tillmacher / taxontabletools Goto Github PK

Hello,
I'm wondering if you see any reason why I couldn't use TTT for output from other pipelines that produce ASV tables rather than OTUs (ANACAPA for example)? Of course the tables will be formatted differently and will need to be modified to fit your template.
Thanks for your thoughts on this.
Sarah

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

Hello! My TaXon tables get consumed after running "Taxonomic resolution" or "Taxonomic richness".
Their file size becomes 0 KB and Excel can't open them, "because the file format or file extension is not vaild." The plots are saved as expected, but I need to backup the TaXon table before running either of the two commands.
Other functions work fine. First I thought that it's a consequence of the warning about non-"binomial taxonomy" in my input table, but I fixed the taxonomy and the problem persists.
I set up TTT on Windows 10 last week.

Hi Till,

I am honoured to inform you that I have earned gold medal in the program crashing category again. I was competing in the 'Read Proportions > Calculate bar chart' section and encountered an [x_x] unexpected error [x_x], despite the accurate plotting of the heatmap and pie chart. This was a first-time occurrence, and the function had previously been functioning properly.

best, Onur.

Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/bin/taxontabletools", line 33, in <module> sys.exit(load_entry_point('taxontabletools==1.4.8', 'console_scripts', 'taxontabletools')()) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/taxontabletools/__main__.py", line 1696, in main read_proportions_bar(taxon_table_7_path, read_proportions_bar_taxonomic_level, path_to_outdirs, width_read_props_bar, heigth_read_props_bar, template, font_size, color_discrete_sequence) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/taxontabletools/read_proportions.py", line 292, in read_proportions_bar plot_df = plot_df.append(df) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/pandas/core/generic.py", line 6204, in __getattr__ return object.__getattribute__(self, name) AttributeError: 'DataFrame' object has no attribute 'append'

Issue: Attempting to work through the tutorial using the tutorial files. However, whenever I reach try to merge replicates using the 'replicate consistency' function or use table filtering to extract Arthropods. I am met with the following message: "Unexpected error: <class 'AttributeError'>.

Issue: Installation fails when trying to install the scikit-bio dependency MacOS

Solution:

• 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 .')

Solution: Downgrade kaleido to version 0.1.0post1

pip3 install kaleido==0.1.0post1

Installation of scikit-bio fails

• Issue: Installation fails when trying to install the scikit-bio dependency hdmedians on Windows
• Solution: Install C++ Build Tools (more information: https://stackoverflow.com/questions/40504552/how-to-install-visual-c-build-tools)