def test_stacked_columns():
'It test the freq histogram'
values = {
'A': [0.66666666666666663, 0.33333333333333331, 0.0, 0.0, 0, 0.0],
'C': [0.33333333333333331, 0.66666666666666663, 0.0, 0.0, 0, 0.0],
'T': [0.0, 0.0, 1.0, 0.33333333333333331, 0, 1.0],
'G': [0.0, 0.0, 0.0, 0.66666666666666663, 0, 0.0]}
colors = {'A':'g', 'C':'b', 'T':'r', 'G':'k'}
fhand = tempfile.NamedTemporaryFile(suffix='.svg')
draw_stacked_columns(values, title='test', fhand=fhand, colors=colors)
fhand.flush()
# from franklin.utils.cmd_utils import call
# call(('eog', fhand.name))
svg = open(fhand.name, 'r').read()
assert '<!-- Created with matplotlib (http://matplotlib' in svg
def create_nucleotide_freq_histogram(sequences, fhand=None, title=None, positions_to_study=30):
"""It writes a especific stacked_columns graphic representing the freq of
each nucleotide per position"""
values = _nucleotide_freq_per_position(sequences, positions_to_study=positions_to_study)
# values should show starting with 1
xvalues = range(len(values.values()[0]))
xvalues.pop(0)
xvalues.append(xvalues[-1] + 1)
if not title:
title = "Nucleotide frequency per position"
colors = {"A": "g", "C": "b", "T": "r", "G": "k"}
xlabel = "Sequence positions"
ylabel = "Nucleotide frequency"
draw_stacked_columns(values, colors, title=title, xlabel=xlabel, ylabel=ylabel, fhand=fhand, xvalues=xvalues)
return values
def create_nucleotide_freq_histogram(sequences, fhand=None, title=None,
positions_to_study=30):
'''It writes a especific stacked_columns graphic representing the freq of
each nucleotide per position'''
values = _nucleotide_freq_per_position(sequences,
positions_to_study=positions_to_study)
#values should show starting with 1
xvalues = range(len(values.values()[0]))
xvalues.pop(0)
xvalues.append(xvalues[-1] + 1)
if not title:
title = 'Nucleotide frequency per position'
colors = {'A':'g', 'C':'b', 'T':'r', 'G':'k'}
xlabel = 'Sequence positions'
ylabel = 'Nucleotide frequency'
draw_stacked_columns(values, colors, title=title, xlabel=xlabel,
ylabel=ylabel, fhand=fhand, xvalues=xvalues)
return values