Re: How to convert gb to gbk to get proper input for mauvealigner?
On Fri, Mar 11, 2016 at 09:28:22AM +0000, Sascha Steinbiss wrote:
> >> a colleague of mine relaised that mauvealigner seems to need gbk files
> >> when running under Linux (while under Win also gb file is working). This
> >> happens when using
> >>
> >> java -Xmx6g -cp /usr/share/java/Mauve.jar org.gel.mauve.contigs.ContigOrderer -output OUTPUTDIR -ref REFERENCE.gbk -draft DRAFT.contigs.fasta
> >>
> >> While under win also REFERENCE.gb is OK this leads to an error under
> >> (the Debian packaged!) mauvealigner (I forgot to ask what version is
> >> used under Win - may be there is a difference as well).
> >
> > As far as I know, gb and gbk are interchangeable extensions for the
> > genbank format.
>
> I am not aware of a systematic difference betweek 'gb' and 'gbk' files
> either.
My colleague found out that simply *renaming* the *.gb file to *.gbk was
sufficient. That totally contradicts my experience that extensions
under Linux are unimportant as long as the content of the file is OK.
So this makes me wonder why mauvealigner works under Windows with the
*.gb files flawlessly (where usually file extensions play some role).
Kind regards
Andreas.
--
http://fam-tille.de
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