59 lines
2.0 KiB
Python
59 lines
2.0 KiB
Python
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#!/usr/bin/env python3
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# -*- coding: UTF-8 -*-
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##https://blog.csdn.net/fanlei_lianjia/article/details/78225857
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import os
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import sys
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from openpyxl import Workbook,load_workbook
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from openpyxl.drawing.image import Image
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if len(sys.argv) != 3:
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print(" ".join(['usage:python',sys.argv[0],'output_dir','tumor']))
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sys.exit()
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output_dir=sys.argv[1]
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tumor=sys.argv[2]
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outputfile=''.join([output_dir,'/report/',tumor,'.report.check.xlsx'])
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wb=Workbook()
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def write_excel(txt_name,sheet):
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f1=open(txt_name,'r',encoding='utf-8')
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lines=f1.readlines()
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for line in lines:
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split_line=line.split('\t')
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sheet.append(split_line)
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wb.save(outputfile)
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inputs={'qc_fail':''.join([output_dir,'/report/','qc_fail.txt']),
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'somatic_filter':''.join([output_dir,'/report/',tumor,'.snp.indel.Somatic.annoall.hg19_multianno_filtered.txt']),
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'hotspot':''.join([output_dir,'/report/',tumor,'.hotspot.snp.indel.filter.anno.hg19_multianno.txt']),
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'germline_filter':''.join([output_dir,'/report/',tumor,'.snp.indel.Germline.anno.hg19_multianno_filtered.txt']),
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'promoter':''.join([output_dir,'/report/',tumor,'.target.promoter.txt']),
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'splicing':''.join([output_dir,'/report/',tumor,'.target.splicing.txt']),
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'fusion':''.join([output_dir,'/report/',tumor,'.fusion.reanno.vcf']),
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'cnv':''.join([output_dir,'/report/',tumor,'.rmdup.cns.cn']),
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'HRR':''.join([output_dir,'/report/',tumor,'.hrr.pre.txt']),
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'HRR':''.join([output_dir,'/report/',tumor,'.hrr.pre.txt']),
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'TMB':''.join([output_dir,'/report/',tumor,'.tmb.txt']),
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'MMR':''.join([output_dir,'/report/',tumor,'.mmr.pre.txt']),
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'immune_predict':''.join([output_dir,'/report/',tumor,'.hpd.pre.txt']),
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'hereditary_cancer_syndrome':''.join([output_dir,'/hereditary/',tumor,'.hereditary.pre.txt'])
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}
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for key,value in inputs.items():
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sheet=wb.create_sheet(key)
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write_excel(value,sheet)
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ws=wb['cnv']
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mr=ws.max_row
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cell='C'+str(mr+4)
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cnv_pic_path=''.join([output_dir,'/report/',tumor,'.cnv.png'])
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image=Image(cnv_pic_path)
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ws.add_image(image,cell)
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wb.save(outputfile)
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del wb['Sheet']
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wb.save(outputfile)
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