except:
FASTQ_FILE_CREATED = 'N'
try:
BARCODE_ENTERED = sys.argv[10]
except:
BARCODE_ENTERED = 'none found'
try:
ONLY_FWD_READS = (sys.argv[11] == 'Y')
except:
ONLY_FWD_READS = False
data_to_display = True
msg_to_user = ""
if FASTQ_FILE_CREATED != 'N':
coverage = SamCoverage(GENOME)
transcript_names = []
transcript_sizes = []
with open(GENOME) as ercc_genome:
for line in ercc_genome:
parsed_line = line.split()
transcript_names.append(parsed_line[0])
transcript_sizes.append(parsed_line[1])
# write counts file and filtered sam file, return stats tuple
counts, all_ercc_counts, total_counts, mean_mapqs = write_output_counts_file(
RAW_SAM_FILE, FILTERED_SAM_FILE, COUNTS_FILE, transcript_names,
ONLY_FWD_READS)
if (total_counts > 0):
percent_total_counts_ercc = '%.2f' % (100 *
(all_ercc_counts / total_counts))
FASTQ_FILE_CREATED = 'N'
try:
BARCODE_ENTERED = sys.argv[10]
except:
BARCODE_ENTERED = 'none found'
try:
ONLY_FWD_READS = (sys.argv[11] == 'Y')
except:
ONLY_FWD_READS = False
data_to_display = True
msg_to_user = ""
if FASTQ_FILE_CREATED != 'N':
coverage = SamCoverage(GENOME)
transcript_names = []
transcript_sizes = []
with open(GENOME) as ercc_genome:
for line in ercc_genome:
parsed_line = line.split()
transcript_names.append(parsed_line[0])
transcript_sizes.append(parsed_line[1])
# write counts file and filtered sam file, return stats tuple
counts, all_ercc_counts, total_counts, mean_mapqs = write_output_counts_file(RAW_SAM_FILE,FILTERED_SAM_FILE,COUNTS_FILE,transcript_names,ONLY_FWD_READS)
if (total_counts > 0):
percent_total_counts_ercc = '%.2f' % (100 * (all_ercc_counts / total_counts))
percent_total_counts_non_ercc = 100 - float(percent_total_counts_ercc)
coverage.parse_sam(FILTERED_SAM_FILE)
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)
template_vars['start_site_coverage'] = results[1]['start_site_coverage']
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'] = results[1]['start_site_coverage']
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)