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()
# GDM: changed to pass filepath name for summary file
SUMMARY_FILE = OUTPUT_DIR + PLUGIN_NAME + '_block.html'
msg_to_user, rsquared = create_summary_block(SUMMARY_FILE, dr,
MINIMUM_RSQUARED)
template = open(SRC + '/ercc_template.html')
page_we_are_making = Template(template.read())
if MINIMUM_COUNTS > 1:
counts_msg = "All transcripts with fewer than " + str(
MINIMUM_COUNTS
) + " counts are shown in the above figure (below the dotted line), but not used in calculating R-squared."
else:
counts_msg = "All transcripts, even those with only 1 count, were used in calculating R-squared."
if BARCODE_ENTERED != 'none found' and BARCODE_ENTERED != '':
barcode = '(' + BARCODE_ENTERED + ')'
else:
barcode = ''
print page_we_are_making.substitute(
dose_response_image=report_components['dose_response_image'],
results_divs=report_components['results_divs'],
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)
template = open(SRC + '/ercc_template.html')
page_we_are_making = Template(template.read())
print page_we_are_making.substitute(dose_response_image = report_components['dose_response_image'],
results_divs = report_components['results_divs'],
ercc_points = ercc_points,
percent_total_counts_non_ercc = percent_total_counts_non_ercc,
percent_total_counts_ercc = percent_total_counts_ercc,
all_ercc_counts = all_ercc_counts,
rsquared = rsquared,
slope = '%.2f' % (dr[2]),
yintercept = '%.2f' % (dr[3]),
N = str(dr[8]),
trendline_points = trendline_points,
color_legend = color_legend,
counts_file = COUNTS_URL,
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()
# GDM: changed to pass filepath name for summary file
SUMMARY_FILE = OUTPUT_DIR+PLUGIN_NAME+'_block.html'
msg_to_user, rsquared = create_summary_block(SUMMARY_FILE,dr,MINIMUM_RSQUARED)
template = open(SRC + '/ercc_template.html')
page_we_are_making = Template(template.read())
if MINIMUM_COUNTS > 1:
counts_msg = "All transcripts with fewer than "+str(MINIMUM_COUNTS)+" counts are shown in the above figure (below the dotted line), but not used in calculating R-squared."
else:
counts_msg = "All transcripts, even those with only 1 count, were used in calculating R-squared."
if BARCODE_ENTERED != 'none found' and BARCODE_ENTERED != '':
barcode = '('+BARCODE_ENTERED+')'
else:
barcode = ''
print page_we_are_making.substitute(dose_response_image = report_components['dose_response_image'],
results_divs = report_components['results_divs'],
ercc_points = ercc_points,
percent_total_counts_non_ercc = percent_total_counts_non_ercc,
percent_total_counts_ercc = percent_total_counts_ercc,
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()
msg_to_user, rsquared = create_summary_block(OUTPUT_DIR,dr,MINIMUM_RSQUARED)
template = open(SRC + '/ercc_template.html')
page_we_are_making = Template(template.read())
if MINIMUM_COUNTS > 1:
counts_msg = "All transcripts with fewer than "+str(MINIMUM_COUNTS)+" counts are shown in the above figure (below the dotted line), but not used in calculating R-squared."
else:
counts_msg = "All transcripts, even those with only 1 count, were used in calculating R-squared."
if BARCODE_ENTERED != 'none found' and BARCODE_ENTERED != '':
barcode = '('+BARCODE_ENTERED+')'
else:
barcode = ''
print page_we_are_making.substitute(dose_response_image = report_components['dose_response_image'],
results_divs = report_components['results_divs'],
ercc_points = ercc_points,
percent_total_counts_non_ercc = percent_total_counts_non_ercc,
percent_total_counts_ercc = percent_total_counts_ercc,