[Bioperl-l] GFF to GTF converter

Alexander Kanapin Alexander.Kanapin at oicr.on.ca
Thu Mar 11 10:56:41 EST 2010

Hi BioPerl gurus,

Does anybody knows a reliable GFF to GTF converter which can generate files acceptable by cufflinks ?

We attempted to convert a drosophila and worm genome GFFs  (taken from Flybase and Wormbase ftp) to GTF with Bio::FeatureIO

#read from a file
my $in  = Bio::FeatureIO->new(-file => $infile , -format => 'GFF');

#write out features
my $out = Bio::FeatureIO->new(-file    => ">$outfile" ,
                           -format  => 'GFF' ,
                           -version => 2.5);

However, we discovered that the resulting file is not compliant with GTF format specifications as they are described here: http://mblab.wustl.edu/GTF22.html
Although, this chunk of code produces CDS and exon entries in the output file, it does not output start codon/stop codon annotations.
Also, we think it misinterprets annotations, so that one do see UTR entries annotated as CDS' or exons.

Many thanks for ideas/notes.


Alexander Kanapin, PhD
Scientific Associate

Ontario Institute for Cancer Research
MaRS Centre, South Tower
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Toronto, Ontario, Canada M5G 0A3
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