Question

我正在尝试创建一个工作流，在该工作流中，我获取一个包含输入文件列表的目录，并通过命令行工具运行它们，并将结果输出到输出目录中。它应该非常简单，而且我已经让它工作了......主要是。

问题在于，无论何时我给它一个输入目录，我都会收到＆＃34;跳过FILE的错误，该文件不存在，或者无法读取＆＃ 34;即使我100％确定文件存在于我的输入目录中。

但是，如果我稍微修改一下代码，然后将其设置为仅输入文件而不是目录，则脚本会像应该的那样运行并完美地完成。

我的输入文件是gzip压缩文件。

这是脚本：

import argparse
import subprocess
import os

parser = argparse.ArgumentParser(description="A RNAseq pipeline for pair-end data")
parser.add_argument("-i", "--inputDir",  help="A input directory containing your gzipped fastq files", required=True)
parser.add_argument("-o", "--outputDir", help="Output directory", required=True)
parser.parse_args()

### Define global variables
args = parser.parse_args()
inputDir = args.inputDir
outputDir = args.outputDir

### Grab all fastq files in input directory
fastq_directory = os.listdir("{}".format(inputDir))
fastq_files = []
for file in fastq_directory:
    fastq_files.append(file)

### Run FastQC
for file in fastq_files:
    fastqc_command = "fastqc --extract -o {} {}".format(outputDir, file)
    subprocess.check_output(['bash', '-c', fastqc_command])

错误：

Skipping 'KO1_R1.fastq.gz' which didn't exist, or couldn't be read
Skipping 'KO1_R2.fastq.gz' which didn't exist, or couldn't be read
Skipping 'KO2_R1.fastq.gz' which didn't exist, or couldn't be read
Skipping 'KO2_R2.fastq.gz' which didn't exist, or couldn't be read
Skipping 'KO3_R1.fastq.gz' which didn't exist, or couldn't be read
Skipping 'KO3_R2.fastq.gz' which didn't exist, or couldn't be read
Skipping 'WT1_R1.fastq.gz' which didn't exist, or couldn't be read
Skipping 'WT1_R2.fastq.gz' which didn't exist, or couldn't be read
Skipping 'WT2_R1.fastq.gz' which didn't exist, or couldn't be read
Skipping 'WT2_R2.fastq.gz' which didn't exist, or couldn't be read
Skipping 'WT3_R1.fastq.gz' which didn't exist, or couldn't be read
Skipping 'WT3_R2.fastq.gz' which didn't exist, or couldn't be read

有什么建议吗？

PS：我知道剧本很糟糕，但我正在学习:)。虽然建议肯定受到欢迎！

Answer 1

尝试更改此内容：

fastq_directory = os.listdir("{}".format(inputDir))
fastq_files = []
for file in fastq_directory:
        fastq_files.append(file)

对此：

fastq_directory = os.listdir("{}".format(inputDir))
fastq_files = []
for file in fastq_directory:
        fastq_files.append(os.path.join(inputDir, file))

这是因为os.listdir()只返回文件名，而不是完整路径。

跳过＆＃39;文件＆＃39;哪个不存在，或者无法读取错误

1 个答案: