在python中，使用os.system调用模块，然后基于该模块调用python模块

Question

I am currently writing a python script.

The ultimate goal here is just to import pysam. But, to do this, first I import a suite of tools known as galaxy, of which pysam is one.

If on the command line I first load galaxy, then enter the python interactive shell, then import pysam, the import is successful.

But, my script is like so:

#!/usr/bin/env python

import subprocess

subprocess.call("module load galaxy/galaxy", shell=True)
subprocess.call("module load ngs-ccts/tabix/0.2.6", shell=True)
import pysam

caddfile=pysam.Tabixfile( "/scratch/share/public_datasets/ngs/databases/CADD/v1.0/whole_genome_SNVs_inclAnno.tsv.gz" )
for gtf in caddfile.fetch(1, 100000, 200000):
    print(gtf)

to me, this seems to recapitulate what I do in the interactive shell, which works.

The script, however, errors and returns:

Traceback (most recent call last):
  File "pysampracticer.py", line 7, in ?
    import pysam
ImportError: No module named pysam

why is it that the script fails to import it while the same series of commands will work on the command line then the python interactive shell, and how should I approach this to recapitulate the results obtained on the interactive shell?

Answer 1

subprocess.call("module load galaxy/galaxy", shell=True)
subprocess.call("module load ngs-ccts/tabix/0.2.6", shell=True)

Loads the modules in sub-processes. It doesn't affect the current process.

Not only that, the two calls create two independent sub-processes. In the first sub-process, the galaxy/galaxy module is loaded but not the ngs-ccts/tabix/0.2.6 modue. In the second sub-process, the ngs-ccts/tabix/0.2.6 is loaded but not the galaxy/galaxy module.