Extracting query and target aligned sequences from Bio.Align.PairwiseAligner

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Extracting query and target aligned sequences from Bio.Align.PairwiseAligner #4630

Open Marysteph opened 4 months ago

Marysteph commented 4 months ago

Hi,

I am developing a module for genotyping antimicrobial resistance. I noticed that the Bio.pairwise2 module has been deprecated, so I wanted to switch to Bio.Align.PairwiseAligner. I couldn't find a way to access the query and target aligned sequences with PairwiseAligner. Any suggestion?

Thanks in advance!

mdehoon commented 4 months ago

Have a look at section 6.2 in the documentation: http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec86 Does that answer your question?