def plot_rRNA_coverage(self):
counts = self.read_file('rRNA_coverage')
coverage_data = {self.name: (self.get_total_reads(), counts, 'blue')}
contaminants.plot_rRNA_coverage(coverage_data,
self.file_names['oligos_sam'],
self.figure_file_names['rRNA_coverage'],
)
def make_rRNA_coverage_plot():
colors = ['b', 'g', 'r', 'c', 'm', 'y', 'k'] * 10
experiments = build_all_experiments(verbose=False)
all_experiments = [exp for exp in experiments['belgium_2014_08_07'].values() if 'FP' in exp.name]
coverage_data = {exp.name: (exp.get_total_reads(), exp.read_file('rRNA_coverage'), color)
for exp, color in zip(all_experiments, colors)}
contaminants.plot_rRNA_coverage(coverage_data,
all_experiments[0].file_names['oligos_sam'],
'belgium_2014_08_07_rRNA_coverage_{0}.pdf',
)
def make_rRNA_coverage_plot():
colors = ['b', 'g', 'r', 'c', 'm', 'y', 'k'] * 10
experiments = build_all_experiments(verbose=False)
all_experiments = [
exp for exp in experiments['belgium_2014_08_07'].values()
if 'FP' in exp.name
]
coverage_data = {
exp.name:
(exp.get_total_reads(), exp.read_file('rRNA_coverage'), color)
for exp, color in zip(all_experiments, colors)
}
contaminants.plot_rRNA_coverage(
coverage_data,
all_experiments[0].file_names['oligos_sam'],
'belgium_2014_08_07_rRNA_coverage_{0}.pdf',
)