How to convert gb to gbk to get proper input for mauvealigner?

[Andreas Tille <andreas@an3as.eu>]

Hi,

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).

The solution of my colleague was to use CloneManager under Windows to do
a gb -> gbk conversion.  Is there any tool in our rich toolset which can
be used here to script this?

Kind regards

        Andreas.

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