TEtoolkit

[DanielaMombach]

Hi, I am trying to run TEtranscripts and got this error in return. Have you seen this before?

File "/mnt/d/TEtranscripts-2.2.3/bin/TEtranscripts", line 32, in <module>
    from TEToolkit.IO.ReadInputs import read_opts2
ImportError: No module named TEToolkit.IO.ReadInputs

Thank you in advance, Daniela

[olivertam]

Hi Daniela,

How did you install TEtranscripts? And what is your command line?

Thanks.

[DanielaMombach]

Yes, I installed v 2.2.3. My command line is: /mnt/d/TEtranscripts-2.2.3/bin/TEtranscripts --format BAM --mode multi -t /mnt/d/srr_cispla/bam/SRR14310043.fastq_Aligned.out.bam /mnt/d/srr_cispla/bam/SRR14310044.fastq_Aligned.out.bam /mnt/d/srr_cispla/bam/SRR14310045.fastq_Aligned.out.bam -c /mnt/d/srr_cispla/bam/SRR14310037.fastq_Aligned.out.bam /mnt/d/srr_cispla/bam/SRR14310038.fastq_Aligned.out.bam /mnt/d/srr_cispla/bam/SRR14310039.fastq_Aligned.out.bam

[DanielaMombach]

From this website https://pypi.org/project/TEtranscripts/#files.

[DanielaMombach]

I think I was able to fix it, thank you for your fast response!

[olivertam]

No problem. Let me know if you encounter more issues.

[olivertam]

No worries. Might I suggest the following if you haven't already done this:

$ export PYTHONPATH="/mnt/d/lib/python3.8/site-packages/:$PYTHONPATH"

This will point python to the location of the TEtranscripts installation. You could either put it in your .bashrc (or .zshrc depending on your shell) to have it activated by default, or just run that command before you use TEtranscripts.

Let me know if you still have issues.

Thanks.