[Biopython] Extract the similarity after using Water in Emboss

[Brian Osborne]

Islam,

I’m looking at the Bio.Emboss code and it seems that, generally speaking, this module runs EMBOSS applications but does not parse their output, which is what would be required to get the “similarity” value.

Also note that in your code example you haven’t yet run water, which you would do like "water_cmd()”. But you can always parse out this similarity value yourself, first by capturing the output, something like this:

>>> water_cmd = WaterCommandline(gapopen=10, gapextend=0.5, stdout=True, auto=True)
>>> water_cmd.asequence = "asis:ACCCGGGCGCGGT"
>>> water_cmd.bsequence = "asis:ACCCGAGCGCGGT"
>>> output = water_cmd()
>>> output
('########################################\n# Program: water\n# Rundate: Tue 21 Feb 2017 13:23:38\n# Commandline: water\n#    -auto\n#    -stdout\n#    -asequence asis:ACCCGGGCGCGGT\n#    -bsequence asis:ACCCGAGCGCGGT\n#    -gapopen 10\n#    -gapextend 0.5\n# Align_format: srspair\n# Report_file: stdout\n########################################\n\n#=======================================\n#\n# Aligned_sequences: 2\n# 1: asis\n# 2: asis\n# Matrix: EDNAFULL\n# Gap_penalty: 10.0\n# Extend_penalty: 0.5\n#\n# Length: 13\n# Identity:      12/13 (92.3%)\n# Similarity:    12/13 (92.3%)\n# Gaps:           0/13 ( 0.0%)\n# Score: 56.0\n# \n#\n#=======================================\n\nasis               1 ACCCGGGCGCGGT     13\n                     |||||.|||||||\nasis               1 ACCCGAGCGCGGT     13\n\n\n#---------------------------------------\n#---------------------------------------\n', '')

Now just use your regex.

Brian O.




> On Feb 19, 2017, at 7:28 PM, Islam Amin <eng.islamamin at gmail.com> wrote:
> 
> 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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