Source code for sequana.protein

import re
import string
import subprocess
from collections import Counter, deque

import colorlog

from sequana.sequence import Sequence

logger = colorlog.getLogger(__name__)


__all__ = ["Protein"]

from sequana.iuapc import amino_acids

aa_letters = list(amino_acids.keys())

from sequana.iuapc import exotic_amino_acids

exotic_aa_letters = list(exotic_amino_acids.keys())




class Protein(Sequence):
    """Simple Protein class

    >>> d = Protein("MALWMRLLPLLALLALWGPD")
    >>> d.check()
    >>> d.stats()

    """

    def __init__(self, sequence, use_exotic_amino_acid=True):
        # make a copy of aa_letters list since we then add elements to it
        super(Protein, self).__init__(sequence, letters=aa_letters[:])
        if use_exotic_amino_acid:
            self._letters += exotic_aa_letters