<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>

CC BY-SA 4.0
2020-10-09T17:46:10.010Z
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.
webNoob13
CC BY-SA 4.0
2020-10-09T15:32:03.987Z
2020-10-09T15:32:03.987Z
dariober
<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>

<machine-learning>
Problems replicating Kover paper results
# 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

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## 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.  

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