[Biopython] pairwise local align subsequence

[Markus Piotrowski]

Am 27.04.2017 um 04:11 schrieb 李团:
> I use pairwise localds to align two sequences, and want to get aligned 
> subsequences, but the result returns fully aligned sequences. How can 
> I get only aligned subsequences?
>
>

Not directly from pairwise2, but you can extract the relevant data from 
the alignment result.

The alignment results is a list of all alignments with the same maximum 
score with the following structure:

     [(aligned_seq1, aligned_seq2, score, start_of_alignment, 
end_of_alignment), (....)]

Unfortunately, also for local alignments, pairwise2 will always return 
the full sequences, even if the beginning and/or end has not been used 
for the alignment. But you can use start_of_alignment, end_of_alignment 
to shorten your sequence like:

 >>> aligned_seq1, aligned_seq2, score, start, end = your_alignment[0]
 >>> seq1_aligned_part = aligned_seq1[start:end]
 >>> seq2_aligned_part = aligned_seq2[start:end]

Markus
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