def get_protein_colors(palette='tab20'):
"""Get protein color dict"""
from Bio.PDB.Polypeptide import aa1
aa1 = list(aa1)
aa1.append('-')
aa1.append('X')
import matplotlib as mpl
from matplotlib import cm
pal = cm.get_cmap(palette, 256)
pal = [mpl.colors.to_hex(i) for i in pal(np.linspace(0, 1, 20))]
pal.append('white')
pal.append('white')
pcolors = {i:j for i,j in zip(aa1,pal)}
return pcolors
def get_sequence_colors(seq):
"""Get colors for a sequence"""
from bokeh.palettes import brewer, viridis, plasma
from Bio.PDB.Polypeptide import aa1
pal = plasma(20)
pal.append('white')
aa1 = list(aa1)
aa1.append('-')
pcolors = {i: j for i, j in zip(aa1, pal)}
text = list(seq)
clrs = {'A': 'red', 'T': 'green', 'G': 'orange', 'C': 'blue', '-': 'white'}
try:
colors = [clrs[i] for i in text]
except:
colors = [pcolors[i] for i in text]
return colors
def get_sequence_colors(seqs, palette='tab20'):
"""Get colors for a sequence"""
from Bio.PDB.Polypeptide import aa1
aa1 = list(aa1)
aa1.append('-')
import matplotlib as mpl
from matplotlib import cm
pal = cm.get_cmap(palette, 256)
pal = [mpl.colors.to_hex(i) for i in pal(np.linspace(0, 1, 20))]
pal.append('white')
pcolors = {i: j for i, j in zip(aa1, pal)}
text = [i for s in list(seqs) for i in s]
clrs = {'A': 'red', 'T': 'green', 'G': 'orange', 'C': 'blue', '-': 'white'}
try:
colors = [clrs[i] for i in text]
except:
colors = [pcolors[i] for i in text]
return colors