added scratch/

scripts/scratch/align_template.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python3
+
+# useful links
+#https://towardsdatascience.com/pairwise-sequence-alignment-using-biopython-d1a9d0ba861f
+#https://www.biostars.org/p/265338/
+
+from Bio import SeqIO
+from Bio import pairwise2
+from Bio.pairwise2 import format_alignment
+import re
+import os
+
+#%%
+os.chdir('/home/tanu/git/LSHTM_analysis/scripts/examples')
+#%%
+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})
+    
+    
+    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
+
+   
+def main():
+    """
+    read file containing reference and pdb_sequence to align
+    """
+    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]] # ref_seq
+    my_pdb_seq = my_dict[my_keys[1]] # pdb_seq
+    
+    fasta_alignment = myalign(my_ref_seq, my_pdb_seq)
+    print('this is my result:', fasta_alignment)
+
+
+if __name__ == '__main__':
+    main()
+
+#%% debug: individually
+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)
+     #print(myid, seq)
+     my_dict.update({myid: seq})
+     
+print(my_dict)
+print(my_dict.keys())
+
+my_keys = list(my_dict.keys())
+alignments = pairwise2.align.globalxx(my_dict[my_keys[0]], my_dict[my_keys[1]])
+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')
+
+#offset = ''
+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')
+
+    
+