def test_plot_from_seq_and_struct(self):
"""plot_from_seq_and_struct helper function should give correct result.
"""
ps_plot = plot_from_seq_and_struct(self.standard_seq,\
self.standard_struct, seqname=self.standard_name)
observed_lines = ps_plot.split('\n')
expected_lines = RNAPLOT_RES.split('\n')
#First 8 lines depend on the runtime. Check after.
self.assertEqual(observed_lines[8:], expected_lines[8:])
def test_plot_from_seq_and_struct(self):
"""plot_from_seq_and_struct helper function should give correct result.
"""
ps_plot = plot_from_seq_and_struct(self.standard_seq,\
self.standard_struct, seqname=self.standard_name)
observed_lines = ps_plot.split('\n')
expected_lines = RNAPLOT_RES.split('\n')
#First 8 lines depend on the runtime. Check after.
self.assertEqual(observed_lines[8:],expected_lines[8:])
def get_rnaplot_postscript(sequence, struct):
"""Returns postscript string for seq and struct.
"""
# Params for RNAplot
params = {"-t": "0", "--pre": "%PreTextHere"}
# Get the postscript list
ps_list = plot_from_seq_and_struct(sequence, struct, params=params).split("\n")
# parse it into prefix and suffix lists
pre_finder = LabeledRecordFinder(is_label_line=lambda x: x.startswith("%PreTextHere"))
prefix, suffix = list(pre_finder(ps_list))
# Remove drawoutline and drawpairs commands form suffix
new_suffix = []
for s in suffix:
if not (s.startswith("drawpairs") or s.startswith("drawoutline")):
new_suffix.append(s)
return "\n".join(prefix), "\n".join(new_suffix)
def get_rnaplot_postscript(sequence, struct):
"""Returns postscript string for seq and struct.
"""
#Params for RNAplot
params = {'-t':'0',\
'--pre':'%PreTextHere'}
#Get the postscript list
ps_list = plot_from_seq_and_struct(sequence,\
struct,params=params).split('\n')
#parse it into prefix and suffix lists
pre_finder = LabeledRecordFinder(\
is_label_line=lambda x: x.startswith('%PreTextHere'))
prefix,suffix = list(pre_finder(ps_list))
#Remove drawoutline and drawpairs commands form suffix
new_suffix = []
for s in suffix:
if not (s.startswith('drawpairs') or s.startswith('drawoutline')):
new_suffix.append(s)
return '\n'.join(prefix), '\n'.join(new_suffix)
def get_rnaplot_postscript(sequence, struct):
"""Returns postscript string for seq and struct.
"""
#Params for RNAplot
params = {'-t':'0',\
'--pre':'%PreTextHere'}
#Get the postscript list
ps_list = plot_from_seq_and_struct(sequence,\
struct,params=params).split('\n')
#parse it into prefix and suffix lists
pre_finder = LabeledRecordFinder(\
is_label_line=lambda x: x.startswith('%PreTextHere'))
prefix,suffix = list(pre_finder(ps_list))
#Remove drawoutline and drawpairs commands form suffix
new_suffix = []
for s in suffix:
if not (s.startswith('drawpairs') or s.startswith('drawoutline')):
new_suffix.append(s)
return '\n'.join(prefix), '\n'.join(new_suffix)
def draw_structure(sequence, struct, indices=None, colors=None, circle_indices=None, square_indices=None, radial=True):
"""Returns a postscript string colored at indices.
sequence: string of sequence characters.
struct: string of ViennaStructure for sequence. Must be valid structure
same length as sequence.
indices: list of indices in sequence that will be colored as a solid
circle.
colors: list of colors, same length as list of indices.
circle_indices: list of indices in sequence to draw an empty circle
around.
square_indices: list of indices in sequence to draw an empty square
around.
radial: draw structue in radial format (default=True).
