#81 WIP checkin

BA9F.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-#  Copyright (C) 2020 Greenweaves Software Limited
+#  Copyright (C) 2020-2024 Greenweaves Software Limited
 #
 #  This program is free software: you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
@@ -14,45 +14,23 @@
 #
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <https://www.gnu.org/licenses/>.
-#
-# BA9F Find the Shortest Non-Shared Substring of Two Strings
 
-import argparse
-from helpers import read_strings
+''' BA9F Find the Shortest Non-Shared Substring of Two Strings'''
+
+from argparse import ArgumentParser
+from os.path import basename
+from time import time
 from snp import SuffixArray
-import time
-from numpy import argmin
 
 def FindShortestNonShared(s,t):
     m = len(s)
     n = len(t)
-    print (m,n)
-    r0,p0,l0 = SuffixArray(s,auxiliary=True,padLCP=True)
-    for i in range(len(r0)):
-        print (f'{i:2d} {r0[i]:2d} {p0[i]:2d}  {l0[i]:2d} {s[r0[i]:]}')
-    r1,p1,l1 = SuffixArray(t,auxiliary=True,padLCP=True)
-    for i in range(len(r1)):
-        print (f'{i:2d} {r1[i]:2d} {p1[i]:2d}  {l1[i]:2d} {t[r1q[i]:]}')
-    #text = s + '$' + t + '#'
-    #r,p,l = SuffixArray(text,auxiliary=True,padLCP=True)
-    #Candidates  = []
-    #Lengths     = []
-    #previous    = -1
-    #for i in range(len(r)):
-        #if r[i]<m:
-            #print (f'{i:2d} {r[i]:2d} {p[i]:2d}  {l[i]:2d} {text[r[i]:]}')
-            #if i==previous+1:
-                #Candidates.append(i)
-                #Lengths.append(l[i])
-            #previous = i
-    #shortest = min(Lengths)
-    #locations = [Candidates[i] for i in range(len(Candidates)) if Lengths[i]==shortest]
-    #for i in locations:
-        #print (f'{i:2d} {r[i]:2d} {p[i]:2d}  {l[i]:2d} {text[r[i]:]}')
+    a2 = SuffixArray(t)
+    return ''
 
 if __name__=='__main__':
-    start = time.time()
-    parser = argparse.ArgumentParser('BA9D Find the Longest Repeat in a String')
+    start = time()
+    parser = ArgumentParser('BA9D Find the Longest Repeat in a String')
     parser.add_argument('--sample',   default=False, action='store_true', help='process sample dataset')
     parser.add_argument('--extra',    default=False, action='store_true', help='process extra dataset')
     parser.add_argument('--rosalind', default=False, action='store_true', help='process Rosalind dataset')
@@ -75,7 +53,7 @@ def FindShortestNonShared(s,t):
         with open(f'{os.path.basename(__file__).split(".")[0]}.txt','w') as f:
             f.write(f'{Result}\n')
 
-    elapsed = time.time()-start
+    elapsed = time()-start
     minutes = int(elapsed/60)
     seconds = elapsed-60*minutes
     print (f'Elapsed Time {minutes} m {seconds:.2f} s')