Having trouble running Desktop version of Pse-in-One

Question

[Jimmy]

I am trying to work with the desktop version of Pse-in-One which can be downloaded from:

http://bliulab.net/Pse-in-One/download/

I am operating using Zsh. I am downloading the program, unzipping it, and then navigating into the directory Downloads/Pse-in-One-1.0.6/Pse-in-One .

Following the Manual http://bliulab.net/Pse-in-One/static/download/Pse-in-One_manual.pdf , I am using a Python 2.7 environment, using pyenv:

pyenv install 2.7
pyenv local 2.7

And I am now trying to run the Example given from the manual. Example 1 is:

kmer.py test.txt output_kmer.txt DNA -k 2 -f svm

This is where the issues begin. Running this by itself doesnt work, and Zsh tells me that the command kmer.py is not found. Of course I assume the issue is that the example doesnt include that you should use the 'python' to execute the kmer.py file, so I modify the command to this:

python kmer.py test.txt output_kmer.txt DNA -k 2 -f svm

But when this is run, all I get is the error: "RuntimeError: Bad magic number in .pyc file"

I get similar issues when I try the other examples listed in the manual ( fyi: the manual sometimes has an en dash – instead of a hypen for flags so be careful when copy/pasting )

I appreciate any assistance in resolving this. I know that there is a web server version of this, but I need to be able to operate this program locally.

Answer 1

[Mensur Dlakic]

Have you tried Googling the last error?

https://www.google.com/search?q=RuntimeError%3A+Bad+magic+number+in+.pyc+file

As it will say in the explanation, this error is triggered by using a wrong version of python. I suggest you type python2 instead, or be sure that you are using the required python version.

[Jimmy]

That was a surprisingly easy fix. Thank you. This command ended up working:

python2 kmer.py example/test.txt output_kmer.txt DNA -k 2 -f svm