Protein sequences#

Note

These docs now use the new_type core objects via the following setting.

import os

# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"

Creating a ProteinSequence with a name#

from cogent3 import make_seq

p = make_seq("THISISAPRQTEIN", "myProtein", moltype="protein")
type(p)

cogent3.core.new_sequence.ProteinSequence

p
0
myProteinTHISISAPRQTEIN

ProteinSequence, length=14

Converting a DNA sequence string to protein sequence string#

from cogent3 import get_code

standard_code = get_code(1)
standard_code.translate("TTTGCAAAC")

'FAN'

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

Converting a nucleic acid sequence object to protein#

from cogent3 import make_seq

nuc = make_seq("TTTGCAAAC", moltype="dna")
pep = nuc.get_translation()
pep
0
NoneFAN

ProteinSequence, length=3

Loading protein sequences from a Phylip file#

from cogent3 import load_aligned_seqs

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