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michaelgruenstaeudl / PACVr

Plastome Assembly Coverage Visualization in R
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Importing a GBK file to create a TxDb object. #6

Closed DelaFuenteJavier closed 3 years ago

DelaFuenteJavier commented 3 years ago

Hi everyone, I am trying to import a GBK in order to create a TxDb object. The file I want to import is this one (note that I changed the extension to .txt to be able to upload it here):

myfile.txt

As I have been recommended I tried to do it in the following way:

gbkFile <- "path/to/my/file.gbk"

gb <- genbankr::readGenBank(gbkFile)

tx <- genbankr::makeTxDbFromGenBank(gb)

However this error shows up:

Error in genbankr::readGenBank(gbkFile) : file does not appear to an existing file or a GBAccession object. Valid file or text argument is required.

Reading other posts I think that the problem might be in the GBK file.

Thanks in advance!

nilsj9 commented 3 years ago

Hi @deLFH as the error message indicates, your file cannot be located. Additionally, your file is missing a "source" feature which is mandatory. See our example: example.gb.