[Bioperl-l] GenBank to GFF conversion tool?

[Jay Hesselberth]

I've been trying to convert GenBank files to GFF format using the
gb_to_gff.pl script provided in bioperl-live/scripts, but it doesn't
seem to process complex sequence features.

For example, when something like join(535378..536418,536417..536485) is
encountered, the GFF line only gets fstart: 535378 and fstop: 536485,
missing the join completely.  I know that wormbase uses separate entries
to describe joins like this (multiple ids associated with the same gene
which can then be joined after the fact).  The script is using
top_SeqFeatures() to extract features; I assume this isn't good enough
to get more complicated features?

Thanks,

Jay

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Jay Hesselberth          jhessel@mail.utexas.edu

University of Texas      (512) 471-6445
2500 Speedway / A4800
Austin, TX  78712