directories fix

frag_package/fragmentation.py

-import random
-
-
-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')
-