ModuleNotFoundError: No module named 'tabix'

[CeballosGene]

I have a problem running your script! I used the following line:
python bin/PGxPOP.py --vcf ./prueba/C11_v1.vcf.gz.tbi --phased --g CYP2D6 --build hg19 -o ./prueba/

And I have the following lines:

Traceback (most recent call last):
  File "/home/rembukai/BIOSOFT/PGxPOP/bin/PGxPOP.py", line 16, in <module>
    import Gene
  File "/home/rembukai/BIOSOFT/PGxPOP/bin/Gene.py", line 8, in <module>
    from Variant import Variant
  File "/home/rembukai/BIOSOFT/PGxPOP/bin/Variant.py", line 2, in <module>
    from DawgToys import clean_chr, iupac_nt
  File "/home/rembukai/BIOSOFT/PGxPOP/bin/DawgToys.py", line 2, in <module>
    import tabix
ModuleNotFoundError: No module named 'tabix'

I have installed tabix along with python in:
/home/rembukai/.local/lib/python3.8/site-packages (0.1)
How can I tell PGxPOP where to find tabix?

Thank you very much

[cariaso]

pip install pytabix will probably solve your problem

…

On Thu, Jan 27, 2022 at 10:19 AM CeballosGene ***@***.***> wrote: I have a problem running your script! I used the following line: python bin/PGxPOP.py --vcf ./prueba/C11_v1.vcf.gz.tbi --phased --gene CYP2D6 --build hg19 -o ./prueba/ And I have the following lines: Traceback (most recent call last): File "/home/rembukai/BIOSOFT/PGxPOP/bin/PGxPOP.py", line 16, in <module> import Gene File "/home/rembukai/BIOSOFT/PGxPOP/bin/Gene.py", line 8, in <module> from Variant import Variant File "/home/rembukai/BIOSOFT/PGxPOP/bin/Variant.py", line 2, in <module> from DawgToys import clean_chr, iupac_nt File "/home/rembukai/BIOSOFT/PGxPOP/bin/DawgToys.py", line 2, in <module> import tabix ModuleNotFoundError: No module named 'tabix' I have installed tabix along with python in: /home/rembukai/.local/lib/python3.8/site-packages (0.1) How can I tell PGxPOP where to find tabix? Thank you very much — Reply to this email directly, view it on GitHub <#9>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAA6TEUCAWF3FEQDVT5PMTDUYFPBNANCNFSM5M6HAXQA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Mike Cariaso http://www.cariaso.com

[CeballosGene]

Thank you very much. I already haver done that and I got:

Requirement already satisfied: pytabix in /home/rembukai/.local/lib/python3.8/site-packages (0.1)

[CeballosGene]

I'm sorry to keep bothering you. But I cant make PGxPP work and it is really important for me to use it.
I unistalled PGxPOP and installed it again.
When I run the line
pip install -r requirements.txt
I obtained the following text:

Requirement already satisfied: numpy==1.15.2 in /home/rembukai/.local/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (1.15.2)
Requirement already satisfied: pyliftover==0.4 in /home/rembukai/.local/lib/python3.8/site-packages (from -r requirements.txt (line 2)) (0.4)
Requirement already satisfied: pytabix==0.1 in /home/rembukai/.local/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (0.1)

Then I run the line to complete the process:
python ./bin/PGxPOP.py --vcf ./pruebas/C11_v1.vcf.gz.tbi --phased --g CYP2D6 --build hg19 -o ./pruebas/

However I obtained this error message:

  File "/home/rembukai/BIOSOFT/PGxPOP/bin/PGxPOP.py", line 11, in <module>
    import numpy as np
ModuleNotFoundError: No module named 'numpy'

First it was the module tabix and now is the module numpy. Please, could you help me to solve this issue. For the last 3 days I have been trying everything without success.