understanding output of cafetutorial_report_analysis.py

[Michał T. Lorenc]

Hi all,

I ran python cafetutorial_report_analysis.py -i report_run1.cafe -o summary_run and it created the following files:

• summary_run_pub.txt
• summary_run_node.txt
• summary_run_fams.txt
• summary_run_anc.txt

Is there any description of the files because at the moment we have a problem interpreting and understand them?

Thank you in advance

Best wishes,

Michal

[Fabio Henrique Kuriki Mendes]

Hi Michal,

If you're using the latest version of CAFE (CAFE 5), you won't need a python script to do anything for you.

Please see https://github.com/hahnlab/CAFE5 under "New functionalities"

"Outputs are now internally parsed by CAFE5 (no external dependencies or scripts necessary) into summary tables."

The github README.md should explain what each file contains and how to interpret the results.

cheers,

Fábio

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[Michał T. Lorenc]

Hi Fabio,

Thank you for your reply. I would like to use CAFE5. I created all input files for CAFE with this instruction https://github.com/harish0201/Analyses_Pipelines/blob/main/7.CAFE.sh . Are those input files still compatible with CAFE5?

By any are you able to update CAFE on bioconda https://github.com/bioconda/bioconda-recipes/tree/25ee21573c577aa1ae899e0f7fbbc848d8a63865/recipes/cafe ?

Thank you in advance,

Best wishes

Michal

[Fabio Henrique Kuriki Mendes]

Hi Michal,

I don't think there are plans to port CAFE on bioconda, but you can ask Ben directly. He'd be the person to tell you what's what in terms of software release.

CAFE 5 should be able to take input in the same format as previous versions of CAFE, unless things have changed. But the output files will be different, and you don't have to run any auxiliary scripts.

From your activity and type of questions you post in this Google group, I predict sooner or later you will be tempted to ask us about CAFE 5. Before you do that, I urge you to read the documentation and tutorial for CAFE 5, check its paper, and put an effort into understanding how CAFE 5 differs from its predecessors.

I hope this helps.

cheers,

Fábio