added script for pairwise alignment

scripts/pdb_align.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+from Bio import SeqIO
+from Bio import pairwise2
+from Bio.pairwise2 import format_alignment
+from align import myalign
+import re
+import os
+os.chdir('/home/tanu/git/LSHTM_analysis/scripts/examples')
+
+
+def main():
+    """
+    align ref_seq and pdb_seq
+    # FIXME: pass command line args i.e filename
+    
+    """
+    my_dict = {}
+    align_fastas_to_align = open('align_fastas.txt', 'r') 
+    for record in SeqIO.parse(align_fastas_to_align,"fasta"):
+         myid = record.id
+         seq = str(record.seq)
+         my_dict.update({myid : seq})
+         
+    my_keys = list(my_dict.keys())
+    my_ref_seq = my_dict[my_keys[0]]
+    my_pdb_seq = my_dict[my_keys[1]]
+        
+    fasta_alignment = myalign(my_ref_seq, my_pdb_seq)
+    print(fasta_alignment)
+    print('class:', type(fasta_alignment))
+    
+   
+if __name__ == '__main__':
+    main()