如何通过 python 调用/运行软件？

Question

I'm trying to make a simple script to run different tasks one by one (one after another) but I don't know how can I run the program by python script. I know that it should be simple: but I couldn't find it any where. my example is this:

samtools merge filename.bam file1.sorted.bam file2.sorted.bam file3.sorted.bam file4.sorted.bam

samtools index filename.bam 
samtools idxstats filename.bam > filename.txt 
samtools pileup -vcf path/filename.fa filename_sorted.bam

I want the python to run the first command and after its finished then goes to the next one! it's important that it wait's until it's finished!

Answer 1

from subprocess import call # call runs an external program and waits for it to quit

for command in ("samtools merge filename.bam file1.sorted.bam file2.sorted.bam file3.sorted.bam file4.sorted.bam", 
                "samtools index filename.bam", 
                "samtools idxstats filename.bam > filename.txt", 
                "samtools pileup -vcf path/filename.fa filename_sorted.bam"):
    # shell=True is so you can handle redirects like in the 3rd command
    call(command, shell=True) 

Answer 2

Use the subprocess module . There are lots of examples at the bottom of the page.