Answers.Body: <p>The single quote at <code>'mycobacterium</code> is not matched so the command prompt is waiting indefinitely for the command to be completed. Maybe you want <code>'mycobacterium tuberculosis/kanamycin/metadata.tsv'</code> (note closing quote)</p>
  
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Answers.Text: 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.
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Body: <p>I am trying to replicate the results for the creator of this repo:  <a href="https://github.com/aldro61/kover2_paper" rel="nofollow noreferrer">https://github.com/aldro61/kover2_paper</a> for genotype to phenotype machine learning interpretable (decision tree) prediction.</p>
  <p>Specifically in the data section when I try to create the dataset as explained here:
  <a href="https://github.com/aldro61/kover2_paper/tree/master/data" rel="nofollow noreferrer">https://github.com/aldro61/kover2_paper/tree/master/data</a></p>
  <p>I make a directory called genomes_dir in the data directory. Then I do:</p>
  <pre><code>python download_genomes.py 'mycobacterium tuberculosis/kanamycin/metadata.tsv' genomes_dir
  </code></pre>
  <p>at the end of the download it tells me that it saved file <code>genome_paths.tsv</code> the data directory, not genomes_dir. So I run command:</p>
  <pre><code>kover dataset create from-tsv --genomic-data genome_paths.tsv ---phenotype-description &quot;Kanamycin resistance&quot; --phenotype-metadata 'mycobacterium tuberculosis/kanamycin/metadata.tsv  --output data_example.kover --progress
  </code></pre>
  <p>and it just hangs with a prompt:</p>
  <pre><code>(kover) nobu@gold3forever:~/Desktop/BioInformatics/ResearchAssistant/kover2_paper/data$ kover dataset create from-tsv --genomic-data genome_paths.tsv ---phenotype-description &quot;Kanamycin resistance&quot; --phenotype-metadata 'mycobacterium tuberculosis/kanamycin/metadata.tsv  --output data_example.kover --progress
  &gt; ^C
  </code></pre>
  <p>it does nothing after hours and hours so I control-C'd to end the process.</p>
  <p>Does anyone have any idea what is happening?</p>
  <p>I also had to install this to get the datasets from PATRIC:  <a href="https://github.com/aldro61/patric_tools" rel="nofollow noreferrer">https://github.com/aldro61/patric_tools</a></p>
  
Tags: <machine-learning>
Title: Problems replicating Kover paper results
ThreadText: # Problems replicating Kover paper results
  
  (Asked by: username_0 on 2020-10-09)
  
  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>
  
  **Tags:** machine-learning
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-10-09. Score: 1
  
  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)
  
  > **Comments:**
  > **username_0**: 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.  
  
  ---
  
  