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Can I also use this to download specific genus? #3

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dutchscientist opened this issue May 9, 2016 · 4 comments
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Can I also use this to download specific genus? #3

dutchscientist opened this issue May 9, 2016 · 4 comments
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@dutchscientist
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As I am a small player with ditto diskspace, and usually only want the genomes from a specific genus, can this be done?
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kblin commented May 9, 2016

From the files provided by NCBI, this is not entirely trivial. I guess a string match on the species_name field would work. I'll add this to my todo list.

@dutchscientist
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OK, it's just that not everyone can afford to download the whole database :)

@kblin kblin self-assigned this May 9, 2016
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kblin commented May 9, 2016

Yes, very good point. I didn't think about that use case before, but it seems pretty obvious now. Thanks a lot for the feedback.

kblin added a commit that referenced this issue May 17, 2016
@kblin
core: Allow do restrict downloads to a specified genus
7232544 
This is based on a simple string match to the organism name provided by NCBI, nothing fancy.
This closes issue #3

Signed-off-by: Kai Blin <kblin@biosustain.dtu.dk>
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kblin commented May 17, 2016

Thanks again for your feedback. In version 0.1.6. that I just released, you can now limit the genus by using the --genus option.
Closed by 7232544

@kblin kblin closed this as completed May 17, 2016
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