an alpha version of a report generator that creats a report of the re…

scripts/qc/alpha_first_time_report_generator.py

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+import docx
+from docx.shared import Inches
+import os
+import glob
+from pdf2image import convert_from_path, convert_from_bytes
+from pdf2image.exceptions import (
+    PDFInfoNotInstalledError,
+    PDFPageCountError,
+    PDFSyntaxError
+)
+# Get the current working directory
+cwd = os.getcwd()
+output_file = input("Enter the desired name of output file (do not include the .docx part): ")
+
+# Print the current working directory
+print("Current working directory: {0}".format(cwd))
+
+#path_to_files = r'/Users/szaheri/Documents/SV/GATK-SV/github_ryan_shared/bwa_dragen_sample_level_comparison/results/bwa/perFamily_plots_tarball/bwa_samples_aligning_with_dragen_perFamily_plots/supporting_plots/sv_inheritance_plots/'
+#folder = r'/Users/szaheri/Documents/SV/GATK-SV/github_ryan_shared/bwa_dragen_sample_level_comparison/results/bwa/perFamily_plots_tarball/bwa_samples_aligning_with_dragen_perFamily_plots/supporting_plots/sv_inheritance_plots/'
+
+path_to_files = os.getcwd()+ '/'
+folder = os.getcwd()+ '/'
+head_tail = os.path.split(cwd)
+
+print(head_tail)
+# print tail part of the path
+print(head_tail[1])
+
+files = [folder + fn for fn in os.listdir(folder) if fn.endswith('.pdf')]
+print(files)
+# Convert them.
+def pic(path, name):
+	images = convert_from_path(path + name) #+ '.pdf'
+	for i in range(len(images)):
+		images[i].save(name[:-4] +str(i) +'.jpg', 'JPEG')
+
+
+#pic(path_to_files,'all.pdf')
+
+
+for filee in glob. glob("*.pdf"):
+	#print(filee)
+	pic(path_to_files,filee)
+
+
+
+mydoc = docx.Document()
+#mydoc = docx.Document("dragen_sample_level.docx")
+mydoc.add_paragraph("This is a report of the " + str(head_tail[0]))
+mydoc.save(str(output_file) + ".docx")
+
+
+files = [folder + fn for fn in os.listdir(folder) if fn.endswith('.pdf')]
+print(files)
+# Convert them.
+#def pic(path, name):
+#	images = convert_from_path(path + name) #+ '.pdf'
+#	for i in range(len(images)):
+#		images[i].save(name +str(i) +'.jpg', 'JPEG')
+
+
+#pic(path_to_files,'all.pdf')
+
+mydoc.add_heading(str(head_tail[1]), 0)
+mydoc.save(str(output_file) + ".docx")
+
+for filee in glob. glob("*.jpg" or "*.png"):
+	print(filee)
+	#pic(path_to_files,filee)
+	mydoc.add_heading(str(filee[:-4]), 1)
+	mydoc.save(str(output_file) + ".docx")
+	mydoc.add_picture(filee, width=Inches(6.0))#, width=docx.shared.Inches(5), height=docx.shared.Inches(5))
+	mydoc.save(str(output_file) + ".docx")
+
+
+for filee in glob. glob("*.png"):
+	print(filee)
+	#pic(path_to_files,filee)
+	mydoc.add_heading(str(filee[:-4]), 1)
+	mydoc.save(str(output_file) + ".docx")
+	mydoc.add_picture(filee, width=Inches(6.0))#, width=docx.shared.Inches(5), height=docx.shared.Inches(5))
+	mydoc.save(str(output_file) + ".docx")
+# You’re free to specify both width and height, but usually you wouldn’t want to. 
+# If you specify only one, python-docx uses it to calculate the properly scaled value of the other. 
+# This way the aspect ratio is preserved and your picture doesn’t look stretched.

