[BioRuby] Bio::GFF::GFF3 error

[Marjan Povolni]

Hello,

I managed to recreate the issue on Ubuntu with ruby-2.0.0-p247, with bio
version 1.4.3 gem, and what solved the issue was updating the bio gem:

gem update bio

That should update the gem to version 1.4.3.0001 (latest), and on my setup
the error message doesn't appear anymore.

Best regards,
Marjan


On Wed, Nov 6, 2013 at 11:47 AM, graham etherington (TSL) <
graham.etherington at sainsbury-laboratory.ac.uk> wrote:

> 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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