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Chnage the TMB number in the blue circle of the report from in-house TMB to Illumina TMB #104

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Merged
xiaoliz0 merged 4 commits into from
Apr 29, 2026
Merged

Chnage the TMB number in the blue circle of the report from in-house TMB to Illumina TMB #104

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35ab3f0
Chnage the TMB number in the blue circle of the report from in-house …
xiaoliz0 Apr 15, 2026
10afde2
Update Script/PRONTO.py
xiaoliz0 Apr 28, 2026
7f22723
Use the suggested codes from Martin and remove the old codes. Give co…
xiaoliz0 Apr 28, 2026
b88c26e
Remove the overwrite conditions.
xiaoliz0 Apr 28, 2026
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100 changes: 44 additions & 56 deletions Script/PRONTO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -806,6 +806,7 @@ def update_ppt_variant_summary_table(data_nrows,DNA_sampleID,RNA_sampleID,TMB_DR
else:
TMB_illumina = "TMB = " + line.split('\t')[1]
TMB_TSO500 = line.split('\t')[1]
TMB_TSO500_nr = round(float(TMB_TSO500.split()[0]))
if(line.split('\t')[2] == 'NA'):
MSI_illumina = "MSI = NA"
msi_text = "-"
Expand Down Expand Up @@ -910,73 +911,60 @@ def update_ppt_variant_summary_table(data_nrows,DNA_sampleID,RNA_sampleID,TMB_DR
tf5.paragraphs[0].text = str(preMTB_appendix_nrows)
tf5.paragraphs[0].font.size = Pt(7)
tf5.paragraphs[0].alignment = PP_ALIGN.CENTER
if(TMB_DRUP_nr >= 0 and TMB_DRUP_nr <= 5 and str_TMB_DRUP != "" and str_TMB_DRUP != "NA"):
roundshape = slide.shapes.add_shape(MSO_SHAPE.OVAL, Cm(7.07), Cm(3.90), Cm(0.58), Cm(0.58))
if(TMB_TSO500 != "" and TMB_TSO500 != "NA"):
if(TMB_TSO500_nr >= 0 and TMB_TSO500_nr <= 5):
roundshape = slide.shapes.add_shape(MSO_SHAPE.OVAL, Cm(7.07), Cm(3.90), Cm(0.58), Cm(0.58))
textbox6 = slide.shapes.add_textbox(Inches(2.74), Inches(1.54), Inches(0.32), Inches(0.21))
if(TMB_TSO500_nr > 5 and TMB_TSO500_nr <= 20):
roundshape = slide.shapes.add_shape(MSO_SHAPE.OVAL, Cm(8.27), Cm(3.90), Cm(0.58), Cm(0.58))
textbox6 = slide.shapes.add_textbox(Cm(8.23), Cm(3.90), Cm(0.58), Cm(0.60))
if(TMB_TSO500_nr > 20):
roundshape = slide.shapes.add_shape(MSO_SHAPE.OVAL, Cm(10.26), Cm(3.90), Cm(0.58), Cm(0.58))
textbox6 = slide.shapes.add_textbox(Cm(10.20), Cm(3.95), Cm(0.58), Cm(0.60))
roundshape.line.color.rgb = RGBColor(255,165,0)
textbox5 = slide.shapes.add_textbox(Inches(2.74), Inches(1.54), Inches(0.32), Inches(0.21))
tf5 = textbox5.text_frame
tf5.paragraphs[0].text = str_TMB_DRUP
tf5.paragraphs[0].font.size = Pt(7)
tf5.paragraphs[0].font.bold = True
tf5.paragraphs[0].alignment = PP_ALIGN.CENTER
tf5.paragraphs[0].font.color.rgb = RGBColor(250,250,250)
if((TMB_DRUP_nr > 5 and TMB_DRUP_nr <= 20) or str_TMB_DRUP == "" or str_TMB_DRUP == "NA"):
roundshape = slide.shapes.add_shape(MSO_SHAPE.OVAL, Cm(8.27), Cm(3.90), Cm(0.58), Cm(0.58))
roundshape.line.color.rgb = RGBColor(255,165,0)
textbox5 = slide.shapes.add_textbox(Cm(8.23), Cm(3.90), Cm(0.58), Cm(0.60))
tf5 = textbox5.text_frame
tf5.paragraphs[0].text = str_TMB_DRUP
tf5.paragraphs[0].font.size = Pt(7)
tf5.paragraphs[0].font.bold = True
tf5.paragraphs[0].alignment = PP_ALIGN.CENTER
tf5.paragraphs[0].font.color.rgb = RGBColor(250,250,250)
if(TMB_DRUP_nr > 20 and str_TMB_DRUP != "" and str_TMB_DRUP != "NA"):
roundshape = slide.shapes.add_shape(MSO_SHAPE.OVAL, Cm(10.26), Cm(3.90), Cm(0.58), Cm(0.58))
roundshape.line.color.rgb = RGBColor(255,165,0)
textbox5 = slide.shapes.add_textbox(Cm(10.20), Cm(3.95), Cm(0.58), Cm(0.60))
tf5 = textbox5.text_frame
tf5.paragraphs[0].text = str_TMB_DRUP