scripts/qc/alpha_second_time_report_generator.py

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+import docx
+from docx.shared import Inches
+import os
+import glob
+from pdf2image import convert_from_path, convert_from_bytes
+from pdf2image.exceptions import (
+    PDFInfoNotInstalledError,
+    PDFPageCountError,
+    PDFSyntaxError
+)
+# Get the current working directory
+cwd = os.getcwd()
+output_file = input("This script assumes that there is already a .docx created \n if this is the first time runing this script please first run the alpha_first_time_report_generator.py \n Enter the name of the already existing output file: ")
+#output_file = "CleftPalete_WGS_GATK-SV"
+# Print the current working directory
+print("Current working directory: {0}".format(cwd))
+
+#path_to_files = r'/Users/szaheri/Documents/SV/GATK-SV/github_ryan_shared/bwa_dragen_sample_level_comparison/results/bwa/perFamily_plots_tarball/bwa_samples_aligning_with_dragen_perFamily_plots/supporting_plots/sv_inheritance_plots/'
+#folder = r'/Users/szaheri/Documents/SV/GATK-SV/github_ryan_shared/bwa_dragen_sample_level_comparison/results/bwa/perFamily_plots_tarball/bwa_samples_aligning_with_dragen_perFamily_plots/supporting_plots/sv_inheritance_plots/'
+
+path_to_files = os.getcwd()+ '/'
+folder = os.getcwd()+ '/'
+head_tail = os.path.split(cwd)
+
+print(head_tail)
+# print tail part of the path
+print(head_tail[1])
+
+files = [folder + fn for fn in os.listdir(folder) if fn.endswith('.pdf')]
+print(files)
+# Convert them.
+def pic(path, name):
+	images = convert_from_path(path + name) #+ '.pdf'
+	for i in range(len(images)):
+		images[i].save(name[:-4] +str(i) +'.jpg', 'JPEG')
+
+
+#pic(path_to_files,'all.pdf')
+
+
+for filee in glob. glob("*.pdf"):
+	#print(filee)
+	pic(path_to_files,filee)
+
+
+
+#mydoc = docx.Document()
+mydoc = docx.Document(str(output_file) + ".docx")
+mydoc.add_paragraph("This is a report of the " + str(head_tail[0]))
+mydoc.save(str(output_file) + ".docx")
+
+
+#mydoc.add_paragraph("This is the second paragraph of a MS Word file.")
+#mydoc.save("my_written_file.docx")
+
+
+files = [folder + fn for fn in os.listdir(folder) if fn.endswith('.pdf')]
+print(files)
+# Convert them.
+#def pic(path, name):
+#	images = convert_from_path(path + name) #+ '.pdf'
+#	for i in range(len(images)):
+#		images[i].save(name +str(i) +'.jpg', 'JPEG')
+
+
+#pic(path_to_files,'all.pdf')
+
+mydoc.add_heading(str(head_tail[1]), 0)
+mydoc.save(str(output_file) + ".docx")
+
+for filee in glob. glob("*.jpg" or "*.png"):
+	print(filee)
+	#pic(path_to_files,filee)
+	mydoc.add_heading(str(filee[:-4]), 1)
+	mydoc.save(str(output_file) + ".docx")
+	mydoc.add_picture(filee, width=Inches(6.0))#, width=docx.shared.Inches(5), height=docx.shared.Inches(5))
+	mydoc.save(str(output_file) + ".docx")
+
+
+for filee in glob. glob("*.png"):
+	print(filee)
+	#pic(path_to_files,filee)
+	mydoc.add_heading(str(filee[:-4]), 1)
+	mydoc.save(str(output_file) + ".docx")
+	mydoc.add_picture(filee, width=Inches(6.0))#, width=docx.shared.Inches(5), height=docx.shared.Inches(5))
+	mydoc.save(str(output_file) + ".docx")
+# You’re free to specify both width and height, but usually you wouldn’t want to. 
+# If you specify only one, python-docx uses it to calculate the properly scaled value of the other. 
+# This way the aspect ratio is preserved and your picture doesn’t look stretched.