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loosolab / UROPA

Universal RObust Peak Annotator
https://uropa-manual.readthedocs.io/
MIT License
15 stars 6 forks source link

besthits output is missing #9

Closed vojtace closed 2 years ago

vojtace commented 2 years ago

Hello, according to the manual there should be three output .bed files when using multiple queries: allhits, finalhits, and besthits. When I run uropa the besthits output is missing. There is no error while executing uropa. I tried it with my data and also with the example data from the manual, with the same result. My version of uropa: 4.0.2 Any advice how to get the besthits file? Thanks!

msbentsen commented 2 years ago

Hi vojtace,

The besthits file is deprecated since 3.0.0, but we forgot to remove it from the documentation. Sorry about the confusion! The besthits file is no longer created, but instead, you can use --output-by-query to get the annotations for each individual query.

I have updated the documentation here on github, but still need to update it on readthedocs. Until then, the docs on output files is available here. Hope that clears up the question.

vojtace commented 2 years ago

Hi, thank you for explaining. The --output-by-query works fine. I also noticed that using the -d parameter results in some more output files, which are also not explained in the manual.

msbentsen commented 2 years ago

Yes, for debugging purposes (-d/--debug), any temporary files are kept within the output folder - but I wouldn't call these regular output files. That is why they are not described in the manual. So if you run uropa with -d, you can safely ignore these files.