Trying to get sequence using sequinr generates error "Error in readLines(socket, n = nelem, ok = FALSE)"
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3.4 years ago
poecile.pal ▴ 50

Good afternoon,

I am trying to get sequence from genbank, using sequinr library.

library("seqinr") 
choosebank("genbank") 
A.thaliana <- query("A.thaliana", "sp=Arabidopsis thaliana AND K=rbcL")

This results in an error:

Error in readLines(socket, n = nelem, ok = FALSE): too few lines read in readLines
Traceback:

1. query("A.thaliana", "sp=Arabidopsis thaliana AND K=rbcL")
2. readLines(socket, n = nelem, ok = FALSE)

Please tell me what this may be related to and how to get the sequence? Thank you in advance!

Best regards, Poecile

gene software error sequence R genome • 1.4k views
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3.4 years ago
zx8754 11k

Google says, try to increase the timeout:

choosebank("genbank", timeout = 20)
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Thank you very much! It works.

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