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applied-bioinformatics / An-Introduction-To-Applied-Bioinformatics

Interactive lessons in bioinformatics.
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Getting error while using blosum 62 instead of blosum 50 #307

Open talhaanwarch opened 5 years ago

talhaanwarch commented 5 years ago

Greetings. I want to use blosum 62 instead of blosum50. i have imported blosum62 using following way

from Bio.SubsMat import MatrixInfo as matlist
blosum62 = matlist.blosum62

but i am getting following error ValueError: One of the sequences contains a character that is not contained in the substitution matrix. Are you using an appropriate substitution matrix for your sequence type (e.g., a nucleotide substitution matrix does not make sense for aligning protein sequences)? Does your sequence contain invalid characters? The offending character(s) is: P, H.

code

from skbio.sequence import Protein
from skbio.alignment import TabularMSA
seq_1 = TabularMSA([seq1])
seq_2 = TabularMSA([seq2])
nw_matrix, traceback_matrix = _compute_score_and_traceback_matrices(
    seq_1, seq_2, 1, 1,blosum62)

sequences are as follows. seq_1=seq1 = Protein("HEAGAWGHEE") seq_2 = Protein("PAWHEAE")