tf5.paragraphs[0].font.size = Pt(7)
tf5.paragraphs[0].font.bold = True
tf5.paragraphs[0].alignment = PP_ALIGN.CENTER
tf5.paragraphs[0].font.color.rgb = RGBColor(250,250,250)
textbox6 = slide.shapes.add_textbox(Inches(6.23), Inches(1.06), Inches(0.97), Inches(0.19))
tf6 = textbox6.text_frame
tf6.paragraphs[0].text = splicing
tf6.paragraphs[0].font.size = Pt(7)
tf6.paragraphs[0].alignment = PP_ALIGN.LEFT
textbox7 = slide.shapes.add_textbox(Inches(6.23), Inches(1.26), Inches(0.97), Inches(0.19))
tf7 = textbox7.text_frame
tf7.paragraphs[0].text = fusion
tf7.paragraphs[0].font.size = Pt(7)
tf6 = textbox6.text_frame
tf6.paragraphs[0].text = str(TMB_TSO500_nr)
tf6.paragraphs[0].font.size = Pt(7)
tf6.paragraphs[0].font.bold = True
tf6.paragraphs[0].alignment = PP_ALIGN.CENTER
tf6.paragraphs[0].font.color.rgb = RGBColor(250,250,250)
textbox7 = slide.shapes.add_textbox(Inches(6.23), Inches(1.06), Inches(0.97), Inches(0.19))
tf7 = textbox7.text_frame
tf7.paragraphs[0].text = splicing
tf7.paragraphs[0].font.size = Pt(7)
tf7.paragraphs[0].alignment = PP_ALIGN.LEFT
textbox8 = slide.shapes.add_textbox(Inches(6.23), Inches(1.26), Inches(0.97), Inches(0.19))
tf8 = textbox8.text_frame
tf8.paragraphs[0].text = fusion
tf8.paragraphs[0].font.size = Pt(7)
tf8.paragraphs[0].alignment = PP_ALIGN.LEFT
if(index == 1):
textbox8 = slide.shapes.add_textbox(Inches(5.14), Inches(2.63), Inches(0.53), Inches(0.25))
tf8 = textbox8.text_frame
tf8.paragraphs[0].text = TMB_DRUP_str
tf8.paragraphs[0].font.size = Pt(8)
tf8.paragraphs[0].alignment = PP_ALIGN.LEFT
textbox9 = slide.shapes.add_textbox(Inches(3.95), Inches(3.70), Inches(0.88), Inches(0.25))
textbox9 = slide.shapes.add_textbox(Inches(5.14), Inches(2.63), Inches(0.53), Inches(0.25))
tf9 = textbox9.text_frame
tf9.paragraphs[0].text = TMB_illumina
tf9.paragraphs[0].text = TMB_DRUP_str
tf9.paragraphs[0].font.size = Pt(8)
tf9.paragraphs[0].alignment = PP_ALIGN.LEFT
textbox10 = slide.shapes.add_textbox(Inches(4.90), Inches(3.84), Inches(1.14), Inches(0.25))
textbox10 = slide.shapes.add_textbox(Inches(3.95), Inches(3.70), Inches(0.88), Inches(0.25))
tf10 = textbox10.text_frame
tf10.paragraphs[0].text = MSI_illumina
tf10.paragraphs[0].text = TMB_illumina
tf10.paragraphs[0].font.size = Pt(8)
tf10.paragraphs[0].alignment = PP_ALIGN.CENTER
if(index == 5):
textbox11 = slide.shapes.add_textbox(Inches(6.03), Inches(2.14), Inches(0.59), Inches(0.25))
tf10.paragraphs[0].alignment = PP_ALIGN.LEFT
textbox11 = slide.shapes.add_textbox(Inches(4.90), Inches(3.84), Inches(1.14), Inches(0.25))
tf11 = textbox11.text_frame
tf11.paragraphs[0].text = TMB_DRUP_str
tf11.paragraphs[0].font.size = Pt(9)
tf11.paragraphs[0].alignment = PP_ALIGN.LEFT
textbox12 = slide.shapes.add_textbox(Inches(6.22), Inches(2.29), Inches(0.88), Inches(0.25))
tf11.paragraphs[0].text = MSI_illumina
tf11.paragraphs[0].font.size = Pt(8)
tf11.paragraphs[0].alignment = PP_ALIGN.CENTER
if(index == 5):
textbox12 = slide.shapes.add_textbox(Inches(6.03), Inches(2.14), Inches(0.59), Inches(0.25))
tf12 = textbox12.text_frame
tf12.paragraphs[0].text = TMB_illumina
tf12.paragraphs[0].text = TMB_DRUP_str
tf12.paragraphs[0].font.size = Pt(9)
tf12.paragraphs[0].alignment = PP_ALIGN.LEFT
tf12.paragraphs[0].alignment = PP_ALIGN.LEFT
textbox13 = slide.shapes.add_textbox(Inches(6.22), Inches(2.29), Inches(0.88), Inches(0.25))
tf13 = textbox13.text_frame
tf13.paragraphs[0].text = TMB_illumina
tf13.paragraphs[0].font.size = Pt(9)
tf13.paragraphs[0].alignment = PP_ALIGN.LEFT
ppt.save(output_ppt_file)
return stable_text

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