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snpeff_ann_somatic_vcf41_to_xlsx.py
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snpeff_ann_somatic_vcf41_to_xlsx.py
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#!/usr/bin/python3
import os,sys,re
from openpyxl import Workbook
from openpyxl import load_workbook
from openpyxl.styles import PatternFill,Font, Color,Fill
input_vcf_filename = str(sys.argv[1]).split('.')[0]
font = Font(name = 'Arial',size=10,bold=True,italic=False,vertAlign=None,underline='none',strike=False,color='FF000000')
xlsx_wb = Workbook()
xlsx_wb_filename = input_vcf_filename + '.' + 'xlsx'
xlsx_wb.active.title = input_vcf_filename[:30]
xlsx_wb_sheet = xlsx_wb.active
xlsx_wb_sheet.sheet_properties.tabColor = "FF9966"
greenFill = PatternFill(start_color='CCFF99',
end_color='CCFF99',
fill_type='solid')
for i in range(1,13):
xlsx_wb_sheet.cell(row = 1, column = i).fill = greenFill
xlsx_wb_sheet.cell(row = 1, column = i).font = font
xlsx_wb_sheet.cell(row = 1, column = 1).value = "Chrom"
xlsx_wb_sheet.cell(row = 1, column = 2).value = "Pos"
xlsx_wb_sheet.cell(row = 1, column = 3).value = "Ref_Allele"
xlsx_wb_sheet.cell(row = 1, column = 4).value = "Alt_Allele"
xlsx_wb_sheet.cell(row = 1, column = 5).value = "Somatic Genotype"
xlsx_wb_sheet.cell(row = 1, column = 6).value = "Somatic Variant Quality"
xlsx_wb_sheet.cell(row = 1, column = 7).value = "Gene"
xlsx_wb_sheet.cell(row = 1, column = 8).value = "HGVS(DNA level)"
xlsx_wb_sheet.cell(row = 1, column = 9).value = "HGVS(Protein level)"
xlsx_wb_sheet.cell(row = 1, column = 10).value = "Variant Annotation"
xlsx_wb_sheet.cell(row = 1, column = 11).value = "Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO"
xlsx_wb_sheet.cell(row = 1, column = 12).value = "COSMICv78"
#冻结首行，设置列宽
xlsx_wb_sheet.freeze_panes = 'A2'
for j in ['A','B','C','D','E','F','G','H','I','J','K','L']:
xlsx_wb_sheet.column_dimensions[j].width = 15
with open(sys.argv[1],'r') as input_vcf:
rowNum = 2
for line in input_vcf:
if line.startswith("#"):
pass
else:
CHROM,POS,ID,REF,ALT,QUAL,FILTER,INFO,FORMAT,NORMAL,TUMOR = line.strip().split("\t")
INFO = INFO.split(';')
QSS = ''
SGT = ''
snpeff_INFO = ''
Gene = ''
Variant_region = ''
HGVS_c = ''
HGVS_p = ''
for item in INFO:
if item.startswith('QSS='):
QSS = item.split('=')[-1]
elif item.startswith('SGT='):
SGT = item.split('=')[-1]
elif item.startswith('ANN='):
snpeff_INFO = item
Gene = item.split('|')[3]
HGVS_c = item.split('|')[9]
HGVS_p = item.split('|')[10]
elif item.startswith('LOF='):
Gene = item.split('|')[1]
elif item.startswith('NMD='):
Gene = item.split('|')[1]
if snpeff_INFO:
Variant_region = snpeff_INFO.split('|')[1]
#for item in snpeff_INFO.split(','):
# Gene = Gene + item.split('|')[3]
# Variant_region = Variant_region + item.split('|')[1]
xlsx_wb_sheet.cell(row = rowNum, column = 1).value = CHROM
xlsx_wb_sheet.cell(row = rowNum, column = 2).value = POS
xlsx_wb_sheet.cell(row = rowNum, column = 3).value = REF
xlsx_wb_sheet.cell(row = rowNum, column = 4).value = ALT
xlsx_wb_sheet.cell(row = rowNum, column = 5).value = SGT
xlsx_wb_sheet.cell(row = rowNum, column = 6).value = QSS
xlsx_wb_sheet.cell(row = rowNum, column = 7).value = Gene
xlsx_wb_sheet.cell(row = rowNum, column = 8).value = HGVS_c
xlsx_wb_sheet.cell(row = rowNum, column = 9).value = HGVS_p
xlsx_wb_sheet.cell(row = rowNum, column = 10).value = Variant_region
xlsx_wb_sheet.cell(row = rowNum, column = 11).value = snpeff_INFO
xlsx_wb_sheet.cell(row = rowNum, column = 12).value = ID
rowNum += 1
xlsx_wb.save(xlsx_wb_filename)