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NickJD / StORF-Reporter

Package to extract Unannotated Regions from prokaryotic genomes report coding and pseudogenised genes delimited by stop codons - Named StORFs (Stop - Open Reading Frames)
GNU General Public License v3.0
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Diversity of input folder names #2

Open Dx-wmc opened 1 year ago

Dx-wmc commented 1 year ago

It's great to see such a great tool, I realized in my own case that if I use a Bakta folder, the fna file needs to be the same as the folder name. For example if my folder is set to Ecoli_23_BAKTA, StORF will only look for Ecoli_23_BAKTA.fna, when in fact the contents of my folder is Ecoli_23.fna. So would it be possible to add an option to cope with this situation.

NickJD commented 1 year ago

Hi. I am currently looking into making it easier and more 'user-driven' for selecting input files and hopefully, I will have some progress on this soon. Thanks for the request.

NickJD commented 11 months ago

Sorry for the delay. Please try v1.2.0 with the "-af" option to provide the alternative filename: StORF-Reporter -anno Bakta Out_Dir -p ./Ecoli_23_BAKTA -af Ecoli_23

elchaarn commented 10 months ago

Hi Nick, I have a similar problem when using the "Multiple_Out_Dirs": https://github.com/NickJD/StORF-Reporter/issues/1 Can you make the above modification for running multiple directories with names different than the file names?