[BioRuby] Bio::GFF::GFF3 error
graham etherington (TSL)
graham.etherington at sainsbury-laboratory.ac.uk
Wed Nov 6 10:47:20 UTC 2013
Hi,
I¹m getting some strange behaviour when trying to create a Bio::GFF::GFF3
object from a gff file.
Here is my test code that throws the error (test_gff.rb):
require 'bio'
Bio::GFF::GFF3.new(File.read("gene.gff"))
Here is my gff file (gene.gff) (validated at
http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online):
##gff-version 3
##sequence-region ctg123 1 1497228
ctg123 . gene 900 9900 . + . ID=gene00001;Name=EDEN
ctg123 . gene 10900 19900 . - . ID=gene00002;Name=EDEN2
Here is the error:
test_gff.rb:2:in `<main>':
/Users/ethering/.rvm/gems/ruby-2.0.0-p247/gems/bio-1.4.3/lib/bio/db/gff.rb:
238: invalid multibyte escape: /[\t\r\n\x00-\x1f\x7f\xfe\xff]/
(SyntaxError)
invalid multibyte escape: /[\s\"\;\t\r\n\x00-\x1f\x7f\xfe\xff]/
There are two things I¹m confused at here.
1. I¹m getting errors for a validated gff file.
2. The errors thrown are coming from the GFF2 code in bio/db/gff.db, as
follows (line numbers provided):
237 # prohibited characters in GFF2 columns
238 PROHIBITED_GFF2_COLUMNS = /[\t\r\n\x00-\x1f\x7f\xfe\xff]/
239
240 # prohibited characters in GFF2 attribute tags
241 PROHIBITED_GFF2_TAGS = /[\s\"\;\t\r\n\x00-\x1f\x7f\xfe\xff]
ruby -v
ruby 2.0.0p247 (2013-06-27 revision 41674) [x86_64-darwin12.5.0]
Any suggestions?
Many thanks,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601
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