#29 converted to standard form

BA5L.py

@@ -1,4 +1,4 @@
-#    Copyright (C) 2019 Greenweaves Software Limited
+#    Copyright (C) 2019-2020 Greenweaves Software Limited
 #
 #    This is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
@@ -11,12 +11,16 @@
 #    GNU General Public License for more details.
 #
 #    You should have received a copy of the GNU General Public License
-#    along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>
 
 # BA5L.py Align Two Strings Using Linear Space
 
-from align import FindMiddleEdge
-from Bio.SubsMat.MatrixInfo import blosum62
+import argparse
+import os
+import time
+from   helpers import read_strings
+from   align import FindMiddleEdge
+from   Bio.Align import substitution_matrices
 
 # alignUsingLinearSpace
 #
@@ -25,7 +29,7 @@
 # Inputs: v
 #         w
 
-def alignUsingLinearSpace(v,w,replace_score=blosum62,indel_cost=5):
+def alignUsingLinearSpace(v,w,replace_score=substitution_matrices.load("BLOSUM62"),indel_cost=5):
     # LinearSpaceAlignment
     #
     # Find longest path between a substring of v[top] v[bottom-1]
@@ -71,7 +75,36 @@ def  LinearSpaceAlignment(top, bottom, left, right):
     DOWN      = 1
     DOWNRIGHT = 2
     LinearSpaceAlignment(0,len(v),0,len(w))
-
+
+    if __name__=='__main__':
+        start = time.time()
+        parser = argparse.ArgumentParser('....')
+        parser.add_argument('--sample',   default=False, action='store_true', help='process sample dataset')
+        parser.add_argument('--rosalind', default=False, action='store_true', help='process Rosalind dataset')
+        args = parser.parse_args()
+        if args.sample:
+            score,s1,t1 = alignUsingLinearSpace('PLEASANTLY','MEANLY')   
+            print (score)
+            print (s1)
+            print (t1) 
+
+        if args.rosalind:
+            Input       = read_strings(f'data/rosalind_{os.path.basename(__file__).split(".")[0]}.txt')
+            fasta       = FastaContent(Input)
+            _,s         = fasta[0]
+            _,t         = fasta[1]
+            score,s1,t1 = alignUsingLinearSpace(s,t)
+
+        with open(f'{os.path.basename(__file__).split(".")[0]}.txt','w') as f:               
+            f.write(f'{score}\n')
+            f.write(f'{s1}\n')
+            f.write(f'{t1}\n')
+
+        elapsed = time.time() - start
+        minutes = int(elapsed/60)
+        seconds = elapsed - 60*minutes
+        print (f'Elapsed Time {minutes} m {seconds:.2f} s')  
+
 if __name__=='__main__':
     from helpers import create_strings    
     print (alignUsingLinearSpace('PLEASANTLY','MEANLY'))