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Error loading the GBK file #9

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DelaFuenteJavier opened this issue Aug 6, 2020 · 0 comments
Open

Error loading the GBK file #9

DelaFuenteJavier opened this issue Aug 6, 2020 · 0 comments

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@DelaFuenteJavier
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DelaFuenteJavier commented Aug 6, 2020

Hi to all.
My intention is to import a GBK file in order to create a TxDb object.
The GBK file is the following one:
myfile.txt but ending in .gbk instead of .txt
This file is annotated with prokka 1.14-dev

So what i do is the following:

smpfile <- system.file("mypath/myfile.gbk", package="genbankr",mustWork = TRUE)
gb<- readGenBank(smpfile)
tx <- makeTxDbFromGenBank(gb)

But when I try to create the smpfile I get the following msg:
"Error in system.file("mypath/myfile.gbk", :
no file found
"

I first thought the problem was in my GBK file but I downloaded other gbk files and it still does not work.

Do you have any clue about what's going on?

I'm pretty new in R so sorry in advance!

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