[Biopython-dev] [Biopython - Feature #3396] (New) Add alignment score, % identity, % similarity, % gaps, etc to EmbossIO

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Wed Nov 28 00:46:22 UTC 2012

Issue #3396 has been reported by Olga Botvinnik.

Feature #3396: Add alignment score, % identity, % similarity, % gaps, etc to EmbossIO

Author: Olga Botvinnik
Status: New
Priority: Normal
Assignee: Olga Botvinnik
Target version: 

As of BioPython 1.59, if an alignment is read in with Bio.AlignIO(handle, 'emboss'), the metadata such as the substitution matrix used, gap_penalty, extend_penalty, identity, similarity, gaps, and score in the header is ignored:

# Aligned_sequences: 4
# 1: IXI_234
# 2: IXI_235
# 3: IXI_236
# 4: IXI_237
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
# Length: 131
# Identity:      95/131 (72.5%)
# Similarity:   127/131 (96.9%)
# Gaps:          25/131 (19.1%)
# Score: 100.0

I edited the EmbossIO.py file to read these metadata and add it as an annotation to each SeqRecord in the MultipleSequenceAlignment object, since the MultipleSequenceAlignment object does not have the option for annotations. I also added the appropriate unit tests. Please let me know if there is a bug in the code that I missed.

For example, for the above alignment, the SeqRecord objects would have the following annotations:

{'identity_denominator': 131, 'matrix': 'EBLOSUM62', 'similarity': 0.8549618320610687, 'similarity_numerator': 112, 'similarity_denominator': 131, 'gaps': 0.1450381679389313, 'identity_numerator': 112, 'gap_penalty': 10.0, 'extend_penalty': 0.5, 'gaps_denominator': 131, 'score': 591.5, 'identity': 0.8549618320610687, 'gaps_numerator': 19}

I decided to keep the numerators and denominators separately from the identity, similarity, and gap percentages just in case a user wanted to do something else with them.

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