Re: How to convert gb to gbk to get proper input for mauvealigner?
Hi, Andreas,
On الخميس 10 آذار 2016 09:05, Andreas Tille wrote:
> 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).
>
As far as I know, gb and gbk are interchangeable extensions for the
genbank format. The genbank format may or may not include the actual
sequence data. If you're passing a genbank file to Mauve, it should be
including the sequence data.
> 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?
>
I'm not aware of any such tools; I've never needed to convert from one
to the other since I usually get a reference sequence from NCBI, where I
can download either type of genbank file directly.
regards
Afif
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
Reply to: