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
if data_to_display:
if (all_ercc_counts < 250):
msg_to_user = "******" + str(
all_ercc_counts
) + ", is not sufficient for a reliable correlation to be calculated."
data_to_display = False
elif (dr[8] < 3):
msg_to_user = "******" + str(
dr[8]
) + ", is not sufficient for a reliable correlation to be calculated."
data_to_display = False
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) data_to_display = True msg_to_user = "" try: report_components = generate_reports(coverage, dr, counts) except ValueError: msg_to_user = "******" data_to_display = False if (all_ercc_counts < 250): msg_to_user = "******"+str(all_ercc_counts)+", is not sufficient for a reliable correlation to be calculated." data_to_display = False elif (dr[8]<3): msg_to_user = "******"+str(dr[8])+", is not sufficient for a reliable correlation to be calculated." data_to_display = False if data_to_display: transcript_names_js, transcript_images_js, transcript_counts_js, transcript_sizes_js, series_params, ercc_points = chart_series_params(counts,transcript_sizes,transcript_names, mean_mapqs,ercc_conc) color_legend = generate_color_legend() msg_to_user, rsquared = create_summary_block(OUTPUT_DIR,dr,MINIMUM_RSQUARED)
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
if data_to_display:
if (all_ercc_counts < 250):
msg_to_user = "******"+str(all_ercc_counts)+", is not sufficient for a reliable correlation to be calculated."
data_to_display = False
elif (dr[8]<3):
msg_to_user = "******"+str(dr[8])+", is not sufficient for a reliable correlation to be calculated."
data_to_display = False
if data_to_display:
transcript_names_js, transcript_images_js, transcript_counts_js, transcript_sizes_js, series_params, ercc_points = chart_series_params(counts,transcript_sizes,transcript_names, mean_mapqs,ercc_conc)
color_legend = generate_color_legend()
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(coverage, dr, counts)
except ValueError:
msg_to_user = "******"
data_to_display = False
if data_to_display:
if (all_ercc_counts < 250):
msg_to_user = "******"+str(all_ercc_counts)+", is not sufficient for a reliable correlation to be calculated."
data_to_display = False
elif (dr[8]<3):
msg_to_user = "******"+str(dr[8])+", is not sufficient for a reliable correlation to be calculated."
data_to_display = False
if data_to_display:
transcript_names_js, transcript_images_js, transcript_counts_js, transcript_sizes_js, series_params, ercc_points = chart_series_params(counts,transcript_sizes,transcript_names, mean_mapqs,ercc_conc)
color_legend = generate_color_legend()
