[Biopython] Error with new biopython with pos_specific_score_matrix()
Sebastian Bassi
sbassi at gmail.com
Thu May 21 21:57:33 UTC 2020
I have a code that used to work I think in 1.52 or so.
This is the code I am testing now in 1.76:
from Bio import AlignIO
from Bio.Align.AlignInfo import SummaryInfo
from Bio.Alphabet import ProteinAlphabet
align = AlignIO.read('samples/cas9align.fasta', 'fasta')
align._alphabet = ProteinAlphabet()
summary = SummaryInfo(align)
summary.pos_specific_score_matrix()
I get
/usr/local/lib/python3.6/dist-packages/Bio/Align/AlignInfo.py
<https://localhost:8080/#> in _guess_consensus_alphabet(self,
ambiguous) 196 if not isinstance(alt, a.__class__):
197 raise ValueError("Alignment contains a sequence
with \
--> 198 an incompatible alphabet.")
199 200 # Check the ambiguous character we are going to
use in the consensus
ValueError: Alignment contains a sequence wit an incompatible alphabet.
The alignment alphabet is protein, so I don't know what is wrong with it.
This is the alignment file I am using:
https://github.com/Serulab/Py4Bio/blob/master/samples/cas9align.fasta
I will appreciate any help.
Best,
SB
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