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21.0 1.0 1.0 1.5 MB

a toolbox for utilize organelle genomic data

License: GNU Affero General Public License v3.0

Python 63.60% PowerShell 0.69% Shell 0.22% Tcl 28.33% Jupyter Notebook 7.16%

genbank organelle plastid visualization

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ktest-vn

ogu's Issues

Skip Alignment

How can I skip the alignment step?

I would like to download my query, apply -unique longest, but NOT align.

I understand the skip_primer, but I also want to -skip_align. -no_divide forces -unique not to execute.

I want to compare alignment characteristics across programs like CLC and BarcodeFinder.

This is an incredible tool by the way!

-Beau

cli.py error as it take false var name in utils

...Trung_conda/OGU-1.3/lib/python3.7/site-packages/OGU/cli.py

Error in
ok1, _ = utils.get_third_party()

Correct in library:
ok1, _ = utils.get_third_party_path()

Initialization font issue in MacOS Sonoma 14.4.1

Hello Dr. Wu,

Thank you for developing this toolkit. It looks cool!
I'm trying OGU and encounter the following font failures when initializing OGU:

$ python -m OGU init

21:48:12 INFO     Failed to extract font properties from /System/Library/Fonts/Apple Color Emoji.ttc: In FT2Font: Could not set the fontsize (invalid pixel size; error code 0x17)
21:48:12 INFO     Failed to extract font properties from /System/Library/Fonts/LastResort.otf: tuple indices must be integers or slices, not str
21:48:13 INFO     Failed to extract font properties from /System/Library/Fonts/Supplemental/NISC18030.ttf: In FT2Font: Could not set the fontsize (invalid pixel size; error code 0x17)
21:48:13 INFO     generated new fontManager
21:48:13 INFO     Try to locate or install all third-party software.
21:48:13 WARNING  Cannot find mafft.bat, try to install. May cost minutes
21:48:13 WARNING  Cannot find iqtree2, try to install. May cost minutes
21:48:14 INFO     Downloading iqtree-2.2.2.2-MacOSX.zip from https://ogu2023.s3.ap-east-1.amazonaws.com/iqtree-2.2.2.2-MacOSX.zip
21:48:14 INFO     Downloading mafft-7.511-mac.zip from https://ogu2023.s3.ap-east-1.amazonaws.com/mafft-7.511-mac.zip
21:48:18 INFO     iqtree-2.2.2.2-MacOSX.zip got. Installing...
21:48:18 INFO     iqtree2 installed successfully.
21:48:20 INFO     mafft-7.511-mac.zip got. Installing...
21:48:21 INFO     mafft.bat installed successfully.
21:48:21 INFO     Got IQTREE.
21:48:21 INFO     Got MAFFT.

I don't believe these errors are fatal, but I wanted to report them in case they can be resolved.
Please let me know if you need more information from me.

Best,
JianJun

Error in evaluate.py code

When I run:

python -m OGU.evaluate -fasta CDS-COX1.fasta

The error was:

File "/home/ktest/pipeline_env/software/environment/Trung_conda/OGU-1.3/lib/python3.7/site-packages/OGU/evaluate.py", line 451, in output_sliding
    plt.style.use('seaborn-v0_8-colorblind')

When I pip install seaborn and change line 451 to seaborn, it fixed !

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