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larel5000

kover2_paper's Issues

error Exception() trying to follow the example

I am trying to follow the example here: https://github.com/aldro61/kover2_paper/tree/master/data

But when I download the mycobacterium tuberculosis data using patric_tools, I don't get a genome_paths.tsv in the genomes_dir but one directory above.

So I try this command from that directory:

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

But I get:

Traceback (most recent call last):
  File "/home/T00057442/RA/kover/kover/bin/kover", line 1192, in <module>
    CommandLineInterface()
  File "/home/T00057442/RA/kover/kover/bin/kover", line 1150, in __init__
    getattr(self, args.command)()
  File "/home/T00057442/RA/kover/kover/bin/kover", line 1170, in dataset
    getattr(dataset_tool, args.command)()
  File "/home/T00057442/RA/kover/kover/bin/kover", line 250, in create
    getattr(creation_tool, args.datasource)()
  File "/home/T00057442/RA/kover/kover/bin/kover", line 97, in from_tsv
    progress_callback=progress)
  File "/home/T00057442/anaconda3/envs/kover/lib/python2.7/site-packages/kover/dataset/create.py", line 155, in from_tsv
    kmer_count = get_kmer_count(tsv_path)
  File "/home/T00057442/anaconda3/envs/kover/lib/python2.7/site-packages/kover/dataset/create.py", line 136, in get_kmer_count
    raise Exception()
Exception

following the data example, I get different output and then a prompt that hangs

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.

What am I doing wrong here?

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