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
