[Bioperl-l] Bio::Tools::GFF parsing error

Scott Cain cain at cshl.edu
Wed Feb 15 11:07:28 EST 2006


Hi Robert,

No column should ever be padded with spaces; GFF columns should always
be separated by a single tab.  Therefore, I don't thing Bio::Tools::GFF
is at fault here.

Scott


On Wed, 2006-02-15 at 11:01 -0500, Robert Buels wrote:
> Hi all,
> 
> I'm parsing a GFF2 file with Bio::Tools::GFF (I would be using 
> FeatureIO, except it purports not to support gff 2), and the file looks 
> like:
> 
> ##gff-version 2
> ##date 2006-02-13
> ##sequence-region C01HBa0088L02.seq 1 120525
> C01HBa0088L02   RepeatMasker    similarity      3537    4267     3.3    
> -       .       Target "Motif:bac_end_repeat_family_345" 1 740
> C01HBa0088L02   RepeatMasker    similarity      4172    4279     2.9    
> +       .       Target "Motif:HRSiTERT00100141" 1 104
> C01HBa0088L02   RepeatMasker    similarity      4267    4323     0.0    
> -       .       Target "Motif:k_29" 150 206
> C01HBa0088L02   RepeatMasker    similarity      4322    4492    26.6    
> +       .       Target "Motif:PRSiTERT00300001" 1960 2129
> C01HBa0088L02   RepeatMasker    similarity      4557    5124    29.5    
> +       .       Target "Motif:PRSiTERT00300001" 2142 2711
> 
> Notice the score column is padded with spaces.
> 
> Bio::Tools::GFF does not like this, and says that ' 3.3' is not a valid 
> score.  My question is, who is wrong here, my input file or 
> Bio::Tools::GFF?  Should Bio::Tools::GFF be able to read this file?
> 
> Rob
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



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