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I am trying to replicate the results for the creator of this repo: https://github.com/aldro61/kover2_paper for genotype to phenotype machine learning interpretable (decision tree) prediction.

Specifically in the data section when I try to create the dataset as explained here: https://github.com/aldro61/kover2_paper/tree/master/data

I make a directory called genomes_dir in the data directory. Then I do:

python download_genomes.py 'mycobacterium tuberculosis/kanamycin/metadata.tsv' genomes_dir

at the end of the download it tells me that it saved file genome_paths.tsv the data directory, not genomes_dir. So I run command:

kover dataset create from-tsv --genomic-data genome_paths.tsv ---phenotype-description "Kanamycin resistance" --phenotype-metadata 'mycobacterium tuberculosis/kanamycin/metadata.tsv  --output data_example.kover --progress

and it just hangs with a prompt:

(kover) nobu@gold3forever:~/Desktop/BioInformatics/ResearchAssistant/kover2_paper/data$ kover dataset create from-tsv --genomic-data genome_paths.tsv ---phenotype-description "Kanamycin resistance" --phenotype-metadata 'mycobacterium tuberculosis/kanamycin/metadata.tsv  --output data_example.kover --progress
> ^C

it does nothing after hours and hours so I control-C'd to end the process.

Does anyone have any idea what is happening?

I also had to install this to get the datasets from PATRIC: https://github.com/aldro61/patric_tools

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The single quote at 'mycobacterium is not matched so the command prompt is waiting indefinitely for the command to be completed. Maybe you want 'mycobacterium tuberculosis/kanamycin/metadata.tsv' (note closing quote)

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  • $\begingroup$ Thanks for the catch but now I'm getting some kmer_count = get_kmer_count(tsv_path) File "/home/nobu/anaconda3/envs/kover/lib/python2.7/site-packages/kover/dataset/create.py", line 136, in get_kmer_count raise Exception() Exception so I'd better check the data I downloaded. $\endgroup$
    – webNoob13
    Commented Oct 9, 2020 at 17:46

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