解析vcfs格式的txt文件

Question

我想用数据框中的以下字段将信息从txt文件提取到dataframe

1) GENEINFO
2) ID
3) POS
4) ALT
5) CLNSIG
6) CLNDN 

The txt file is here

我编写了以下代码，试图从文件中获取信息，但不知道如何继续。你能帮我介绍一些做那件事的想法吗

import io
import os
import pandas as pd


def read_vcf(path):
    with open('clinvar_final.txt', 'r') as f:
        lines = [l for l in f if not l.startswith('##')]
    return pd.read_csv(
        io.StringIO(''.join(lines)),
        dtype={'#CHROM': str, 'POS': int, 'ID': str, 'REF': str, 'ALT': str,
               'QUAL': str, 'FILTER': str, 'INFO': str},
        sep='\t'
    ).rename(columns={'#CHROM': 'CHROM'})

Answer 1

你可以阅读它

df = pd.read_csv('clinvar_final.txt', comment='#', sep='\t')

在这之后，您将有一个tabel，其中包含列2）ID3）POS4）ALT

print(df[['ID', 'POS', 'ALT']].head())

给予

       ID      POS ALT
0  475283  1014O42   A
1  542074  1O14122   T
2  183381  1014143   T
3  542075  1014179   T
4  475278  1014217   T

其他信息（1）GENEINFO5）CLNSIG6）CLNDN）作为一个字符串在列INFO中，您可以使用regex将它们添加到分隔的列中

df['GENEINFO'] = df['INFO'].str.extract('GENEINFO=([^;]*)')
df['CLNSIG'] = df['INFO'].str.extract('CLNSIG=([^;]*)')
df['CLNDN'] = df['INFO'].str.extract('CLNDN=([^;]*)')

print(df['GENEINFO'].head())
print(df['CLNSIG'].head())
print(df['CLNDN'].head())

结果

0    ISG15:9636
1    ISG15:9636
2    ISG15:9636
3    ISG15:9636
4    ISG15:9636
Name: GENEINFO, dtype: object

0                    Benign
1    Uncertain_significance
2                Pathogenic
3    Uncertain_significance
4                    Benign
Name: CLNSIG, dtype: object

0    Immunodeficiency_38_with_basal_ganglia_calcifi...
1    Immunodeficiency_38_with_basal_ganglia_calcifi...
2    Immunodeficiency_38_with_basal_ganglia_calcifi...
3    Immunodeficiency_38_with_basal_ganglia_calcifi...
4    Immunodeficiency_38_with_basal_ganglia_calcifi...
Name: CLNDN, dtype: object

---

import pandas as pd

df = pd.read_csv('clinvar_final.txt', comment='#', sep='\t')

print(df.columns)

print(df[['ID', 'POS', 'ALT']].head())

df['GENEINFO'] = df['INFO'].str.extract('GENEINFO=([^;]*)')
df['CLNSIG'] = df['INFO'].str.extract('CLNSIG=([^;]*)')
df['CLNDN'] = df['INFO'].str.extract('CLNDN=([^;]*)')

print(df['GENEINFO'].head())
print(df['CLNSIG'].head())
print(df['CLNDN'].head())