"""
seq_len_scale = int(len(sequence) / 50.0)
if seq_len_scale < 1:
circle_scale_size = 0.0
square_scale_size = 0.0
else:
# Get circle radius. Proportional to sequence length
circle_scale_size = (0.02 / seq_len_scale) / 4.0
# Get edge size. Proportional to sequence length
square_scale_size = (0.03 / seq_len_scale) / 4.0
circle_radius = 0.02 - circle_scale_size
square_edge_size = 0.03 - square_scale_size
if indices is None:
indices = []
if colors is None:
colors = []
if circle_indices is None:
circle_indices = []
if square_indices is None:
square_indices = []
if len(indices) != len(colors):
raise ValueError, "indices and colors must be equal sized lists"
if radial:
params = {"-t": "0"}
else:
params = {"-t": "1"}
# Get the postscript list
ps_list = plot_from_seq_and_struct(sequence, struct, params=params).split("\n")
# Parse out seq, coords, and pairs
seq, coords, pair_list = RnaPlotParser(ps_list)
coords = scale_coords(coords)
# get letters
letters = make_letters(coords, list(seq))
# get pairs
pairs = make_pairs(coords, pair_list)
# get outline
outline = make_outline(coords)
# get labels
labels, label_coords = make_labels(coords)
# get plain circle coords
circle_coords = [coords[i] for i in circle_indices]
circle_faces = ["white"] * len(circle_coords)
circle_edges = ["black"] * len(circle_coords)
plain_circles = make_circles(circle_coords, circle_faces, circle_edges, radius=circle_radius)
# get motif circles
motif_coords = [coords[i] for i in indices]
motif_circles = make_circles(motif_coords, colors, colors, fill=True, radius=circle_radius)
# Get square coords
square_coords = [coords[i] for i in square_indices]
plain_squares = make_boxes(square_coords, edge_size=square_edge_size)
axis = gca()
axis.set_axis_off()
all_coords = coords + label_coords
set_axis_limits(axis, all_coords)
for l in [letters, pairs, outline, motif_circles, plain_circles, plain_squares, labels]:
for shape in l:
axis.add_artist(shape)
fig = gcf()
largest = max([fig.get_figheight(), fig.get_figwidth()])
fig.set_figheight(largest)
fig.set_figwidth(largest)
def draw_structure(sequence,struct,indices=None,colors=None,\
circle_indices=None, square_indices=None,radial=True):
"""Returns a postscript string colored at indices.
sequence: string of sequence characters.
struct: string of ViennaStructure for sequence. Must be valid structure
same length as sequence.
indices: list of indices in sequence that will be colored as a solid
circle.
colors: list of colors, same length as list of indices.
circle_indices: list of indices in sequence to draw an empty circle
around.
square_indices: list of indices in sequence to draw an empty square
around.
radial: draw structue in radial format (default=True).
"""
seq_len_scale = int(len(sequence)/50.)
if seq_len_scale < 1:
circle_scale_size = 0.
square_scale_size = 0.
else:
#Get circle radius. Proportional to sequence length
circle_scale_size = (.02/seq_len_scale)/4.0
#Get edge size. Proportional to sequence length
square_scale_size = (.03/seq_len_scale)/4.0
circle_radius = .02 - circle_scale_size
square_edge_size = .03 - square_scale_size
if indices is None:
indices = []
if colors is None:
colors = []
if circle_indices is None:
circle_indices = []
if square_indices is None:
square_indices = []
if len(indices) != len(colors):
raise ValueError, 'indices and colors must be equal sized lists'
if radial:
params = {'-t':'0'}
else:
params = {'-t':'1'}
#Get the postscript list
ps_list = plot_from_seq_and_struct(sequence,\
struct,params=params).split('\n')
#Parse out seq, coords, and pairs
seq, coords, pair_list = RnaPlotParser(ps_list)
coords = scale_coords(coords)
#get letters
letters = make_letters(coords, list(seq))
#get pairs
pairs = make_pairs(coords, pair_list)
#get outline
outline = make_outline(coords)
#get labels
labels,label_coords = make_labels(coords)
#get plain circle coords
circle_coords = [coords[i] for i in circle_indices]
circle_faces = ['white']*len(circle_coords)
circle_edges = ['black']*len(circle_coords)
plain_circles = make_circles(circle_coords,circle_faces, circle_edges,\
radius=circle_radius)
#get motif circles
motif_coords = [coords[i] for i in indices]
motif_circles = make_circles(motif_coords,colors,colors,fill=True,\
radius=circle_radius)
#Get square coords
square_coords = [coords[i] for i in square_indices]
plain_squares = make_boxes(square_coords,edge_size=square_edge_size)
axis = gca()
axis.set_axis_off()
all_coords = coords + label_coords
set_axis_limits(axis, all_coords)
for l in [letters, pairs, outline, motif_circles, plain_circles, \
plain_squares,labels]:
for shape in l:
axis.add_artist(shape)
fig = gcf()
largest = max([fig.get_figheight(), fig.get_figwidth()])
fig.set_figheight(largest)
fig.set_figwidth(largest)
