Question: How to fetch gene bank flat file (.gb) in R
0
gravatar for Neu
6 months ago by
Neu10
India
Neu10 wrote:

Hello, I need to fetch gene bank flat file of bacteria (Mycobacterium_smegmatis) in R. I have tried using Biofiles. It's not working and generating the error as below

Error in biofiles::gbRecord(mito.path) : 
  'rcd' must be the path to GenBank or Embl flat file or an 'efetch' object containing GenBank records

Please suggest me how can I do that.

Thank you

R • 146 views
ADD COMMENTlink modified 6 months ago by WouterDeCoster43k • written 6 months ago by Neu10
3

Please provide the code that gives this error.

ADD REPLYlink written 6 months ago by zx87549.1k

What the error message says is that mito.path is not a valid path to a Genbank file nor an efetch object. If you're trying to read a file, make sure that it's accessible to your script.

ADD REPLYlink written 6 months ago by Jean-Karim Heriche21k
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