added script for pairwise alignment

scripts/align.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+from Bio import SeqIO
+from Bio import pairwise2
+from Bio.pairwise2 import format_alignment
+import re
+import os
+#%%
+def myalign(ref_seq, pdb_seq):
+
+    myalign_dict = {}
+    alignments = pairwise2.align.globalxx(ref_seq, pdb_seq)  
+    #alignments = pairwise2.align.localxx(ref, struct)
+
+    match = []
+
+    for a, b in zip(alignments[0][0], alignments[0][1]):
+            if a == b:
+                    match.append('|')
+            else:
+                    match.append(' ')
+
+
+    #print(match)
+    print(alignments[0][0])
+    print("".join(match))
+    print(alignments[0][1])
+
+    result_align = alignments[0][1]
+    #print(result_align)
+    print('===============================================================\n')
+
+    # update dict
+    myalign_dict.update({'aligned_fasta': result_align})
+        
+    # find start and end of match    
+    aa_regex = '\w'
+    m = re.search(aa_regex, result_align)
+    #m = my_match.span()
+    offset = m.start()
+    offset_end = m.end()
+
+    print('start of match:', offset
+    , '\nend of match:', offset_end)
+    print('===============================================================\n')
+    
+    # update dict
+    myalign_dict.update({'start_match' : offset})
+    myalign_dict.update({'end_match' : offset_end})
+
+    return myalign_dict
+