Copy number variation study using CNOGpro

Question

[Neu]

Hi,

I want to study copy number variation using CNOGpro. Below are my commands. Please help me to resolve the generated errors.

library("reutils")
library("biofiles")

b_file <- reutils::efetch("CP002806", "nuccore", rettype = "gbwithparts", retmode = "text")
bk_file <- biofiles::gbRecord(gb_file)
gbkfile <- biofiles::gbRecord(gb_file)

CNOGpro(hitsfile, gbkfile, windowlength = 100, name = "C. psittaci")

Error Reading contents of GenBank file... Error in readLines(con = gbkfile) : 'con' is not a connection

Thank you

[zx8754]

Check if the class class(gbkfile) is a connection. readLines 1st argument con expects a connection.

Read about ?connections