解决问题：BadGzipFile: Not a gzipped file (b‘ve‘)

相关资料

论文：Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas
代码：https://github.com/greenelab/pancancer
参考：https://cloud.tencent.com/developer/article/1729308

问题描述

在运行下面一段代码时
语句：rnaseq_full_df = pd.read_table(‘data/pancan_rnaseq_freeze.tsv.gz’, index_col=0)
报错：BadGzipFile: Not a gzipped file (b’ve’)

import os
import math
import torch  # pythorch 模块
import itertools
import warnings

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt

from torch import nn

T = True
F = False
%matplotlib inline
%config InlineBackend.figure_format = 'svg'

warnings.filterwarnings("ignore")
plt.rc('font', family='Times New Roman')
plt.rcParams['figure.figsize'] = (4, 3)
my_colors = ["#1EB2A6", "#ffc4a3", "#e2979c", "#F67575"]

# 数据导入
rnaseq_full_df = pd.read_table('data/pancan_rnaseq_freeze.tsv.gz', index_col=0)
mutation_df = pd.read_table('data/pancan_mutation_freeze.tsv.gz', index_col=0)
sample_freeze = pd.read_table('data/sample_freeze.tsv', index_col=0)
mut_burden = pd.read_table('data/mutation_burden_freeze.tsv')

解决方法

更改.tsv.gz文件的扩展名为.tsv，对应修改程序文件名即可。

# 数据导入
rnaseq_full_df = pd.read_table('data/pancan_rnaseq_freeze.tsv', index_col=0)
mutation_df = pd.read_table('data/pancan_mutation_freeze.tsv', index_col=0)