Chnage the TMB number in the blue circle of the report from in-house TMB to Illumina TMB #104
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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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…TMB to Illumina TMB. And the number needs to be rounded. This is the request from national molecular biology group. GitHub issue 100.
tonjegul
approved these changes
Apr 15, 2026
marrip
reviewed
Apr 15, 2026
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marrip
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marrip
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Hey, I think your changes are quite straight forward but I would consider to make this part in the code DRYer. Please have a look at my suggestion and let me know what you think
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| if(TMB_TSO500_nr >= 0 and TMB_TSO500_nr <= 5 and TMB_TSO500 != "" and TMB_TSO500 != "NA"): | ||
| roundshape = slide.shapes.add_shape(MSO_SHAPE.OVAL, Cm(7.07), Cm(3.90), Cm(0.58), Cm(0.58)) | ||
| 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].text = str(TMB_TSO500_nr) | ||
| 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"): | ||
| if((TMB_TSO500_nr > 5 and TMB_TSO500_nr <= 20) or TMB_TSO500 == "" or TMB_TSO500 == "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].text = str(TMB_TSO500_nr) | ||
| 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"): | ||
| if(TMB_TSO500_nr > 20 and TMB_TSO500 != "" and TMB_TSO500 != "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].text = str(TMB_TSO500_nr) | ||
| 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) |
Collaborator
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could we make this whole part DRYer. I see there is a lot of repetition which seems unnecessary? Maybe something like:
Suggested change
| 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)) | |
| textbox5 = 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)) | |
| textbox5 = slide.shapes.add_textbox(Cm(8.23), Cm(3.90), Cm(0.58), Cm(0.60)) | |
| if(TMB_TSO500_nr > 20 and TMB_TSO500 != "" and TMB_TSO500 != "NA"): | |
| roundshape = slide.shapes.add_shape(MSO_SHAPE.OVAL, Cm(10.26), Cm(3.90), Cm(0.58), Cm(0.58)) | |
| textbox5 = slide.shapes.add_textbox(Cm(10.20), Cm(3.95), Cm(0.58), Cm(0.60)) | |
| roundshape.line.color.rgb = RGBColor(255,165,0) | |
| tf5 = textbox5.text_frame | |
| tf5.paragraphs[0].text = str(TMB_TSO500_nr) | |
| 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) |
I changed the logic in if((TMB_TSO500_nr > 5 and TMB_TSO500_nr <= 20) or TMB_TSO500 == "" or TMB_TSO500 == "NA") because I thought it was a mistake that it would also handle TMB_TSO500 == "" to be empty and TMB_TSO500to beNA` but I can adjust it for this case if I got it wrong. Just let me know
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Request from the national molecular biology group:
Change the TMB number in the blue circle of report from in-house TMB to Illumina TMB. And the number will be rounded when reading into the report.