#73 started exploratory code

BA9F.py

@@ -17,12 +17,30 @@
 
 import argparse
 from helpers import read_strings
-#from snp import SuffixTree   
+from snp import SuffixArray  
 import time
+from numpy import argmin
 
-def FindLongestRepeat(string):
-    pass
-
+def FindShortestNonShared(s,t):
+    text = s + '$' + t + '#'
+    r,p,lcp = SuffixArray(text,auxiliary=True,padLCP=True)
+    Candidates = []
+    Rejects    = []
+    for i in range(len(r)):
+        if r[i]<= len(s)+ 2:
+            Candidates.append((i,text[r[i]:]))
+        print (f'{i:2d} {r[i]:2d} {lcp[i]:2d} {l} {text[r[i]:]}')
+    Pairs           = []
+    previous_from_s = False
+    for i in range(len(lcp)):
+        from_s          = r[i]<len(s)+2
+        if from_s and previous_from_s:
+            Pairs.append(i) 
+        previous_from_s = from_s
+    candidate_LCPs = [lcp[i] if i in  Pairs else len(lcp) for i in range(len(lcp))]
+    index          = argmin(candidate_LCPs)
+    return text[r[index]:r[index]+candidate_LCPs[index]]    
+
 if __name__=='__main__':
     start = time.time()
     parser = argparse.ArgumentParser('BA9D Find the Longest Repeat in a String')
@@ -31,12 +49,22 @@ def FindLongestRepeat(string):
     parser.add_argument('--rosalind', default=False, action='store_true', help='process Rosalind dataset')
     args = parser.parse_args()
     if args.sample:
-        print (FindLongestRepeat('ATATCGTTTTATCGTT'))
+        print (FindShortestNonShared('CCAAGCTGCTAGAGG','CATGCTGGGCTGGCT'))
 
     if args.extra:
-        pass
+        Input,Expected  = read_strings('data/ShortestNonSharedSubstring.txt',init=0)       
+        Actual          = FindShortestNonShared(Input[0],Input[1])
+        print (len(Expected[0]),len(Actual))
+        print (Expected[0])
+        print (Actual) 
+
     if args.rosalind:
-        pass
+        Input  = read_strings(f'data/rosalind_{os.path.basename(__file__).split(".")[0]}.txt')    
+        Result = FindShortestNonShared(Input[0],Input[1])
+        print (Result)
+        with open(f'{os.path.basename(__file__).split(".")[0]}.txt','w') as f:
+            f.write(f'{Result}\n')
+
     elapsed = time.time()-start
     minutes = int(elapsed/60)
     seconds = elapsed-60*minutes

data/ShortestNonSharedSubstring.txt

@@ -0,0 +1,5 @@
+Input
+GAGCGATGTGTAAAGACGGGCCTAGTGTGTTATTGGTGAGGATCCGCAAATTCCGCTTTAACATCGCTCAACCGTCCACGAGCAGCTCGCGGCTTGTTTGATTTTGCTCACCCGGAACTAAGCCTTCAATAATTGCGGGACACTTCTACTTTCCATGTATTAAAACCTTATAATTCCGAGAGACTGACATTTTAACCCAGGGATTCTCGGGGCTTGTAGGTCACTGGCGTTAGCTCTGCCAATGTTCTTCATCGCCGAAATTAAACTCGTGACCTTGCCCTACGGTTTGAAACGTTGGATTCCTAGCATTCGGTGCAACGGGAGTTCCATACCAGCAGTTAAGGACCGGGTTGCCCCGTCCCACTACGAGCAGCCGTTAGAAAACAGTTCTACCGGAGGCTATCCCGCACCACGGGTTTTCTTAGTGAAAGGGACTGCGCAGCCATCGAAGAGTAGGGGGAGTCAGAGAGAGGCAGGCTTGTTGGGCTGATACATCTAGTTTACTAAATAGCCTTAATGGCGTCCCCCTCTTCGTTGATGCGCGTGGCCTGTGAAATTAGGCAGGGCCCAATGAGCAAGGCTGATTACTATCTAATTGCAGAGCGCAATGCTCTCATATATTATTATCCATGAATCTCATTTCACTAATCAGAAACGTG
+CACCTCGTCAATACAACAAAAGGCGGCTCGCTTAAAGGGCGCAGCTAGTTCCTCCCCCTCTCATTGGGACATAGTCAACCTGCTAATCCGGATTCGAATGGATTATTCCGTAATTGAACGGTAATTTAGTGAGCTTCGCAGTAAACGATAGATGCGAGCTCTAGCAGGCCACTGACTATATAAACGCCAACACTAGTGCCGTGCATGGACGACTCGATGTACTATAGATTTGCACAGGTATGACCGGAGGAGCGGGACTGCCTAGGCTATAGGGAACGGGGAGTATTGGGAGCCTTTTAGGCCCTCGTCATATCCCTTAACGTTCCCGCGCAGCTAAATTGTGGAACCGGAAAACAATGGATCTGCTTATTTTTGTAGGCTTGGTTAAGCGAAACGGATCAAAATAAACAAAGAATTAATCAATGAACTAACCAACGAAGTAAGCAAGGATATACATAGATTTATTCATTGATCTATCCATCGATGTATGCATGGACACAGACTTACTCACTGACCTACCCACCGACGTACGCACGGAGAGTTAGTCAGTGAGCTAGCCAGCGAGGTAGGCAGGGTTTTCTTTGTTCCTTCGTTGCTTGGTCTCTGTCCCTCCGTCGCTCGGTGTGCCTGCGTGGCTGGGCCCCGCCGGCGCGGGGAAA
+Output
+AAACC