In [1]:
%matplotlib inline
%load_ext autoreload
%autoreload 2
import logging
from eden.util import configure_logging
configure_logging(logging.getLogger(), verbosity=2)
given the RFAM id of a family we retrieve it from the RFAM online database composing the correspondent URL
In [2]:
rfam_id = 'RF00005' #tRNA
In [3]:
from eden_rna.io.rfam import load
seqs = list(load(rfam_id, range(6)))
In [4]:
from eden_rna.sequence import fold
graphs = fold(seqs)
In [5]:
from eden.display import draw_graph_set
opts={'n_graphs_per_line':2, 'size':1, 'vertex_border':False, 'vertex_size':200, 'font_size':9, 'vertex_alpha':0.6,
'vertex_color':'_label_', 'colormap':'Set3', 'prog':'circo', 'size_x_to_y_ratio':10}
draw_graph_set(graphs, **opts)
In [6]:
from eden_rna.rnafold import fold
graphs = fold(seqs)
In [7]:
from eden.display import draw_graph_set
opts={'n_graphs_per_line':2,'size':7, 'vertex_border':False, 'vertex_size':200, 'font_size':9, 'vertex_alpha':0.6,
'vertex_color':'_label_', 'colormap':'Set3'}
draw_graph_set(graphs, **opts)
In [8]:
from eden_rna.rnaplfold import fold
params = dict(window_size = 250,
max_bp_span = 150,
hard_threshold=0.5,
avg_bp_prob_cutoff = 0.1,
max_num_edges = 2,
no_lonely_bps=True,
nesting=True)
graphs = fold(seqs, **params)
opts={'n_graphs_per_line':2,'size':7, 'vertex_border':False, 'vertex_size':200, 'font_size':9, 'vertex_alpha':0.6,
'vertex_color':'_label_', 'colormap':'Set3', 'ignore_for_layout':'nesting'}
draw_graph_set(graphs, **opts)
In [9]:
from eden_rna.rnashapes import fold
params = dict(shape_type=5, energy_range=35, max_num=3, split_components=True)
graphs = fold(seqs, **params)
opts={'n_graphs_per_line':3,'size':7, 'vertex_border':False, 'vertex_size':200, 'font_size':9, 'vertex_alpha':0.6,
'vertex_color':'_label_', 'colormap':'Set3', 'ignore_for_layout':'nesting'}
draw_graph_set(graphs, **opts)