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

Robert Buels rmb32 at cornell.edu
Wed Feb 15 11:01:07 EST 2006


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

-- 
Robert Buels
SGN Bioinformatics Analyst
252A Emerson Hall, Cornell University
Ithaca, NY  14853
Tel: 607-255-2360
rmb32 at cornell.edu
http://www.sgn.cornell.edu




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