I got some diffculties when run rMATs

Question

[younglin113]

I had tried to analyze the mRNA alternative splicing situation with a reported tool, named rMATs. But I was stuck when I try to test this tool following its tutorial which is posted in http://rnaseq-mats.sourceforge.net/user_guide.htm,and the test line is :

/software/biosoft/software/python2.7.2/bin/python2.7 rMATS-turbo-Linux-UCS2/rmats.py --b1 b1.txt --b2 b2.txt --gtf gtf/Homo_sapiens.Ensembl.GRCh37.72.gtf --od bam_test -t paired --readLength 101 --cstat 0.0001 --libType fr-unstranded

but quickly I got this error :

Traceback (most recent call last):
File "rMATS-turbo-Linux-UCS2/rmats.py", line 17, in <module>
from rmatspipeline import run_pipe
ImportError: libpython2.7.so.1.0: cannot open shared object file: No such file or directory

I really don't know how to fix this. I will be deeply appreciate it if you can give me some advice. Thanks!!!

[younglin113]

I am really thankful for your answers. I actually searched the web for solutions, but I sort of am not in the sudoers files. So I can't install libpython2.7 myself. Maybe I should contact the administrator to solve this. Thanks anyway, Kevin!

[Kevin Blighe]

Yes, they should be able to install it. Good luck!

Answer 1

[Kevin Blighe]

If you search for "ImportError: libpython2.7.so.1.0: cannot open shared object file: No such file or directory" in a search engine, you will see many solutions posted on other forums. Please try one to see if it helps.

Either the library is not installed or your Python path variable is not set properly such that this library would be included. To see if it is even installed, type: locate libpython2.7.so.1.0.

If it's not even installed, then you can install with (On Ubuntu):

sudo apt-get install libpython2.7
sudo apt-get install libatlas3-base

If it's installed, you'll see the directory in which it's located. You can then add this to your LD_LIBRARY_PATH variable. Note that you can also add the directory of libraries in the script run-time with, for example (as I do here: A: How to download all sequences of a list of proteins for a particular organism ):

import sys
sys.path.append('/usr/local/lib/python2.7/dist-packages/')

Thanks,

Kevin