[SOLVED] iterate through files in python script and execute bash command

iterate through files in python script and execute bash command

I am trying to write a python script that loops through SAM files in a directory and uses samtools view to convert those SAM files to BAM files. Here's what I have, but am struggling with how to input the SAM file (i) into the bash command in the last line.

import os
import glob
for i in glob.iglob('/file/path/to/files/*.sam'):
      os.system("samtools view -S -b %i > %i.bam" %i)

Thank you for your help!

Solution

You might be best using classic string concatenation techniques to achieve this. You can basically just add the result into the os.system call.

You could rewrite it to something like:

import os
import glob

for file in glob.iglob('/file/path/to/files/*.sam');
    command = "samtools view -S -b " + str(file) + " > " + str(file) + ".bam"
    os.system(command)

You could even use the format option instead:

command = "samtools view -S -b {} > {}.bam".format(file, file)

The python documentation does a good job about explaining how you can do these sorts of operations.