Using the ! magic I can access env type environment variables, but not ones defined in my terminal, or .bashrc.
$://balter/chip-seq-analysis/chipseq$ echo $hg38
//genomes/hg38/release-85/Homo_sapiens.GRCh38.dna.primary_assembly.fa
[email protected]://balter/chip-seq-analysis/chipseq$ ipython
Python 2.7.12 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:42:40)
Type "copyright", "credits" or "license" for more information.
IPython 5.1.0 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.
In [1]: !echo $hg38
In [2]: !echo $SHELL
/usr/bin/bash
In [3]:
解决方案
if your variables are not exported, no subprocess can access them, python or not.
foo=value
is only seen by the current process (here: bash)
but if you do (in your .bashrc):
export foo
or set & export:
export foo=value
then the variable becomes visible by subprocesses. That's your fix.
BTW, to get an env. variable in python, the real python way is:
import os
print(os.getenv("foo"))