97 lines
3.3 KiB
Python
Executable File
97 lines
3.3 KiB
Python
Executable File
#!/usr/bin/env python3
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#-*-coding:utf-8-*-
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import sys
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import json
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import pandas as pd
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def read_position_file(positions_filename):
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# 读取 csv 文件中的位点信息
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positions = []
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df = pd.read_csv(positions_filename, sep='\t')
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for p in df['end']:
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positions.append(int(p))
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return positions
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def process_positions(sample_vcf, positions):
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# 统计样本杂合率
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result_dict = {}
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# 读取VCF文件为DataFrame,624会出现nan值
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df = pd.read_csv(sample_vcf, sep='\t', comment='#', header=None, names=range(11))
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for j in positions:
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result_dict[j] = {'count': 0, 'sum': 0}
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# 筛选出符合条件的行
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filtered_df = df[(df[0] == "chrX") & (df[1] == j)]
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# 处理每行数据，处理624的nan
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for index, row in filtered_df.iterrows():
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if pd.isna(row[10]):
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genotype_str = row[9].split(":")[4]
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else:
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genotype_str = row[9].split(":")[5]
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if genotype_str.endswith('%'):
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genotype = float(genotype_str[:-1]) / 100 # 将百分数转换为小数
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else:
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genotype = float(genotype_str)
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result_dict[j]['sum'] += genotype
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if genotype <= 0.9 and genotype >= 0.1:
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result_dict[j]['count'] += 1
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return result_dict
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def write_output(result_dict):
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# 计算平均杂合率
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sum_i = 0
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count_i = 0
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average_i = 0
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for key, value in result_dict.items():
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sum_i += value['count']
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count_i += 1
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average_i = sum_i / count_i if count_i > 0 else 0
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return average_i
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def sex_detect_probe(average_i):
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# 判断性别
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if average_i == 0.0:
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sample_sex_probe = "男"
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else:
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sample_sex_probe = "女"
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return sample_sex_probe
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def sex_detect_lims(filename):
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# 从 JSON 文件中读取 LIMS 中的性别信息
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with open(filename, 'r', encoding= "utf-8") as json_file:
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config_data = json.load(json_file)
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sample_sex_lims = config_data["data"][0]["gender"]
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return sample_sex_lims
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def sex_detect(sample_sex_probe, sample_sex_lims):
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# 比较样本推断的性别和 LIMS 中的性别
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if sample_sex_probe == sample_sex_lims:
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return "性别一致"
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else:
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v1 = f"性别不一致(计算结果:{sample_sex_probe}"
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v2 = f"lims:{sample_sex_lims})"
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return v1+","+v2
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def main(out_dir, sample_name):
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sample_vcf = out_dir + "/mutation/" + sample_name + ".snp.indel.Germline.anno.hg19_multianno.vcf"
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position_file = "/dataseq/jmdna/codes/public/gender.bed"
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positions = read_position_file(position_file)
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result_dict = process_positions(sample_vcf, positions)
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average_i = write_output(result_dict)
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sample_sex_probe = sex_detect_probe(average_i)
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post_json_file = out_dir + "/qc/" + sample_name + "_post.json"
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sample_sex_lims = sex_detect_lims(post_json_file)
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result_data = sex_detect(sample_sex_probe, sample_sex_lims)
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return result_data
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if __name__ == "__main__":
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if len(sys.argv) < 2:
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print("usage: python3 sex_detect.py out_dir sample_name")
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sys.exit()
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out_dir = sys.argv[1]
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sample_name = sys.argv[2]
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main(out_dir,sample_name)
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