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Arkadiy-Garber / MagicLamp

A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.
GNU General Public License v3.0
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R figure output when running the YfGenie.py #14

Closed azam17 closed 9 months ago

azam17 commented 1 year ago

Hi, how do we get the R figure when running the YfGenie.py? im just using the existing hmm inside the hmms folder

Arkadiy-Garber commented 1 year ago

Hi, thanks for your interest in MagicLamp! Unfortunately, the recent update of this software removes its ability to automatically generate plots. That feature was very buggy and clunky, and I consider the main output files to be the CSV files.

If you'd like to generate similar R plots, all the R code to do so is present in this location: RSCRIPTS. Sorry for the bad naming of variables (these scripts were originally written for FeGenie). But you should be able to plug in the output CSV files into this.

Let me know if you have any questions, and sorry for the inconvenience. Arkadiy

azam17 commented 1 year ago

okay thanks for the reply. i will try using the R codes. one question comes to mind. if i have multiple genomes, how do i combine the multiple output CSV the into one as the input data for the R codes

Arkadiy-Garber commented 1 year ago

Sounds good. Let me know if you have any other issues.

Cheers, Arkadiy

azam17 commented 1 year ago

I have a question which is irrelevant to the original question. When using a fasta file as an input, is it required to include both the gff file and the protein sequence in fasta format file?

Arkadiy-Garber commented 1 year ago

Yup, all three file types are mandatory input.

I recommend using Prokka or Bakta to generate the gff file and protein sequences.

https://github.com/oschwengers/bakta

https://github.com/tseemann/prokka