Ejemplo n.º 1
0
            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'],
Ejemplo n.º 2
0
  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,
Ejemplo n.º 3
0
    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,
Ejemplo n.º 4
0
  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,