Protein sequences

Creating a ProteinSequence with a name

from cogent3 import PROTEIN

p = PROTEIN.make_seq("THISISAPRQTEIN", "myProtein")
type(p)
str(p)
'THISISAPRQTEIN'

Converting a DNA sequence string to protein sequence string

from cogent3.core.genetic_code import DEFAULT as standard_code

standard_code.translate("TTTGCAAAC")
'FAN'

Conversion to a ProteinSequence from a DnaSequence is shown in Translate a DnaSequence to protein.

Loading protein sequences from a Phylip file

from cogent3 import load_aligned_seqs

seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein")