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)
ercc_conc = load_ercc_conc(filter=counts.keys(), pool=ERCC_POOL_NBR)
ercc_conc.sort()
dr = dose_response(coverage, ercc_conc, counts, MINIMUM_COUNTS)
trendline_points = generate_trendline_points(dr)
else:
msg_to_user = "******" + BARCODE_ENTERED + ", is not found. This is most likely to result when the barcode is typed incorrectly, or the run was originally processed with a Torrent Suite version less than 3.4."
data_to_display = False
if data_to_display:
try:
report_components = generate_reports(OUTPUT_DIR, coverage, dr, counts)
except ValueError:
msg_to_user = "******"
data_to_display = False
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)
ercc_conc = load_ercc_conc(filter = counts.keys(), pool = ERCC_POOL_NBR)
ercc_conc.sort()
dr = dose_response(coverage,ercc_conc,counts,MINIMUM_COUNTS)
trendline_points = generate_trendline_points(dr)
else:
msg_to_user = "******"+BARCODE_ENTERED+", is not found. This is most likely to result when the barcode is typed incorrectly, or the run was originally processed with a Torrent Suite version less than 3.4."
data_to_display = False
if data_to_display:
try:
report_components = generate_reports(OUTPUT_DIR, coverage, dr, counts)
except ValueError:
msg_to_user = "******"
data_to_display = False