Exemplo n.º 1
0
 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'],
                                    )
Exemplo n.º 2
0
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',
                                   )
Exemplo n.º 3
0
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',
    )