First iteration of terminal fragment selector

fragmentation.py

+import pandas as pd
+import random
+import numpy as np
+
+dna_seq = {
+    "ATAACATGTGGATGGCCAGTGGTCGGTTGTTACACGCCTACCGCGATGCTGAATGACCCGGACTAGAGTGGCGAAATTTATGGCGTGTGACCCGTTATGC": 100,
+    "TCCATTTCGGTCAGTGGGTCATTGCTAGTAGTCGATTGCATTGCCATTCTCCGAGTGATTTAGCGTGACAGCCGCAGGGAACCCATAAAATGCAATCGTA": 100
+}
+
+mean_length = 12
+std = 1
+
+term_frags = []
+for seq, counts in dna_seq.items():
+    for _ in range(counts):
+        n_cuts = int(len(seq)/mean_length)
+        cuts = random.sample(range(1,len(seq)-1), n_cuts)
+        cuts.sort()
+        cuts.insert(0,0)
+        term_frag = ""
+        for i, val in enumerate(cuts):
+            if i == len(cuts)-1:
+                fragment = seq[val:cuts[-1]]
+            else:
+                fragment = seq[val:cuts[i+1]]
+            if mean_length-std <= len(fragment) <= mean_length+std:
+                term_frag = fragment
+        if term_frag == "":
+            continue
+        else:
+            term_frags.append(term_frag)
+    
+with open('terminal_frags.txt', 'w') as f:
+    for line in term_frags:
+        f.write(line)
+        f.write('\n')
+