[Bioperl-l] bp_genbank2gff.pl bug

Fields, Christopher J cjfields at illinois.edu
Wed Nov 9 14:51:48 EST 2011


Scott,

It would remain in the repo history if it is removed, otherwise we can probably set up an 'unmaintained' folder.  Either would prevent it from being packaged and installed in future versions.  

(Speaking of, we should discuss (w/ Lincoln) about possible splitting out Bio::DB::SeqFeature/GFF and related code/tests/etc into it's own distribution, in line with slimming down core modules)

chris

On Nov 9, 2011, at 12:43 PM, Scott Cain wrote:

> 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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