template_vars['start_site_coverage_pct'] = results[1]['start_site_coverage_pct']
template_vars['unique_start_sites'] = results[1]['unique_start_sites']
template_vars['start_site_complexity'] = results[1]['start_site_complexity']
template_vars['contig_cv'] = results[1]['contig_cv']
results_divs += (result_div % template_vars)
plot_coverage(contig[1], starts[1], path = image_name)
results_divs += '</div>'
report_components['results_divs'] = results_divs
report_components['updates'] = proc_update
return report_components
if __name__=='__main__':
coverage = SamCoverage(GENOME)
if len(sys.argv) == 2: coverage.parse_sam(sys.argv[1])
else: coverage.parse_sam(TEST_SAM)
threshold = 1
counts = {}
for ercc, count in coverage.count_iter():
if count >= threshold:
counts[ercc] = count
ercc_conc = load_ercc_conc(filter = counts.keys())
dr = dose_response(coverage, ercc_conc)
generate_reports(coverage, dr)
template_vars['start_site_coverage_pct'] = results[1]['start_site_coverage_pct']
template_vars['unique_start_sites'] = results[1]['unique_start_sites']
template_vars['start_site_complexity'] = results[1]['start_site_complexity']
template_vars['contig_cv'] = results[1]['contig_cv']
results_divs += (result_div % template_vars)
plot_coverage(contig[1], starts[1], path = outdir+image_name)
results_divs += '</div>'
report_components['results_divs'] = results_divs
report_components['updates'] = proc_update
return report_components
if __name__=='__main__':
coverage = SamCoverage(GENOME)
if len(sys.argv) == 2: coverage.parse_sam(sys.argv[1])
else: coverage.parse_sam(TEST_SAM)
threshold = 1
counts = {}
for ercc, count in coverage.count_iter():
if count >= threshold:
counts[ercc] = count
ercc_conc = load_ercc_conc(filter = counts.keys())
dr = dose_response(coverage, ercc_conc)
generate_reports(coverage, dr)
