# coding: utf-8

# In[32]:

import seq_align

from Bio import SeqIO,Seq

# In[22]:

score_mat = seq_align.build_scoring_matrix(set(["A","T","G","C"]),10,-10,0)

# In[33]:

seq_recs = SeqIO.parse("/Users/richard/Downloads/rosalind_lcsq.txt","fasta")

seq_x,seq_y = [str(seq.seq) for seq in seq_recs]

# In[34]:

align_mat = seq_align.compute_alignment_matrix(seq_x, seq_y, score_mat, True)

# In[35]:

_,align1,align2 = seq_align.compute_global_alignment(seq_x,seq_y,score_mat,align_mat)

print align1

print align2

# In[36]:

res = ''.join([align1[i] for i in range(len(align1)) if align1[i]!= '-' and align2[i]!='-'])

# In[37]:

with open ("/Users/richard/Downloads/output",'w') as file:

file.write(res)