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all_edit.py

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+from __future__ import print_function
+from random import sample, choice
+import sys
+import string
+import datetime as d
+
+
+def all_edit():
+    length_cutoff = int(input("Enter length cutoff:"))
+    edit_dis = int(input("enter edit distance:"))
+
+    repeat_file = open("all_repeats_1-6nt.txt","r")
+
+    repeats_out = dict()
+    new_motifs = list()
+    #motif_fallback = dict()
+    #repeat_lengths = []
+    out_file = open("output_edit.txt","wt")
+
+    motif_lengths = []
+
+    for line in repeat_file:
+        motif_dict = dict()
+
+        L = line.strip().split('\t')
+        motif = L[0]
+        motif_length = int(L[2])
+
+        if motif_length not in motif_lengths:
+            motif_lengths.append(motif_length)
+        i=0
+        input_seq_length = motif_length
+        while i < motif_length and input_seq_length < length_cutoff:
+            motif += motif[i]
+            i += 1
+            if i >= motif_length:
+                i = 0
+            input_seq_length = len(motif)
+
+        motif_dict['class'] = L[1]
+        motif_dict['motif_length'] = motif_length
+        motif_dict['strand'] = L[3]
+        repeats_out[motif] = motif_dict
+        new_motifs.append(motif) #consists of all the motifs of specified length
+
+    """
+    accessing the newly formed motifs 
+    """
+
+    #print(repeats_out[new_motifs[9]]['class'])
+    alphabet = ['A','T','G','C']
+    i=0
+    #print(rand_indices)
+    for repeats in new_motifs:
+        rand_indices = sample(list(range(0,length_cutoff)),edit_dis)
+        for ind in rand_indices:
+            rep = list(repeats)
+            alphabet.remove(rep[ind])
+            rep[ind]=choice(alphabet)
+            repeats = "".join(rep)
+            l_repeats = len(repeats)
+            alphabet = ['A','T','G','C']
+            #print(rand_indices)
+            #print(repeats[ind])
+        #print(repeats)
+        #print(new_motifs[0])
+        #break
+        """
+        compare each changed repeat with 
+        other repeats in new_motifs except itself
+        (use wagner fisher now)
+        in this for loop only!
+        """
+        print("=============",file = out_file)
+        print(new_motifs[i],file = out_file)
+        i=i+1
+        print(repeats,file = out_file)
+        print("=============",file = out_file)
+
+        for ext_rep in new_motifs:
+            #print(new_motifs[2])
+            cal_edit_dis = wagner_fisher(repeats, l_repeats, ext_rep, length_cutoff)
+            #print(cal_edit_dis)
+            #print(ext_rep,repeats_out[ext_rep]['class'])
+            if(edit_dis == cal_edit_dis):
+                print(ext_rep,repeats_out[ext_rep]['class'],cal_edit_dis, file = out_file)
+
+
+
+
+
+
+
+
+
+
+def wagner_fisher(s1, len_s1, s2, len_s2):
+
+    d = {}
+
+    #Make to use O(min(n,m)) space
+    #print(s1,s2)
+    if len_s1 > len_s2:
+        s1, s2 = s2, s1
+        len_s1, len_s2 = len_s2, len_s1
+    for i in range(-1, len_s1 + 1):
+        d[(i, -1)] = i + 1
+    for j in range(-1, len_s2 + 1):
+        d[(-1, j)] = j + 1
+
+    for i in range(len_s1):
+        for j in range(len_s2):
+            if s1[i] == s2[j]:
+                d[i, j] = d[i - 1, j - 1]
+            else:
+                d[(i, j)] = min(
+                    d[(i - 1, j)] + 1,  # deletion
+                    d[(i, j - 1)] + 1,  # insertion
+                    d[(i - 1, j - 1)] + 1,  # substitution
+                )
+    return d[len_s1 - 1, len_s2 - 1]
+
+
+
+
+
+
+
+st = d.datetime.now()    
+all_edit()
+print(d.datetime.now()-st).total_seconds()