[Biopython] Extract the similarity after using Water in Emboss

Islam Amin eng.islamamin at gmail.com
Mon Feb 20 00:28:32 UTC 2017


Dear All.
I would like to get the similarity between two sequences, I have found that
there is attributes called "similarity" but I this it is boolean value, is
there any way to get the similarity value between two sequences instead of
writing a text file.

from Bio.Emboss.Applications import WaterCommandline
water_cmd = WaterCommandline(gapopen=10, gapextend=0.5)
water_cmd.asequence = "asis:ACCCGGGCGCGGT"
water_cmd.bsequence = "asis:ACCCGAGCGCGGT"
print water_cmd.similarity
> None
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