Unable to used TTT

[Rishikeshklaxmi]

Hey Macher

I am not able to use the TTT. I have python version 3.9 in my Mac. I have prepare the Table Taxon file as suggested but this is showing error in the TTT. Could you please help me in the same.

Regards Rishikesh

[Rishikeshklaxmi]

[Rishikeshklaxmi]

[onurdogan]

Hi Rishikeshklaxmi and Till, I may be able to assist you, as I have several gold medals in the program crash category across multiple sections. Could you please provide the latest message that appears in the terminal after clicking the Exit button in the Error window? best, Onur.

[Rishikeshklaxmi]

Hey Dogan

Thank you for your swift response. Yesterday I uninstalled python3.9 from my mac. I created an environment in Anaconda for python3.8 (See screenshot in attachment). Then I tried to install taxontabletools but it showed "ERROR: Failed building wheel for scikit-bio" in installation.(screenshot attached).

I am also attaching some of my data as Taxontable, please look into it. Is it fine for the use?

Thanks and regards

Rishikesh

On Tue, Oct 10, 2023 at 5:57 PM Onur Doğan @.***> wrote:

Hi Rishikeshklaxmi and Till, I may be able to assist you, as I have several gold medals in the program crash category across multiple sections. Could you please provide the latest message that appears in the terminal after clicking the Exit button in the Error window? best, Onur.

— Reply to this email directly, view it on GitHub https://github.com/TillMacher/TaxonTableTools/issues/9#issuecomment-1755280634, or unsubscribe https://github.com/notifications/unsubscribe-auth/BB7ZP4DBOLVKDHDJI6C35V3X6U5KZAVCNFSM6AAAAAA5YOH6NSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJVGI4DANRTGQ . You are receiving this because you authored the thread.Message ID: @.***>

[onurdogan]

Hi again,

I have not seen any screenshots and/or related data in the attachment, but have you ever tried this code to execute the installation: conda install -c conda-forge scikit-bio.

And, I would also check if my OTUs are the same (or sorting OTU_1, OTU _2, OTU_3 or number in total) in both Read and Taxonomy files; sometimes, one can be >OTU_1 (with greater than sign) and the other is OTU_1.

Onur

[Rishikeshklaxmi]

Hey In the previous message i have attached in your mail. I am attaching them here now. Also when i run "conda install -c conda-forge scikit-bio." code again an error occured please have a look.

1.arthropoda_data.xlsx

[onurdogan]

Heya,

Here is some information about my Python version, scikit-bio, and the PATH.

Additionally, after a quick glance through the TaXon table provided and comparing it with mine, I noticed that my TaXon table's header begins with:

• ID instead of IDs
• and my OTUs (or ESVs) are sorting like OTU_1, OTU_2, ... OTU_1652 instead of OTU1, OTU2, ... OTU1652.

Python version:

Python 3.9.10 

scikit-bio:

Name: scikit-bio
Version: 0.5.6
Summary: Data structures, algorithms and educational resources for bioinformatics.
Home-page: http://scikit-bio.org
Author: scikit-bio development team
Author-email: gregcaporaso@gmail.com
License: BSD-3-Clause
Location: /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages
Requires: CacheControl, decorator, hdmedians, IPython, lockfile, matplotlib, natsort, numpy, pandas, scikit-learn, scipy
Required-by: taxontabletools

PATH:

echo $PATH | tr ":" "\n" 

/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/bin
/usr/local/bin/ncbi-blast-2.13.0+/bin
/usr/local/bin
/Library/Frameworks/Python.framework/Versions/3.9/bin
/Library/Frameworks/Python.framework/Versions/3.11/bin
/Library/Frameworks/Python.framework/Versions/3.10/bin
/usr/bin/phyton
/usr/local/bin
/usr/local/sbin
/usr/local/bin
/Library/Frameworks/Python.framework/Versions/3.9/bin
/Library/Frameworks/Python.framework/Versions/3.11/bin
/Library/Frameworks/Python.framework/Versions/3.10/bin
/usr/local/bin
/System/Cryptexes/App/usr/bin
/usr/bin
/bin
/usr/sbin
/sbin
/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin
/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin
/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin
/opt/X11/bin

enjoy, Onur.

[Rishikeshklaxmi]

Dear Onur Thank you for sharing the details. I have installed python version 3.9.10. But i think the issue is with the installation of scikit-bio. when is tried to solve this issue as mentioned in the issue 4 a wall of error comes (attached). I tried my best to solve this but the problem not resolved. "Install brew on your Mac (https://brew.sh/) Install gcc using brew $ brew install gcc Install openssl using brew $ brew install openssl Install wget using brew $ brew install wget Install geos using brew $ brew install geos Then follow this: https://stackoverflow.com/questions/68839809/issues-with-scikit-bio-on-mac-m1 Hint: If you do not use the default version of Python in your PATH you have to specify the installation: $ python3.9 setup.py install (instead of just 'install .')"

[onurdogan]

We recently experienced the same issue when trying to install scikit-bio on our laboratory Mac -not M1 or M2-. Although I cannot remember the exact steps we took, it is likely that we installed Xcode etc. and maybe uninstalled other Python versions then setting the PATH correctly. I will also inform my colleague that we have solved the problem.

[Rishikeshklaxmi]

Thank you meanwhile a am also trying to solve this issue

[TillMacher]

Hey all,

first, apologies for the silence over the past months! I am aware of the various issues that have arisen over the past year regarding TTT, particularly with the installation process. Unfortunately, due to limited time for programming over the past 1.5 years, I haven’t been able to address these issues sooner. And the paid subscription of PySimpleGUI is also kind of rendering TTT 1.0 useless... However, I am currently working on TTT v2.0, which will bring improvements in performance, layout, and ease of installation. I think that TTT v2.0 will be ready for launch by November :)

Cheers, Till