gravy.py

# -*- coding: utf-8 -*-
"""
Created on Thu Apr 20 19:52:05 2017

@author: vgor
"""
import re
from collections import Counter

#acording to J. Mol. Biol. 157:105-132(1982).
AA_hidropaticity = {
    "A":  1.800,
    "R": -4.500,
    "N": -3.500,
    "D": -3.500,
    "C":  2.500,
    "Q": -3.500,
    "E": -3.500,
    "G": -0.400,
    "H": -3.200,
    "I":  4.500,
    "L":  3.800,
    "K": -3.900,
    "M":  1.900,
    "F":  2.800,
    "P": -1.600,
    "S": -0.800,
    "T": -0.700,
    "W": -0.900,
    "Y": -1.300,
    "V":  4.200
    }

#Regex to select letters that are not in standard FASTA format
invalidFasta = re.compile("[^{}]".format("".join(AA_hidropaticity.keys())))

def gravy(sequence):
    """
    Calculate GRAVY measure
    """
    sequence = re.sub(invalidFasta, "", sequence)
    return sum([AA_hidropaticity[aa] for aa in sequence]) / len(sequence)

def AAContent(sequence, frequencies=True):
    """
    Calculate amino acid composition
    """
    AACont = Counter(sequence)

    if frequencies:
        for k, v in AACont.items():
            AACont[k] = float(v)/len(sequence)

    return AACont