How to run prepDE.py3?
1
0
Entering edit mode
14 months ago
SH • 0

Hello,

  • I ran stringtie and obtained merge.gtf as a result. Now, I want to run prepDE.py3 to obtain gene.csv and transcript.csv. I thought prepDE.py3 was a function that was embedded together with stringtie when I installed it.
  • However, when I type "./prepDE.py3" or "prepDE.py3" in the Ubuntu terminal, it shows an error message "command not found".
  • Currently, "sudo apt-get install python3-pip" has been completed. After that, I tried "sudo pip3 install prepDE.py3", but it shows an error message "ERROR: Could not find a version that satisfies the requirement prepDE.py3 (from versions: none) ERROR: No matching distribution found for prepDE.py3".
  • So, I downloaded prepDE.py3 in the working folder by executing "wget https://github.com/gpertea/stringtie/raw/master/prepDE.py3". In conclusion, I want to run prepDE.py3 in the Ubuntu terminal. How can I do it?

Thank you in advance for your help.

prepDE.py3 stringtie • 1.6k views
ADD COMMENT
0
Entering edit mode
14 months ago
Barry Digby ★ 1.3k

The shebang in prepDE.py3 looks for the first version of python3 installed in your path (#!/usr/bin/env python3) so if you have python3, just type python prepDE.py3 :)

If your base python is 2.7 install python3.* in an environment using conda

ADD COMMENT

Login before adding your answer.

Traffic: 1492 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6