An auxiliary script that might help condensing pathway tab files

cruizperez / MicrobeAnnotator

Pipeline for metabolic annotation of microbial genomes

Artistic License 2.0

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An auxiliary script that might help condensing pathway tab files #96

Open AhmedElsherbini opened 3 months ago

AhmedElsherbini commented 3 months ago

Hi all,

Firstly, thank you for developing this nice tool.

Recently, I made this simple script that helps me to work with your pathway completeness tab files file. My script aims to condense your tab file from many genomes into two condensed CSV files, one for the detailed pathway "column 2" and one for the pathway group "column 3" per isolate.

Firstly, if you have any feedback, I will be happy to get it. I hope I can benefit other colleagues with this script.

Best regards, Ahmed

cruizperez commented 3 months ago

Hi Ahmed! Thank you for your script! I will check it out soon as I think it would be very useful to parse the results from MA. I am currently refactoring the entire tool to address all the issues that have been raised and that I unfortunately haven't had the chance to address. I will reach out as soon as I am in the results module, and we can chat about incorporating it! In the meantime, I am going to test it with some testing results I have. Thank you!

AhmedElsherbini commented 3 months ago

Thank you @cruizperez .

I will be happy to have your feedback. I am open for

One quick question, do you believe that the pathway completeness will be radically different when using --light mode?

Best, Ahmed