abalter abalter - 18 days ago 9
Bash Question

How to access shell variable in ipython

Using the

!
magic I can access
env
type environment variables, but not ones defined in my terminal, or
.bashrc
.

$:/<path>/balter/chip-seq-analysis/chipseq$ echo $hg38
/<path>/genomes/hg38/release-85/Homo_sapiens.GRCh38.dna.primary_assembly.fa
balter@exalab3:/<path>/balter/chip-seq-analysis/chipseq$ 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]:

Answer

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"))