[Bioperl-l] bp_genbank2gff.pl bug

Scott Cain scott at scottcain.net
Wed Nov 9 13:43:00 EST 2011


Hi Chris,

Actually, removing it from the distribution (but letting it remain in the
code repository) is not a bad idea.  I can't really think of a down side.

Scott


2011/11/9 Fields, Christopher J <cjfields at illinois.edu>

> Scott,
>
> Do we want to add that caveat to the bp_genbank2gff.pl documentation (or
> remove it altogether)?
>
> chris
>
> On Nov 9, 2011, at 10:12 AM, Scott Cain wrote:
>
> > Hi Angel,
> >
> > I would suggest using bp_genbank2gff3.pl, as it is more actively
> > maintained; the bp_genbank2gff.pl script hasn't really been touched in
> many
> > years, and I imagine it's suffering from some serious code rot.
> >
> > Scott
> >
> >
> > 2011/11/9 Angel Zaballos <azaballos at isciii.es>
> >
> >> Running bp_genbank2gff.pl got this:
> >>
> >> [root at localhost zaballos]# bp_genbank2gff.pl -stdout -accession
> >> AAXT01000001.1 > babesichr3.gff
> >> Replacement list is longer than search list at
> >> /usr/share/perl5/Bio/Range.pm line 251.
> >>
> >>
> >>
> >> Ángel Zaballos
> >> Unidad de Genómica
> >> Centro Nacional de Microbiología-ISCIII
> >> Carretera Majadahonda-Pozuelo, Km 2,2
> >> 28220-Majadahonda
> >>
> >> Tel: 918223994
> >> mail:  azaballos at isciii.es
> >>
> >>
> >>
> >>
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> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain
> dot
> > net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > Ontario Institute for Cancer Research
> >
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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