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Re-format the CNV overview plots in ppt report. issue76 #77

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xiaoliz0 merged 1 commit into from
Aug 27, 2025
Merged

Re-format the CNV overview plots in ppt report. issue76 #77

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31 changes: 20 additions & 11 deletions Script/PRONTO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1119,20 +1119,27 @@ def update_clinical_tsoppi_file(InPreD_clinical_tsoppi_data_file,sample_id,if_ge
fw.close()


def pdf_page_image_to_ppt(pdf_file,pages,output_ppt_file):
def pdf_page_image_to_ppt(pdf_file,output_ppt_file,pages,width_scale,height_scale):
ppt = Presentation(output_ppt_file)
for page_num in pages:
images = convert_from_path(pdf_file, first_page=page_num, last_page=page_num)
slide = ppt.slides.add_slide(ppt.slide_layouts[6])
image_width = ppt.slide_width * width_scale
image_height = ppt.slide_height * height_scale
for i in range(0, len(pages)):
images = convert_from_path(pdf_file, first_page=pages[i], last_page=pages[i])
if not images:
logging.warning("The page number {} in {} is not found!".format(page_num, pdf_file))
logging.warning("The page number {} in {} is not found!".format(pages[i], pdf_file))
continue
slide = ppt.slides.add_slide(ppt.slide_layouts[6])
image_path = "temp_page_{}.jpg".format(page_num)
image_path = "temp_page_{}.jpg".format(pages[i])
images[0].save(image_path, 'JPEG')
slide.shapes.add_picture(image_path, left=0, top=0, width=ppt.slide_width, height=ppt.slide_height)
if(len(pages) == 1):
image_top = ppt.slide_height/4
else:
image_top = image_height*i
slide.shapes.add_picture(image_path, left=0, top=image_top, width=image_width, height=image_height)
os.remove(image_path)
ppt.save(output_ppt_file)




def usage(exit_status = 0):
print ("""Usage: python3 %s
Expand Down Expand Up @@ -1526,11 +1533,13 @@ def main(argv):
slide8_table_nrows = insert_table_to_ppt(slide8_table_data_file,slide8_table_ppSlide,slide8_table_name,slide8_header_left,slide8_header_top,slide8_header_width,slide8_table_left,slide8_table_top,slide8_table_width,slide8_table_height,slide8_table_font_size,slide8_table_header,output_ppt_file,if_print_rowNo,table8_column_width)

# Insert the CNV_overveiw_plots pictures A2, B3 and C1 into report.
A2_to_extract=[2]
pdf_page_image_to_ppt(CNV_overview_plots_pdf,output_ppt_file,A2_to_extract,width_scale=1,height_scale=0.5)
if(DNA_normal_sampleID != ""):
pages_to_extract = [2, 5, 6]
B3_C1_to_extract = [5, 6]
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@marrip marrip Jul 4, 2025

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just a minor comment here, the variable B3_C1_to_extract does not help me understand what it holds - pages_to_extract was more self-explanatory. May I ask the reasoning behind the change?

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@marrip marrip Jul 4, 2025

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ah, looking at line 1536, it is to make the destinction between A2_to_extract and B3_C1_to_extract. What do A2, B3 and C1 stand for?

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@xiaoliz0 xiaoliz0 Jul 4, 2025

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Hi Martin, A2, B3 and C1 are the CNV plot image names in the TSOPPI results. And there will be conditions to extract different plots into the report.

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@marrip marrip Jul 8, 2025

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thanks for the clarification. Maybe you could just add a comment about it to make sure anybody reading your code understands ☺️

else:
pages_to_extract = [2, 4, 5]
pdf_page_image_to_ppt(CNV_overview_plots_pdf,pages_to_extract,output_ppt_file)
B3_C1_to_extract = [4, 5]
pdf_page_image_to_ppt(CNV_overview_plots_pdf,output_ppt_file,B3_C1_to_extract,width_scale=1,height_scale=0.5)

# Change slides order.
ppt = Presentation(output_ppt_file)
Expand Down