self):
+ # What will be returned
+ return "Scores:\n{}\nPrev_pos:\n{}\n\n".format(self.print_scores(), self.print_prev_pos())
+
+ # self representation for print
+ def print_scores(self):
+ """ Output the values of the matrix """
+ # What will be returned
+ ret_scores = ". . "
+ # Print top_seq
+ for i in self.seq_top:
+ ret_scores += " {} ".format(i)
+ # New line
+ ret_scores += "\n"
+ # For each line
+ for ind, i in enumerate(self.matrix):
+ # Print seq_left
+ if ind > 0:
+ ret_scores += "{} ".format(self.seq_left[ind-1])
+ else:
+ ret_scores += ". "
+ # For each column
+ for j in i:
+ # If this cell has no value
+ if j.score is None:
+ # Add a dot to the return
+ ret_scores += (" . ")
+ # If this cell is not empty
+ else:
+ # Add its content to the return
+ tmp_val = str(j.score)
+ if len(tmp_val) == 1:
+ ret_scores += " " + tmp_val + " "
+ if len(tmp_val) == 2:
+ ret_scores += tmp_val + " "
+ if len(tmp_val) == 3:
+ ret_scores += tmp_val
+ # Always add a space after the value we add
+ ret_scores += " "
+ # End of this line, go to next line
+ ret_scores += "\n"
+ # Return the content of the Matrix
+ return ret_scores
+
+ # self representation for print
+ def print_prev_pos(self):
+ """ Output the values of the matrix """
+ # What will be returned
+ ret_prev_pos = ". . "
+ # Print top_seq
+ for i in self.seq_top:
+ ret_prev_pos += " {} ".format(i)
+ # New line
+ ret_prev_pos += "\n"
+ # For each line
+ for ind, i in enumerate(self.matrix):
+ # Print seq_left
+ if ind > 0:
+ ret_prev_pos += "{} ".format(self.seq_left[ind-1])
+ else:
+ ret_prev_pos += ". "
+ # For each column
+ for j in i:
+ # If this cell has no value
+ if j.prev_pos is None:
+ # Add a dot to the return
+ ret_prev_pos += (". ")
+ # If this cell is not empty
+ else:
+ # Add its content to the return
+ tmp_val = str(j.prev_pos)
+ ret_prev_pos += tmp_val
+ # Always add a space after the value we add
+ ret_prev_pos += " "
+ # End of this line, go to next line
+ ret_prev_pos += "\n"
+ # Return the content of the Matrix
+ return ret_prev_pos
+
+ def initialize(self):
+ """ Initialize the matrix, i.e. fill the first line and column """
+ # First cell is 0
+
+ def fill_matrix(self):
+ """ Fill-up the matrix """
+
+ def global_alignment(self):
+ """ Make a global alignment of two sequences """
+
+
+def main():
+ """ The main of TP3"""
+ mat = DynamicMatrix("ACGGCTAT", "ACTGTAG", 2, -1, -2)
+ #mat.initialize()
+ #mat.fill_matrix()
+ #print(mat)
+ #al_seq_top, al_seq_left, score = mat.global_alignment()
+ #nice_display(al_seq_top, al_seq_left, score)
+
+# Launch the main
+main()
+# Exit without error
+exit(0)
+# Always put one extra return line
--
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