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1 Examples
0
Source : genome_protein_plots.py
with GNU General Public License v3.0
from michellejlin
with GNU General Public License v3.0
from michellejlin
def protein_annotation(first):
protein_locs = []
protein_names = []
protein_lengths = []
# Shades in every other protein region. Provides warning if proteins overlap.
for i in range(0, proteins.shape[0]):
if(i==0):
x1 = 0
elif(proteins.iloc[i,1] < proteins.iloc[i-1,2]) and first:
print('WARNING: Protein-' + str(proteins.iloc[i,0]) + ' is overlapping with Protein-' + str(proteins.iloc[i-1,0]))
print('Analysis will continue but the visualization for these two proteins will look a little funny. Often the fix for this is simply deleting the small ancilary proteins that overlapping from the gff file and using the -f and -g flags. For more help see the readme.')
x1 = proteins.iloc[i,1]
else:
x1 = proteins.iloc[i,1]
if(i==proteins.shape[0]-1):
x2 = proteins.iloc[i,2]
else:
x2 = proteins.iloc[(i+1),1]
if(i%2==0):
genome_plot.add_layout(BoxAnnotation(left=x1, right=x2, fill_alpha=0.1, fill_color='green'))
protein_locs.append((x1+x2)/2)
protein_lengths.append(x2-x1)
protein_names.append(proteins.iloc[i,0])
if(os.stat("mat_peptides_additions.txt").st_size!=0):
# Makes arrows for mature peptides.
for i in range(0, mat_peptides_list.shape[0]):
x1 = mat_peptides_list.iloc[i,1]
x2 = mat_peptides_list.iloc[i,2]
genome_plot.add_layout(Arrow(end = VeeHead(size=20, fill_color = "cadetblue", fill_alpha = 0.3, line_alpha = 0),
line_color = "cadetblue", line_width = 20, x_start = x1, x_end = x2,
y_start = 5, y_end = 5, line_alpha = 0.3))
# Adds protein labels as tick marks.
genome_plot.xaxis.ticker = protein_locs
protein_locs2 = []
for protein_loc in protein_locs:
str_protein_loc = str(protein_loc)
## print("old str_protein_loc" + str_protein_loc)
if ".0" in str_protein_loc:
str_protein_loc = str_protein_loc.split('.')[0]
## print("split" + str_protein_loc)
protein_locs2.append(int(str_protein_loc))
else:
protein_locs2.append(float(str_protein_loc))
genome_plot.xaxis.major_label_overrides = dict(zip(protein_locs2, protein_names))
return protein_names,protein_lengths
# Creates the legend and configures some of the toolbar stuff.
def configurePlot(g):