Error reading gff file into R (with read.gff from the ape package)

Question

[ramiroricardo]

Dear all,

I was trying to read a gff3 genome file into R, but I get the following error:

Error in scan(file, w, sep = "\t", quote = "", quiet = TRUE, na.strings = na.strings,  : 
  scan() expected 'an integer', got 'TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC'

Has anyone seen this and/or knows how to solve it?

Thanks,

Ramiro

[Devon Ryan]

Few parsers handle GFF files with sequence information. The simplest solution is to just delete the sequence information off of the end.

[pyjiang2]

I encountered the same problem. It is because there are fasta files at the end. Try grep -n ">" gff_file to find the fasta files, and then just take the lines before that into a new file which won't give this error.

[venu]

May be you can try import.gff function from rtracklayer.