bowtie2, and python script

Question

[qudrat.nii]

Hello, Everytime I run my script it shows "bad file descriptor" in terminal. Following is my script. Please help

import os
import subprocess
import shlex
fastq1 = []
fastq2 = []
path = os.listdir('kud')
for files in path:
    if '_1' in files:
        fastq1.append(files)
    if '_2' in files:
        fastq2.append(files)
for i,j in zip(fastq1,fastq2):
    command = "bowtie2 -x bt2_base -1 i -2 j -S z.sam"
    cmd = shlex.split(command)
    subprocess.run(cmd,shell=False,stdout=subprocess.PIPE,stderr=subprocess.PIPE,universal_newlines=True)

Answer 1

[Asaf]

Just a guess - the file names you are passing don't have the directory name ('kud') but I don't know.

Anyhow, I would highly suggest to avoid running such scripts and using proper workflow managing software such as nextflow, snakemake or other. 99% chance that what you are trying to run was already implemented in nf-core and you just need to run the pipeline.

Answer 2

[barslmn]

This is still related to your old thread. bowtie2, and python script. Why start a new one?

You're trying to use variables inside a string.

x = 5
s = "x"
print(s)

This will just print string x and not the int 5. In your example you're setting command string with literal characters i and j and not with their values. Instead, you just do some string formatting.

# here are some examples.
x = 5
y = 6
s = f"x is {x} y is {y}"

You can read more about string formatting in python docs.

[qudrat.nii]

Even after string formating, i.e f"(-1 {i} -2 {j})" it is showing problem of "bowtie2-align exited with value 2\n')"

[barslmn]

Why do you have parenthesis? Shouldn't look like this?

f"-1 {i} -2 {j}"